Project ID: plumID:22.004
Stderr for source: input_files/Aldol_reaction/2_Sampling/plumed.dat
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#! 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 In file included from /home/runner/opt/include/plumed_master/core/../tools/Tools.h:27, from /home/runner/opt/include/plumed_master/core/Action.h:28, from /home/runner/opt/include/plumed_master/core/ActionAtomistic.h:25, from /home/runner/opt/include/plumed_master/core/Colvar.h:25, from Contacts.GygNVm.cpp:22: /home/runner/opt/include/plumed_master/core/../tools/Tensor.h:98: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 98 | #pragma acc enter data copyin(this[0:1], d, d[0:n*m-1]) | /home/runner/opt/include/plumed_master/core/../tools/Tensor.h:102: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 102 | #pragma acc exit data delete( d[0:n*m-1], d, this[0:1]) | In file included from /home/runner/opt/include/plumed_master/core/ActionAtomistic.h:27: /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:94: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 94 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:100: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 100 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:102: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 102 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:108: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 108 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:112: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 112 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:116: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 116 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:120: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 120 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/core/../tools/Pbc.h:123: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 123 | #pragma acc routine seq | In file included from /home/runner/opt/include/plumed_master/core/Colvar.h:27: /home/runner/opt/include/plumed_master/core/../tools/Matrix.h:100: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 100 | #pragma acc enter data copyin(this[0:1],sz,data[0:sz]) | /home/runner/opt/include/plumed_master/core/../tools/Matrix.h:103: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 103 | #pragma acc exit data delete(data[0:sz],sz,this[0:1]) | /home/runner/opt/include/plumed_master/core/../tools/Matrix.h:117: warning: ignoring ‘#pragma acc enter’ [-Wunknown-pragmas] 117 | #pragma acc enter data copyin(this[0:1]) | /home/runner/opt/include/plumed_master/core/../tools/Matrix.h:123: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 123 | #pragma acc exit data delete( this[0:1]) | In file included from Contacts.GygNVm.cpp:34: /home/runner/opt/include/plumed_master/tools/SwitchingFunction.h:182: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 182 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/tools/SwitchingFunction.h:190: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 190 | #pragma acc routine seq | Contacts.GygNVm.cpp: In static member function ‘static void PLMD::colvar::Contacts::registerKeywords(PLMD::Keywords&)’: Contacts.GygNVm.cpp:77:26: warning: ‘void PLMD::Keywords::addOutputComponent(const std::string&, const std::string&, const std::string&)’ is deprecated: Use addOutputComponent with four argument and specify valid types for value from scalar/vector/matrix/grid [-Wdeprecated-declarations] 77 | keys.addOutputComponent("c", "default", "contacts"); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /home/runner/opt/include/plumed_master/core/Action.h:27: /home/runner/opt/include/plumed_master/core/../tools/Keywords.h:268:8: note: declared here 268 | void addOutputComponent( const std::string& name, const std::string& key, const std::string& descr ); | ^~~~~~~~~~~~~~~~~~ Contacts.GygNVm.cpp: In constructor ‘PLMD::colvar::Contacts::Contacts(const PLMD::ActionOptions&)’: Contacts.GygNVm.cpp:93:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 93 | for(unsigned int i=0; i<num_atomsa; i++) | ~^~~~~~~~~~~ Contacts.GygNVm.cpp:99:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 99 | for(unsigned int i=0; i<num_atomsb; i++) | ~^~~~~~~~~~~ Contacts.GygNVm.cpp:124:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 124 | for(unsigned int i=0;i<num_atomsa;++i){ | ~^~~~~~~~~~~ Contacts.GygNVm.cpp:129:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 129 | for(unsigned int i=0;i<num_atomsb;++i){ | ~^~~~~~~~~~~ terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError' what(): (tools/Keywords.cpp:483) void PLMD::Keywords::addFlag(std::string_view, bool, std::string_view) +++ assertion failed: !defaultValue the second argument to addFlag must be false COMPONENTS [pkrvmbietmlfzoi:07996] *** Process received signal *** [pkrvmbietmlfzoi:07996] Signal: Aborted (6) [pkrvmbietmlfzoi:07996] Signal code: (-6) [pkrvmbietmlfzoi:07996] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7fdc74c45330] [pkrvmbietmlfzoi:07996] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7fdc74c9eb2c] [pkrvmbietmlfzoi:07996] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7fdc74c4527e] [pkrvmbietmlfzoi:07996] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7fdc74c288ff] [pkrvmbietmlfzoi:07996] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ff5)[0x7fdc750a5ff5] [pkrvmbietmlfzoi:07996] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb0da)[0x7fdc750bb0da] [pkrvmbietmlfzoi:07996] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x7fdc750a5a55] [pkrvmbietmlfzoi:07996] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5a6f)[0x7fdc750a5a6f] [pkrvmbietmlfzoi:07996] [ 8] plumed_master(+0x146dd)[0x55d8cb7fd6dd] [pkrvmbietmlfzoi:07996] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7fdc74c2a1ca] [pkrvmbietmlfzoi:07996] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7fdc74c2a28b] [pkrvmbietmlfzoi:07996] [11] plumed_master(+0x15365)[0x55d8cb7fe365] [pkrvmbietmlfzoi:07996] *** End of error message ***