+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/local/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log
+ su pbulk -c '"$@"' make /opt/local/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log
===> Building for plumed-2.8.0nb2
/opt/local/bin/gmake lib
gmake[1]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0'
/opt/local/bin/gmake -C src
gmake[2]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src'
/opt/local/bin/gmake -C lib
gmake[3]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
/opt/local/bin/gmake dirslinks
gmake[4]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
*** Updating links to used modules in all directories ***
/opt/local/bin/gmake ../analysis.links ../asmjit.links ../bias.links ../blas.links ../cltools.links ../colvar.links ../config.links ../core.links ../function.links ../generic.links ../gridtools.links ../isdb.links ../lapack.links ../lepton.links ../main.links ../mapping.links ../molfile.links ../multicolvar.links ../reference.links ../secondarystructure.links ../setup.links ../tools.links ../vatom.links ../vesselbase.links ../wrapper.links ../xdrfile.links
gmake[5]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
/opt/local/bin/gmake -C ../analysis links
/opt/local/bin/gmake -C ../asmjit links
/opt/local/bin/gmake -C ../bias links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit'
/opt/local/bin/gmake -C ../blas links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas'
/opt/local/bin/gmake -C ../cltools links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias'
/opt/local/bin/gmake -C ../colvar links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools'
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar'
/opt/local/bin/gmake -C ../config links
/opt/local/bin/gmake -C ../core links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/config'
Nothing to do in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/config
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/config'
/opt/local/bin/gmake -C ../function links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
/opt/local/bin/gmake -C ../generic links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/function'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/function
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core'
/opt/local/bin/gmake -C ../gridtools links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic'
/opt/local/bin/gmake -C ../isdb links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/function'
/opt/local/bin/gmake -C ../lapack links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack'
/opt/local/bin/gmake -C ../lepton links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools'
/opt/local/bin/gmake -C ../main links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton'
/opt/local/bin/gmake -C ../mapping links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/mapping'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/mapping
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main'
/opt/local/bin/gmake -C ../molfile links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile'
/opt/local/bin/gmake -C ../multicolvar links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb'
/opt/local/bin/gmake -C ../reference links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/reference'
/opt/local/bin/gmake -C ../secondarystructure links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/mapping'
/opt/local/bin/gmake -C ../setup links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar'
/opt/local/bin/gmake -C ../tools links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup'
/opt/local/bin/gmake -C ../vatom links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure'
/opt/local/bin/gmake -C ../vesselbase links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/tools'
/opt/local/bin/gmake -C ../wrapper links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper'
Nothing to do in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase'
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper'
/opt/local/bin/gmake -C ../xdrfile links
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/xdrfile'
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/xdrfile
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/xdrfile'
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vatom'
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase'
gmake[5]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
gmake[4]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
/opt/local/bin/gmake dirs
gmake[4]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
*** Compiling all directories ***
/opt/local/bin/gmake ../analysis ../asmjit ../bias ../blas ../cltools ../colvar ../config ../core ../function ../generic ../gridtools ../isdb ../lapack ../lepton ../main ../mapping ../molfile ../multicolvar ../reference ../secondarystructure ../setup ../tools ../vatom ../vesselbase ../wrapper ../xdrfile
gmake[5]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
/opt/local/bin/gmake -C ../analysis obj
/opt/local/bin/gmake -C ../asmjit obj
