+ 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' 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 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/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/analysis' /opt/local/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/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/cltools' /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/function' /opt/local/bin/gmake -C ../gridtools links gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/core' /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/gridtools' /opt/local/bin/gmake -C ../lapack links 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]: 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/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/lepton' /opt/local/bin/gmake -C ../main 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]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/lapack' /opt/local/bin/gmake -C ../mapping 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]: 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/mapping' /opt/local/bin/gmake -C ../secondarystructure links gmake[6]: Entering directory '/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/local/bin/gmake -C ../setup links 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/vatom' /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/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 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' gmake[6]: Entering directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/asmjit' compiling AnalysisBase.cpp compiling arch.cpp compiling ABMD.cpp compiling assembler.cpp compiling codebuilder.cpp compiling codecompiler.cpp compiling codeemitter.cpp compiling Average.cpp compiling Bias.cpp compiling codeholder.cpp compiling constpool.cpp compiling BiasValue.cpp compiling cpuinfo.cpp compiling func.cpp compiling AverageVessel.cpp compiling ExtendedLagrangian.cpp compiling Committor.cpp compiling External.cpp compiling DataCollectionObject.cpp compiling LWalls.cpp compiling EuclideanDissimilarityMatrix.cpp compiling globals.cpp compiling MaxEnt.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 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 { | ^~~~~~~~~~~~~~~~ compiling MetaD.cpp 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 Histogram.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( 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 MovingRestraint.cpp compiling x86builder.cpp compiling PBMetaD.cpp compiling Restraint.cpp compiling ReweightBase.cpp compiling ReweightBias.cpp compiling x86compiler.cpp compiling ReweightMetad.cpp compiling x86inst.cpp compiling x86instimpl.cpp compiling ReweightTemperaturePressure.cpp compiling x86internal.cpp compiling ReweightWham.cpp compiling x86logging.cpp compiling UWalls.cpp compiling x86operand.cpp compiling x86operand_regs.cpp compiling x86regalloc.cpp gmake[6]: Leaving directory '/home/pbulk/build/math/plumed/work/plumed-2.8.0/src/bias' 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~ 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