[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir conf28578.dir
<.> /usr/bin/mkdir -p conf28578.dir
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p .
<.> /usr/bin/mkdir -p -p .
[*] c++ --version
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 --version -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -v
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -V
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -V -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -qversion
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -qversion -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -g -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -g -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] cc --version
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 --version -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] cc -v
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] cc -V
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -V -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] cc -qversion
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -qversion -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] cc -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include conftest.c
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.c -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2
[*] cc -c -g -I/opt/local/include -I/usr/include conftest.c
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -g -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.c -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2
[*] cc -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -I/opt/local/include -I/usr/include conftest.c
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.c -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2
[*] f77 --version
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong --version -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] f77 -v
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong -v -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] f77 -V
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong -V -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] f77 -qversion
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong -qversion -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] f77 -c conftest.F
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong -c conftest.F -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] f77 -c -g conftest.f
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong -c -g conftest.f -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] cc -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -I/opt/local/include -I/usr/include conftest.c
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC conftest.c -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2
[*] cc -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.c -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.c -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c -MM -MFconftest.d conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c -MM -MFconftest.d conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -fopenmp -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lgsl -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -E -I/opt/local/include -I/usr/include conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -E -I/home/pbulk/build/math/plumed/work/.buildlink/include conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lgsl -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -I/opt/local/include -I/usr/include -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 conftest.cpp -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -o conftest -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib conftest.cpp -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ --print-prog-name=ld
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 --print-prog-name=ld -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ --print-prog-name=ar
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 --print-prog-name=ar -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-main.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-f.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest-g.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -o conftest.exe conftest-main.o conftest-both.a -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -lumem
[*] cc -c conftest-main.c
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c conftest-main.c -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] cc conftest.o conftest-main.o -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -o conftest.exe
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 conftest.o conftest-main.o -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -o conftest.exe -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include -lumem
[*] cc conftest.o conftest-main.o -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -lstdc++ -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -o conftest.exe
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gcc -fcommon -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 conftest.o conftest-main.o -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib -lstdc++ -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -o conftest.exe -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc -gdwarf-2 -I/home/pbulk/build/math/plumed/work/.buildlink/include -lumem
[*] f77 -c conftest-main.f90
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong -c conftest-main.f90 -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/home/pbulk/build/math/plumed/work/.buildlink/include -fPIC -Wall -pedantic -std=c++11 -c conftest.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] f77 conftest.o conftest-main.o -L/opt/local/lib -Wl,-R/opt/local/lib -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -lstdc++ -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -o conftest.exe
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/gfortran -m64 -fstack-protector-strong conftest.o conftest-main.o -L/home/pbulk/build/math/plumed/work/.buildlink/lib -Wl,-rpath,/opt/local/lib -lstdc++ -lfftw3 -lgsl -lz -ldl -llapack -lblas -lcblas -lblas -o conftest.exe -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] /home/pbulk/build/math/plumed/work/.tools/bin/pkg-config --variable=prefix bash-completion
<.> set args --variable=prefix bash-completion; shift; PKG_CONFIG_LIBDIR=/home/pbulk/build/math/plumed/work/.buildlink/lib/amd64/pkgconfig:/home/pbulk/build/math/plumed/work/.buildlink/lib/pkgconfig:/home/pbulk/build/math/plumed/work/.buildlink/share/pkgconfig false  "$@"
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir conf48785.dir
<.> /usr/bin/mkdir -p conf48785.dir
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p .
<.> /usr/bin/mkdir -p -p .
