+ 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
/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]: 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]: 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/asmjit'
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/asmjit
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/analysis
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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit'
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar'
/opt/local/bin/gmake -C ../config links
Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar
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 ../core links
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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/colvar'
/opt/local/bin/gmake -C ../function 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core'
/opt/local/bin/gmake -C ../generic links
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/cltools'
/opt/local/bin/gmake -C ../gridtools 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
/opt/local/bin/gmake -C ../isdb links
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]: 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/generic'
/opt/local/bin/gmake -C ../lepton links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack'
/opt/local/bin/gmake -C ../main 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]: 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main'
/opt/local/bin/gmake -C ../mapping links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lepton'
/opt/local/bin/gmake -C ../molfile links
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]: 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/gridtools'
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile'
/opt/local/bin/gmake -C ../multicolvar links
/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]: 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/reference'
/opt/local/bin/gmake -C ../secondarystructure 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/isdb'
/opt/local/bin/gmake -C ../setup links
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/mapping'
/opt/local/bin/gmake -C ../tools links
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/multicolvar'
/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]: 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 ../vesselbase links
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/vesselbase'
Verify modules and create links in /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/secondarystructure'
/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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/wrapper'
/opt/local/bin/gmake -C ../xdrfile links
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/tools'
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
/opt/local/bin/gmake -C ../blas obj
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas'
compiling blas.cpp
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias'
compiling ABMD.cpp
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit'
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis'
compiling arch.cpp
compiling AnalysisBase.cpp
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/blas'
/opt/local/bin/gmake -C ../cltools obj
gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools'
compiling CLTool.cpp
compiling assembler.cpp
{ ../maketools/make-scripts-options.sh ; cat completion.sh ; }| ../maketools/xxd > completion.xxd
../../scripts/selector.sh: line 219: python: command not found
compiling Driver.cpp
compiling codebuilder.cpp
In file included from xdrfile/xdrfile_trr.h:1,
from Driver.cpp:38:
xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37:
xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
In file included from xdrfile/xdrfile_xtc.h:1,
from Driver.cpp:39:
xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
compiling codecompiler.cpp
compiling DriverDouble.cpp
compiling Bias.cpp
In file included from xdrfile/xdrfile_trr.h:1,
from Driver.cpp:38,
from DriverDouble.cpp:23:
xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37:
xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
In file included from xdrfile/xdrfile_xtc.h:1,
from Driver.cpp:39:
xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
compiling Average.cpp
compiling codeemitter.cpp
compiling codeholder.cpp
compiling BiasValue.cpp
compiling constpool.cpp
compiling cpuinfo.cpp
compiling ExtendedLagrangian.cpp
compiling AverageVessel.cpp
compiling func.cpp
compiling DriverFloat.cpp
compiling Committor.cpp
In file included from xdrfile/xdrfile_trr.h:1,
from Driver.cpp:38,
from DriverFloat.cpp:23:
xdrfile/../../xdrfile/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
In file included from xdrfile/../../xdrfile/xdrfile_trr.h:37:
xdrfile/../../xdrfile/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
In file included from xdrfile/xdrfile_xtc.h:1,
from Driver.cpp:39:
xdrfile/../../xdrfile/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment]
5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
|
compiling External.cpp
compiling DataCollectionObject.cpp
compiling LWalls.cpp
compiling EuclideanDissimilarityMatrix.cpp
compiling MaxEnt.cpp
compiling globals.cpp
compiling GenExample.cpp
compiling inst.cpp
compiling logging.cpp
compiling operand.cpp
compiling osutils.cpp
compiling regalloc.cpp
compiling FarthestPointSampling.cpp
compiling runtime.cpp
compiling string.cpp
compiling MetaD.cpp
compiling utils.cpp
compiling vmem.cpp
compiling GenTemplate.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!");
| ~~~~~~^~~~~~~~~
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 Histogram.cpp
compiling x86assembler.cpp
compiling Info.cpp
compiling Manual.cpp
compiling PdbRenumber.cpp
compiling LandmarkSelectionBase.cpp
compiling SimpleMD.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 SumHills.cpp
compiling MovingRestraint.cpp
compiling PBMetaD.cpp
compiling kT.cpp
compiling pesmd.cpp
compiling Completion.cpp
compiling x86inst.cpp
compiling x86instimpl.cpp
gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools'
compiling x86internal.cpp
compiling x86logging.cpp
compiling x86operand.cpp
compiling x86operand_regs.cpp
compiling x86regalloc.cpp
compiling Restraint.cpp
compiling ReweightBase.cpp
compiling ReweightBias.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 ReweightMetad.cpp
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-2024Q4-x86_64/math/plumed
*** Error code 1
Stop.
bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-2024Q4-x86_64/math/plumed