/opt/local/bin/gmake -C ../bias obj
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias'
compiling AnalysisBase.cpp
compiling ABMD.cpp
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit'
compiling arch.cpp
compiling assembler.cpp
compiling codebuilder.cpp
compiling codecompiler.cpp
compiling Average.cpp
compiling Bias.cpp
compiling codeemitter.cpp
compiling codeholder.cpp
compiling BiasValue.cpp
compiling constpool.cpp
compiling cpuinfo.cpp
compiling AverageVessel.cpp
compiling func.cpp
compiling ExtendedLagrangian.cpp
compiling Committor.cpp
compiling External.cpp
compiling DataCollectionObject.cpp
compiling EuclideanDissimilarityMatrix.cpp
compiling LWalls.cpp
compiling globals.cpp
compiling inst.cpp
compiling MaxEnt.cpp
compiling logging.cpp
compiling FarthestPointSampling.cpp
compiling operand.cpp
compiling osutils.cpp
compiling regalloc.cpp
compiling runtime.cpp
compiling string.cpp
compiling Histogram.cpp
compiling MetaD.cpp
compiling utils.cpp
compiling vmem.cpp
vmem.cpp:284:13: warning: 'bool PLMD::asmjit::vMemMgrCheckTree(VMemMgr*)' defined but not used [-Wunused-function]
284 | static bool vMemMgrCheckTree(VMemMgr* self) noexcept {
| ^~~~~~~~~~~~~~~~
vmem.cpp: In member function 'PLMD::asmjit::Error PLMD::asmjit::VMemMgr::release(void*)':
vmem.cpp:883:1: warning: dangling pointer 'q' to 'head' may be used [-Wdangling-pointer=]
883 | }
| ^
vmem.cpp:420:10: note: 'head' declared here
420 | RbNode head = { { nullptr, nullptr }, 0, 0 };
| ^~~~
compiling x86assembler.cpp
MetaD.cpp: In constructor 'PLMD::bias::MetaD::MetaD(const PLMD::ActionOptions&)':
MetaD.cpp:1232:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
1232 | if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from GRID while other do not!");
| ~~~~~~^~~~~~~~~
MetaD.cpp:1297:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
1297 | if(result!=0&&result!=mpi_nw_) error("in this WALKERS_MPI run some replica have restarted from FILE while other do not!");
| ~~~~~~^~~~~~~~~
compiling LandmarkSelectionBase.cpp
compiling LandmarkStaged.cpp
LandmarkStaged.cpp: In member function 'virtual void PLMD::analysis::LandmarkStaged::selectLandmarks()':
LandmarkStaged.cpp:69:42: error: call of overloaded 'sqrt(unsigned int)' is ambiguous
69 | unsigned int m = static_cast<int>( sqrt(n*N) );
| ~~~~^~~~~
In file included from /usr/include/math.h:35,
from /opt/local/gcc13/include/c++/13.3.0/bits/std_abs.h:40,
from /opt/local/gcc13/include/c++/13.3.0/cstdlib:81,
from /opt/local/gcc13/include/c++/13.3.0/ext/string_conversions.h:43,
from /opt/local/gcc13/include/c++/13.3.0/bits/basic_string.h:4109,
from /opt/local/gcc13/include/c++/13.3.0/string:54,
from core/../../core/Action.h:25,
from core/../../core/ActionPilot.h:25,
from core/ActionPilot.h:1,
from AnalysisBase.h:25,
from LandmarkSelectionBase.h:25,
from LandmarkStaged.cpp:22:
/usr/include/iso/math_iso.h:232:28: note: candidate: 'long double std::sqrt(long double)'
232 | inline long double sqrt(long double __X) { return __sqrtl(__X); }
| ^~~~
/usr/include/iso/math_iso.h:183:22: note: candidate: 'float std::sqrt(float)'
183 | inline float sqrt(float __X) { return __sqrtf(__X); }
| ^~~~
/usr/include/iso/math_iso.h:77:15: note: candidate: 'double std::sqrt(double)'
77 | extern double sqrt(double);
| ^~~~
gmake[6]: *** [../maketools/make.rules:21: LandmarkStaged.o] Error 1
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
gmake[5]: *** [Makefile:426: ../analysis] Error 2
gmake[5]: *** Waiting for unfinished jobs....
compiling x86builder.cpp
compiling x86compiler.cpp
compiling MovingRestraint.cpp
compiling PBMetaD.cpp
compiling x86inst.cpp
compiling x86instimpl.cpp
compiling x86internal.cpp
compiling x86logging.cpp
compiling Restraint.cpp
compiling ReweightBase.cpp
compiling x86operand.cpp
compiling ReweightBias.cpp
compiling x86operand_regs.cpp
compiling x86regalloc.cpp
compiling ReweightMetad.cpp
compiling zone.cpp
zone.cpp:223:13: warning: 'bool PLMD::asmjit::ZoneHeap_hasDynamicBlock(ZoneHeap*, ZoneHeap::DynamicBlock*)' defined but not used [-Wunused-function]
223 | static bool ZoneHeap_hasDynamicBlock(ZoneHeap* self, ZoneHeap::DynamicBlock* block) noexcept {
| ^~~~~~~~~~~~~~~~~~~~~~~~
compiling ReweightTemperaturePressure.cpp
compiling ReweightWham.cpp
compiling UWalls.cpp
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias'
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit'
gmake[5]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
gmake[4]: *** [Makefile:128: dirs] Error 2
gmake[4]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
gmake[3]: *** [Makefile:111: all] Error 2
gmake[3]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib'
gmake[2]: *** [Makefile:8: lib] Error 2
gmake[2]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src'
gmake[1]: *** [Makefile:32: lib] Error 2
gmake[1]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0'
gmake: *** [Makefile:21: all] Error 2
*** Error code 2
Stop.
bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/plumed
*** Error code 1
Stop.
bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/plumed