+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/plumed-2.8.0nb2/work.log ===> Building for plumed-2.8.0nb2 /opt/pkg/bin/gmake lib gmake[1]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0' /opt/pkg/bin/gmake -C src gmake[2]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src' /opt/pkg/bin/gmake -C lib gmake[3]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' /opt/pkg/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/pkg/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/pkg/bin/gmake -C ../analysis links /opt/pkg/bin/gmake -C ../asmjit links /opt/pkg/bin/gmake -C ../bias links /opt/pkg/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' 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/bias gmake[6]: Leaving directory '/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/asmjit' /opt/pkg/bin/gmake -C ../cltools links 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/asmjit gmake[6]: Entering 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/asmjit' Verify modules and create links in /home/pbulk/build/math/plumed/work/plumed-2.8.0/src/cltools /opt/pkg/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/bias' /opt/pkg/bin/gmake -C ../config 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/pkg/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/pkg/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/cltools' /opt/pkg/bin/gmake -C ../generic links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core' /opt/pkg/bin/gmake -C ../gridtools 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]: 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/function' /opt/pkg/bin/gmake -C ../isdb links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/generic' /opt/pkg/bin/gmake -C ../lapack links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/gridtools' /opt/pkg/bin/gmake -C ../lepton links 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]: 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/lapack' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' /opt/pkg/bin/gmake -C ../main links 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/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/lepton' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/main' /opt/pkg/bin/gmake -C ../mapping links /opt/pkg/bin/gmake -C ../molfile links gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/molfile' 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/molfile 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/molfile' /opt/pkg/bin/gmake -C ../multicolvar links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack' /opt/pkg/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/isdb' /opt/pkg/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/reference' /opt/pkg/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/pkg/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/multicolvar' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/setup' /opt/pkg/bin/gmake -C ../vatom links /opt/pkg/bin/gmake -C ../vesselbase 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/vesselbase' gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/secondarystructure' /opt/pkg/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 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/wrapper' /opt/pkg/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/pkg/bin/gmake dirs gmake[4]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lib' *** Compiling all directories *** /opt/pkg/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/pkg/bin/gmake -C ../analysis obj /opt/pkg/bin/gmake -C ../asmjit obj gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/analysis' compiling AnalysisBase.cpp /opt/pkg/bin/gmake -C ../bias obj gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' compiling Average.cpp compiling arch.cpp gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' compiling ABMD.cpp compiling assembler.cpp compiling codebuilder.cpp compiling codecompiler.cpp compiling AverageVessel.cpp compiling Bias.cpp compiling codeemitter.cpp compiling codeholder.cpp compiling constpool.cpp compiling cpuinfo.cpp compiling func.cpp compiling BiasValue.cpp compiling Committor.cpp compiling DataCollectionObject.cpp compiling globals.cpp compiling ExtendedLagrangian.cpp compiling inst.cpp compiling logging.cpp compiling EuclideanDissimilarityMatrix.cpp compiling FarthestPointSampling.cpp compiling operand.cpp compiling osutils.cpp compiling External.cpp compiling regalloc.cpp compiling runtime.cpp compiling string.cpp compiling Histogram.cpp compiling LandmarkSelectionBase.cpp compiling utils.cpp compiling vmem.cpp compiling LWalls.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 compiling LandmarkStaged.cpp compiling MaxEnt.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( sqrt(n*N) ); | ~~~~^~~~~ In file included from /usr/include/math.h:35, from /opt/tools/gcc13/include/c++/13.3.0/bits/std_abs.h:40, from /opt/tools/gcc13/include/c++/13.3.0/cstdlib:81, from /opt/tools/gcc13/include/c++/13.3.0/ext/string_conversions.h:43, from /opt/tools/gcc13/include/c++/13.3.0/bits/basic_string.h:4109, from /opt/tools/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]: *** Waiting for unfinished jobs.... compiling x86builder.cpp 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 x86compiler.cpp compiling MetaD.cpp compiling x86inst.cpp compiling x86instimpl.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 x86internal.cpp compiling x86logging.cpp compiling x86operand.cpp compiling x86operand_regs.cpp compiling x86regalloc.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 MovingRestraint.cpp compiling PBMetaD.cpp compiling Restraint.cpp compiling ReweightBase.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' compiling ReweightBias.cpp 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[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-upstream-trunk/math/plumed *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/math/plumed