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p reference
<.> /usr/bin/mkdir -p -p reference
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p config
<.> /usr/bin/mkdir -p -p config
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p vesselbase
<.> /usr/bin/mkdir -p -p vesselbase
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p gridtools
<.> /usr/bin/mkdir -p -p gridtools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p reference
<.> /usr/bin/mkdir -p -p reference
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p molfile
<.> /usr/bin/mkdir -p -p molfile
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p multicolvar
<.> /usr/bin/mkdir -p -p multicolvar
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p xdrfile
<.> /usr/bin/mkdir -p -p xdrfile
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p bias
<.> /usr/bin/mkdir -p -p bias
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p config
<.> /usr/bin/mkdir -p -p config
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p reference
<.> /usr/bin/mkdir -p -p reference
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p lepton
<.> /usr/bin/mkdir -p -p lepton
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p xdrfile
<.> /usr/bin/mkdir -p -p xdrfile
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p lepton
<.> /usr/bin/mkdir -p -p lepton
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p bias
<.> /usr/bin/mkdir -p -p bias
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p blas
<.> /usr/bin/mkdir -p -p blas
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p colvar
<.> /usr/bin/mkdir -p -p colvar
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p vesselbase
<.> /usr/bin/mkdir -p -p vesselbase
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p asmjit
<.> /usr/bin/mkdir -p -p asmjit
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p reference
<.> /usr/bin/mkdir -p -p reference
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p wrapper
<.> /usr/bin/mkdir -p -p wrapper
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p function
<.> /usr/bin/mkdir -p -p function
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p cltools
<.> /usr/bin/mkdir -p -p cltools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p reference
<.> /usr/bin/mkdir -p -p reference
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p vesselbase
<.> /usr/bin/mkdir -p -p tools
<.> /usr/bin/mkdir -p -p vesselbase
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p vesselbase
<.> /usr/bin/mkdir -p -p vesselbase
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p gridtools
<.> /usr/bin/mkdir -p -p gridtools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p reference
<.> /usr/bin/mkdir -p -p reference
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p lapack
<.> /usr/bin/mkdir -p -p lapack
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p vesselbase
<.> /usr/bin/mkdir -p -p vesselbase
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p lepton
<.> /usr/bin/mkdir -p -p lepton
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p core
<.> /usr/bin/mkdir -p -p core
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p tools
<.> /usr/bin/mkdir -p -p tools
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p bias
<.> /usr/bin/mkdir -p -p bias
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir -p analysis
<.> /usr/bin/mkdir -p -p analysis
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir deps
<.> /usr/bin/mkdir -p deps
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir deps
<.> /usr/bin/mkdir -p deps
[*] /home/pbulk/build/math/plumed/work/.tools/bin/mkdir deps
<.> /usr/bin/mkdir -p deps
[*] c++ -c -MM -MFAnalysisBase.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AnalysisBase.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFAnalysisBase.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp AnalysisBase.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFABMD.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ABMD.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFABMD.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ABMD.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFarch.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp arch.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFarch.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp arch.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp arch.cpp -o arch.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp arch.cpp -o arch.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ABMD.cpp -o ABMD.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ABMD.cpp -o ABMD.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AnalysisBase.cpp -o AnalysisBase.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp AnalysisBase.cpp -o AnalysisBase.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFassembler.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp assembler.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFassembler.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp assembler.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp assembler.cpp -o assembler.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp assembler.cpp -o assembler.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFcodebuilder.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codebuilder.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFcodebuilder.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codebuilder.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codebuilder.cpp -o codebuilder.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codebuilder.cpp -o codebuilder.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFcodecompiler.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codecompiler.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFcodecompiler.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codecompiler.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codecompiler.cpp -o codecompiler.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codecompiler.cpp -o codecompiler.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFAverage.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Average.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFAverage.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Average.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Average.cpp -o Average.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Average.cpp -o Average.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFBias.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Bias.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFBias.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Bias.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Bias.cpp -o Bias.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Bias.cpp -o Bias.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFcodeemitter.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codeemitter.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFcodeemitter.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codeemitter.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codeemitter.cpp -o codeemitter.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codeemitter.cpp -o codeemitter.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFcodeholder.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codeholder.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFcodeholder.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codeholder.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp codeholder.cpp -o codeholder.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp codeholder.cpp -o codeholder.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFBiasValue.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasValue.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFBiasValue.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasValue.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFconstpool.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp constpool.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFconstpool.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp constpool.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasValue.cpp -o BiasValue.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp BiasValue.cpp -o BiasValue.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp constpool.cpp -o constpool.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp constpool.cpp -o constpool.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFcpuinfo.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp cpuinfo.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFcpuinfo.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp cpuinfo.