Project ID: plumID:20.015
Stderr for source: 2-EMMI/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.DHANNf.cpp: In constructor ‘PLMD::isdb::EMMIVOX::EMMIVOX(const PLMD::ActionOptions&)’: EMMIVox.DHANNf.cpp:328:52: warning: ‘double PLMD::PlumedMain::DeprecatedAtoms::getKBoltzmann() const’ is deprecated: Use Action::getKBoltzmann(). [-Wdeprecated-declarations] 328 | if(temp>0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from EMMIVox.DHANNf.cpp:24: /home/runner/opt/include/plumed_master/core/PlumedMain.h:102:12: note: declared here 102 | double getKBoltzmann() const ; | ^~~~~~~~~~~~~ EMMIVox.DHANNf.cpp:329:37: 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] 329 | else kbt_=plumed.getAtoms().getKbT(); | ~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from EMMIVox.DHANNf.cpp:24: /home/runner/opt/include/plumed_master/core/PlumedMain.h:104:12: note: declared here 104 | double getKbT() const ; | ^~~~~~ EMMIVox.DHANNf.cpp: In member function ‘void PLMD::isdb::EMMIVOX::write_model_overlap(long int)’: EMMIVox.DHANNf.cpp:536:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 536 | for(int i=0; i<ovmd_.size(); ++i) { | ~^~~~~~~~~~~~~ EMMIVox.DHANNf.cpp: In member function ‘std::vector PLMD::isdb::EMMIVOX::read_exp_errors(std::string)’: EMMIVox.DHANNf.cpp:670:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 670 | for(unsigned i=0; i<nexp; ++i) { | ~^~~~~ EMMIVox.DHANNf.cpp: In member function ‘void PLMD::isdb::EMMIVOX::get_exp_data(std::string)’: EMMIVox.DHANNf.cpp:801:22: 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] 801 | if(GMM_d_beta_[i]>=GMM_d_grps_.size()) error("Check Beta values"); terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (core/PlumedMain.cpp:986) void PLMD::PlumedMain::readInputWords(const std::vector<std::__cxx11::basic_string >&, const bool&) ERROR I cannot understand line: EMMIVOX LABEL=gmm TEMP=303.15 NL_STRIDE=50 NL_CUTOFF=0.5 NS_CUTOFF=1.0 ATOMS=protein-h DATA_FILE=map_zoned_align.dat NORM_DENSITY=2068.185 RESOLUTION=0.1 VOXEL=0.1012 NOISETYPE=MARGINAL SIGMA_MIN=0.2 STATUS_FILE=EMMIStatus WRITE_STRIDE=2500 Maybe a missing space or a typo? [fv-az1198-456:08119] *** Process received signal *** [fv-az1198-456:08119] Signal: Aborted (6) [fv-az1198-456:08119] Signal code: (-6) [fv-az1198-456:08119] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f039b242520] [fv-az1198-456:08119] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f039b2969fc] [fv-az1198-456:08119] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f039b242476] [fv-az1198-456:08119] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f039b2287f3] [fv-az1198-456:08119] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa4f26)[0x7f039b6a4f26] [fv-az1198-456:08119] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xb6d9c)[0x7f039b6b6d9c] [fv-az1198-456:08119] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xb6e07)[0x7f039b6b6e07] [fv-az1198-456:08119] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(__cxa_rethrow+0x4b)[0x7f039b6b70bb] [fv-az1198-456:08119] [ 8] plumed_master(+0x12e7f)[0x55a1c9865e7f] [fv-az1198-456:08119] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f039b229d90] [fv-az1198-456:08119] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f039b229e40] [fv-az1198-456:08119] [11] plumed_master(+0x13115)[0x55a1c9866115] [fv-az1198-456:08119] *** End of error message *** </pre>