Project ID: plumID:23.024
Stderr for source: examples/driverTests/plumed_C45.dat
Download: zipped raw stdout - zipped raw stderr
#! Only the first 1000 rows of the error file are shown below #! To inspect the full error file, please download the zipped raw stderr file above WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">> ../../src/pines/PINES.kRcDjY.cpp: In static member function ‘static void PLMD::PINES::PINES::registerKeywords(PLMD::Keywords&)’: ../../src/pines/PINES.kRcDjY.cpp:158:3: error: ‘componentsAreNotOptional’ was not declared in this scope 158 | componentsAreNotOptional(keys); | ^~~~~~~~~~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp: In constructor ‘PLMD::PINES::PINES::PINES(const PLMD::ActionOptions&)’: ../../src/pines/PINES.kRcDjY.cpp:356:69: warning: ‘bool PLMD::PlumedMain::DeprecatedAtoms::usingNaturalUnits() const’ is deprecated: Use Action::usingNaturalUnits(). [-Wdeprecated-declarations] 356 | mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from ../../src/pines/PINES.kRcDjY.cpp:19: /home/runner/opt/include/plumed_master/core/PlumedMain.h:108:10: note: declared here 108 | bool usingNaturalUnits() const ; | ^~~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:356:76: error: ‘atoms’ was not declared in this scope; did you mean ‘Atoms’? 356 | mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()); | ^~~~~ | Atoms ../../src/pines/PINES.kRcDjY.cpp:379:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__gnu_cxx::__alloc_traits<std::allocator, unsigned int>::value_type’ {aka ‘unsigned int’} [-Wsign-compare] 379 | if(rind==Presind[j]) { ../../src/pines/PINES.kRcDjY.cpp:416:11: warning: unused variable ‘rind’ [-Wunused-variable] 416 | int rind=mypdb.getResidueNumber(anum); | ^~~~ ../../src/pines/PINES.kRcDjY.cpp:1012:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<PLMD::VectorGeneric<3> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1012 | for (int i = 0; i < ann_deriv.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp: In member function ‘virtual void PLMD::PINES::PINES::prepare()’: ../../src/pines/PINES.kRcDjY.cpp:1090:11: warning: unused variable ‘buffer’ [-Wunused-variable] 1090 | int buffer=10; | ^~~~~~ ../../src/pines/PINES.kRcDjY.cpp: In member function ‘virtual void PLMD::PINES::PINES::calculate()’: ../../src/pines/PINES.kRcDjY.cpp:1337:12: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1337 | stride=comm.Get_size(); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1338:10: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1338 | rank=comm.Get_rank(); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1512:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1512 | if(sb_count > max_solv_atoms) { | ~~~~~~~~~^~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1567:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1567 | if(nl_small[j]->size() >= max_solv_atoms) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1575:44: warning: comparison of integer expressions of different signedness: ‘std::vector ::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1575 | if(sb_count - A0[i].size() < max_solv_atoms) { | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1589:25: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1589 | if(!doserial && comm.initialized()) { | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1620:11: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1620 | comm.Barrier(); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1625:11: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1625 | comm.Allgather(&dim,1,&Vdim[0],1); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1640:11: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1640 | comm.Allgather(&OrdVec[0],Nprec,&OrdVecAll[0],Nprec); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1642:11: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1642 | comm.Allgatherv(&Atom0F[0],Atom0F.size(),&Atom0FAll[0],&Vdim[0],&Vpos[0]); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1643:11: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1643 | comm.Allgatherv(&Atom1F[0],Atom1F.size(),&Atom1FAll[0],&Vdim[0],&Vpos[0]); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1656:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 1656 | for(unsigned m=0; m<OrdVecAll[i+l*Nprec]; m++) { ../../src/pines/PINES.kRcDjY.cpp:1668:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} [-Wsign-compare] 1668 | for(unsigned m=0; m<OrdVec[i]; m++) { ../../src/pines/PINES.kRcDjY.cpp:1723:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1723 | if(limit > max_solv_atoms) { | ~~~~~~^~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1704:10: warning: unused variable ‘dosorting’ [-Wunused-variable] 1704 | bool dosorting=dosort[j]; | ^~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1801:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1801 | if(limit > max_solv_atoms) { | ~~~~~~^~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1826:16: warning: unused variable ‘tPINES’ [-Wunused-variable] 1826 | double tPINES = sfs[j].calculate(dm*Fvol, dfunc); | ^~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1848:20: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1848 | if (!serial && comm.initialized() ) { | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1856:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1856 | comm.Barrier(); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1860:11: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1860 | comm.Sum(cPINES[j][k]); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1861:27: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1861 | cPINES[j][k] /= comm.Get_size(); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1870:15: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1870 | comm.Sum(ann_deriv[i][j][k]); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1871:37: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1871 | ann_deriv[i][j][k] /= comm.Get_size(); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1877:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1877 | comm.Sum(&m_virial[0][0],9); | ^~~~ In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/OFile.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Log.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:30, from /home/runner/opt/include/plumed_master/colvar/../core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/colvar/../core/Colvar.h:25, from /home/runner/opt/include/plumed_master/colvar/Colvar.h:24, from ../../src/pines/PINES.kRcDjY.cpp:17: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1902:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1902 | if( (limit > max_solv_atoms) && (solv_blocks != 0) ){ | ~~~~~~^~~~~~~~~~~~~~~~ ../../src/pines/PINES.kRcDjY.cpp:1771:8: warning: unused variable ‘Nder’ [-Wunused-variable] 1771 | bool Nder=CompDer; | ^~~~ ../../src/pines/PINES.kRcDjY.cpp:1772:8: warning: unused variable ‘Scalevol’ [-Wunused-variable] 1772 | bool Scalevol=Svol; | ^~~~~~~~ terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (core/PlumedMain.cpp:1282) void PLMD::PlumedMain::load(const string&) An error happened while executing command env PLUMED_ROOT='/home/runner/opt/lib/plumed_master' PLUMED_VERSION='2.10.0-dev' PLUMED_HTMLDIR='/home/runner/opt/share/doc/plumed_master' PLUMED_INCLUDEDIR='/home/runner/opt/include' PLUMED_PROGRAM_NAME='plumed_master' PLUMED_IS_INSTALLED='yes' "/home/runner/opt/lib/plumed_master"/scripts/mklib.sh -n -o ./../../src/pines/PINES.2.10.0-dev.so ../../src/pines/PINES.cpp [fv-az842-842:39722] *** Process received signal *** [fv-az842-842:39722] Signal: Aborted (6) [fv-az842-842:39722] Signal code: (-6) [fv-az842-842:39722] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f3b38042520] [fv-az842-842:39722] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f3b380969fc] [fv-az842-842:39722] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f3b38042476] [fv-az842-842:39722] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f3b380287f3] [fv-az842-842:39722] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa2b9e)[0x7f3b384a2b9e] [fv-az842-842:39722] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae20c)[0x7f3b384ae20c] [fv-az842-842:39722] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xae277)[0x7f3b384ae277] [fv-az842-842:39722] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(__cxa_rethrow+0x4b)[0x7f3b384ae52b] [fv-az842-842:39722] [ 8] plumed_master(+0x14274)[0x55cdc322a274] [fv-az842-842:39722] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f3b38029d90] [fv-az842-842:39722] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f3b38029e40] [fv-az842-842:39722] [11] plumed_master(+0x14ed5)[0x55cdc322aed5] [fv-az842-842:39722] *** End of error message *** </pre>