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp cpuinfo.cpp -o cpuinfo.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp cpuinfo.cpp -o cpuinfo.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFAverageVessel.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageVessel.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFAverageVessel.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageVessel.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageVessel.cpp -o AverageVessel.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp AverageVessel.cpp -o AverageVessel.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFfunc.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp func.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFfunc.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp func.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp func.cpp -o func.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp func.cpp -o func.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFExtendedLagrangian.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ExtendedLagrangian.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFExtendedLagrangian.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ExtendedLagrangian.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ExtendedLagrangian.cpp -o ExtendedLagrangian.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ExtendedLagrangian.cpp -o ExtendedLagrangian.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFCommittor.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Committor.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFCommittor.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Committor.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Committor.cpp -o Committor.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Committor.cpp -o Committor.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFExternal.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp External.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFExternal.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp External.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp External.cpp -o External.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp External.cpp -o External.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFDataCollectionObject.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DataCollectionObject.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFDataCollectionObject.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp DataCollectionObject.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp DataCollectionObject.cpp -o DataCollectionObject.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp DataCollectionObject.cpp -o DataCollectionObject.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFEuclideanDissimilarityMatrix.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFEuclideanDissimilarityMatrix.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFLWalls.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LWalls.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFLWalls.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp LWalls.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LWalls.cpp -o LWalls.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp LWalls.cpp -o LWalls.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp -o EuclideanDissimilarityMatrix.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp EuclideanDissimilarityMatrix.cpp -o EuclideanDissimilarityMatrix.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFglobals.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp globals.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFglobals.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp globals.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp globals.cpp -o globals.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp globals.cpp -o globals.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFinst.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp inst.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFinst.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp inst.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFMaxEnt.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFMaxEnt.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp inst.cpp -o inst.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp inst.cpp -o inst.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp -o MaxEnt.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp MaxEnt.cpp -o MaxEnt.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFlogging.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp logging.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFlogging.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp logging.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp logging.cpp -o logging.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp logging.cpp -o logging.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFFarthestPointSampling.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FarthestPointSampling.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFFarthestPointSampling.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp FarthestPointSampling.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFoperand.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp operand.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFoperand.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp operand.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp FarthestPointSampling.cpp -o FarthestPointSampling.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp FarthestPointSampling.cpp -o FarthestPointSampling.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp operand.cpp -o operand.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp operand.cpp -o operand.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFosutils.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFosutils.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp -o osutils.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp osutils.cpp -o osutils.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFregalloc.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFregalloc.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp -o regalloc.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp regalloc.cpp -o regalloc.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFruntime.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFruntime.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp -o runtime.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp runtime.cpp -o runtime.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFstring.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp string.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFstring.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp string.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp string.cpp -o string.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp string.cpp -o string.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFHistogram.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Histogram.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFHistogram.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Histogram.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Histogram.cpp -o Histogram.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Histogram.cpp -o Histogram.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFMetaD.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MetaD.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFMetaD.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp MetaD.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFutils.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp utils.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFutils.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp utils.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp utils.cpp -o utils.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp utils.cpp -o utils.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MetaD.cpp -o MetaD.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp MetaD.cpp -o MetaD.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFvmem.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp vmem.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFvmem.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp vmem.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp vmem.cpp -o vmem.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp vmem.cpp -o vmem.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86assembler.