Project ID: plumID:22.018
Stderr for source: LAT1/plumed.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">> EMMIVox.U7Z3q7.cpp: In constructor ‘PLMD::isdb::EMMIVOX::EMMIVOX(const PLMD::ActionOptions&)’: EMMIVox.U7Z3q7.cpp:327:52: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKBoltzmann() const’ is deprecated: Use Action::getKBoltzmann(). [-Wdeprecated-declarations] 327 | if(temp>0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from EMMIVox.U7Z3q7.cpp:24: /home/runner/opt/include/plumed_master/core/PlumedMain.h:102:12: note: declared here 102 | double getKBoltzmann() const ; | ^~~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:328:37: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKbT() const’ is deprecated: Use Action::getkBT() N.B. this function also reads the TEMP keyword from the input for you. [-Wdeprecated-declarations] 328 | else kbt_=plumed.getAtoms().getKbT(); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from EMMIVox.U7Z3q7.cpp:24: /home/runner/opt/include/plumed_master/core/PlumedMain.h:104:12: note: declared here 104 | double getKbT() const ; | ^~~~~~ EMMIVox.U7Z3q7.cpp:376:20: error: invalid use of incomplete type ‘class PLMD::Communicator’ 376 | unsigned mpisize=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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:383:13: error: invalid use of incomplete type ‘class PLMD::Communicator’ 383 | nrep_ = multi_sim_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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:385:14: error: invalid use of incomplete type ‘class PLMD::Communicator’ 385 | replica_ = multi_sim_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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp: In member function ‘void PLMD::isdb::EMMIVOX::write_model_overlap(long int)’: EMMIVox.U7Z3q7.cpp:535:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 535 | for(int i=0; i<ovmd_.size(); ++i) { | ~^~~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp: In member function ‘std::vector PLMD::isdb::EMMIVOX::read_exp_errors(std::string)’: EMMIVox.U7Z3q7.cpp:669:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 669 | for(unsigned i=0; i<nexp; ++i) { | ~^~~~~ EMMIVox.U7Z3q7.cpp: In member function ‘void PLMD::isdb::EMMIVOX::get_exp_data(std::string)’: EMMIVox.U7Z3q7.cpp:800:22: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator , int>::value_type’ {aka ‘int’} and ‘std::vector<std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 800 | if(GMM_d_beta_[i]>=GMM_d_grps_.size()) error("Check Beta values"); EMMIVox.U7Z3q7.cpp: In member function ‘void PLMD::isdb::EMMIVOX::doMonteCarloScale()’: EMMIVox.U7Z3q7.cpp:1082:5: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1082 | multi_sim_comm.Sum(&new_scale, 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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:1083:5: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1083 | multi_sim_comm.Sum(&new_off, 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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:1103:28: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1103 | if(!no_aver_ && nrep_>1) multi_sim_comm.Sum(&new_ene, 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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:1116:5: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1116 | multi_sim_comm.Sum(&do_update, 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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:1127:30: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1127 | if(!no_aver_ && nrep_>1) multi_sim_comm.Sum(&GMMid_der_[0], GMMid_der_.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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp: In member function ‘virtual void PLMD::isdb::EMMIVOX::calculate()’: EMMIVox.U7Z3q7.cpp:1334:5: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1334 | multi_sim_comm.Sum(&ovmd_[0], ovmd_.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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:1383:5: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1383 | multi_sim_comm.Sum(&GMMid_der_[0], GMMid_der_.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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ EMMIVox.U7Z3q7.cpp:1384:5: error: invalid use of incomplete type ‘class PLMD::Communicator’ 1384 | multi_sim_comm.Sum(&ene_, 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 EMMIVox.U7Z3q7.cpp:22: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (core/PlumedMain.cpp:1260) void PLMD::PlumedMain::load(const string&) An error happened while executing command env PLUMED_ROOT="/home/runner/opt/lib/plumed_master" env PLUMED_VERSION="2.10.0-dev" env PLUMED_HTMLDIR="/home/runner/opt/share/doc/plumed_master" env PLUMED_INCLUDEDIR="/home/runner/opt/include" env PLUMED_PROGRAM_NAME="plumed_master" env PLUMED_IS_INSTALLED="yes" "/home/runner/opt/lib/plumed_master"/scripts/mklib.sh EMMIVox.cpp [fv-az1433-905:68965] *** Process received signal *** [fv-az1433-905:68965] Signal: Aborted (6) [fv-az1433-905:68965] Signal code: (-6) [fv-az1433-905:68965] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7feebee42520] [fv-az1433-905:68965] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7feebee969fc] [fv-az1433-905:68965] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7feebee42476] [fv-az1433-905:68965] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7feebee287f3] [fv-az1433-905:68965] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa4f26)[0x7feebf2a4f26] [fv-az1433-905:68965] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xb6d9c)[0x7feebf2b6d9c] [fv-az1433-905:68965] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xb6e07)[0x7feebf2b6e07] [fv-az1433-905:68965] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(__cxa_rethrow+0x4b)[0x7feebf2b70bb] [fv-az1433-905:68965] [ 8] plumed_master(+0x12e7f)[0x55807732ee7f] [fv-az1433-905:68965] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7feebee29d90] [fv-az1433-905:68965] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7feebee29e40] [fv-az1433-905:68965] [11] plumed_master(+0x13115)[0x55807732f115] [fv-az1433-905:68965] *** End of error message *** </pre>