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86assembler.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86assembler.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86assembler.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86assembler.cpp -o x86assembler.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86assembler.cpp -o x86assembler.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFLandmarkSelectionBase.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFLandmarkSelectionBase.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp -o LandmarkSelectionBase.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkSelectionBase.cpp -o LandmarkSelectionBase.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFLandmarkStaged.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFLandmarkStaged.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp -o LandmarkStaged.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp LandmarkStaged.cpp -o LandmarkStaged.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86builder.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86builder.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86builder.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86builder.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86builder.cpp -o x86builder.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86builder.cpp -o x86builder.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86compiler.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86compiler.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp -o x86compiler.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86compiler.cpp -o x86compiler.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFMovingRestraint.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFMovingRestraint.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp -o MovingRestraint.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp MovingRestraint.cpp -o MovingRestraint.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFPBMetaD.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PBMetaD.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFPBMetaD.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp PBMetaD.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp PBMetaD.cpp -o PBMetaD.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp PBMetaD.cpp -o PBMetaD.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86inst.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86inst.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp -o x86inst.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86inst.cpp -o x86inst.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86instimpl.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86instimpl.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86instimpl.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86instimpl.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86instimpl.cpp -o x86instimpl.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86instimpl.cpp -o x86instimpl.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86internal.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86internal.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86internal.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86internal.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86internal.cpp -o x86internal.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86internal.cpp -o x86internal.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86logging.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86logging.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp -o x86logging.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86logging.cpp -o x86logging.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFRestraint.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Restraint.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFRestraint.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Restraint.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp Restraint.cpp -o Restraint.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp Restraint.cpp -o Restraint.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFReweightBase.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBase.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFReweightBase.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBase.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBase.cpp -o ReweightBase.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBase.cpp -o ReweightBase.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86operand.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86operand.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand.cpp -o x86operand.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand.cpp -o x86operand.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFReweightBias.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFReweightBias.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86operand_regs.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand_regs.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86operand_regs.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand_regs.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp -o ReweightBias.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightBias.cpp -o ReweightBias.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand_regs.cpp -o x86operand_regs.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86operand_regs.cpp -o x86operand_regs.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFx86regalloc.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86regalloc.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFx86regalloc.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86regalloc.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp x86regalloc.cpp -o x86regalloc.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp x86regalloc.cpp -o x86regalloc.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFReweightMetad.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightMetad.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFReweightMetad.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightMetad.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightMetad.cpp -o ReweightMetad.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightMetad.cpp -o ReweightMetad.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFzone.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp zone.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFzone.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp zone.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp zone.cpp -o zone.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp zone.cpp -o zone.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFReweightTemperaturePressure.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFReweightTemperaturePressure.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp -o ReweightTemperaturePressure.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightTemperaturePressure.cpp -o ReweightTemperaturePressure.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFReweightWham.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFReweightWham.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp -o ReweightWham.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp ReweightWham.cpp -o ReweightWham.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -MM -MFUWalls.d -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -MM -MFUWalls.d -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc
[*] c++ -c -I/opt/local/include -I/usr/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/local/include -I/usr/include -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp -o UWalls.o
<.> /home/pbulk/build/math/plumed/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -c -I/home/pbulk/build/math/plumed/work/.buildlink/include '-DPACKAGE_NAME="PLUMED"' '-DPACKAGE_TARNAME="plumed"' '-DPACKAGE_VERSION="2"' '-DPACKAGE_STRING="PLUMED 2"' '-DPACKAGE_BUGREPORT=""' '-DPACKAGE_URL=""' -D__PLUMED_LIBCXX11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1 -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1 -D__PLUMED_HAS_ASMJIT=1 -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_RTLD_DEFAULT=1 -D__PLUMED_HAS_CHDIR=1 -D__PLUMED_HAS_SUBPROCESS=1 -D__PLUMED_HAS_GETCWD=1 -D__PLUMED_HAS_POPEN=1 -D__PLUMED_HAS_EXECINFO=1 -D__PLUMED_HAS_ZLIB=1 -D__PLUMED_HAS_GSL=1 -D__PLUMED_HAS_FFTW=1 -DNDEBUG=1 -D_REENTRANT=1 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -fPIC -Wall -pedantic -std=c++11 -fopenmp UWalls.cpp -o UWalls.o -specs=/home/pbulk/build/math/plumed/work/.cwrapper/specs.pkgsrc