Project ID: plumID:21.005
Stderr for source: SF-prof/plumed_structure_factor_OO.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">>
../codes/StructureFactor_sphericallyAveraged.WPeWaX.cpp: In constructor ‘PLMD::colvar::StructureFactor_sphericallyAveraged::StructureFactor_sphericallyAveraged(const PLMD::ActionOptions&)’:
../codes/StructureFactor_sphericallyAveraged.WPeWaX.cpp:184:41: warning: ‘int PLMD::PlumedMain::DeprecatedAtoms::getNatoms() const’ is deprecated [-Wdeprecated-declarations]
184 | NumAtom_=plumed.getAtoms().getNatoms();
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from ../codes/StructureFactor_sphericallyAveraged.WPeWaX.cpp:8:
/home/runner/opt/include/plumed/core/PlumedMain.h:106:9: note: declared here
106 | int getNatoms() const ;
| ^~~~~~~~~
../codes/StructureFactor_sphericallyAveraged.WPeWaX.cpp:190:108: warning: ‘int PLMD::PlumedMain::DeprecatedAtoms::getNatoms() const’ is deprecated [-Wdeprecated-declarations]
190 | log.printf(" over a total of N_tot=%d, considering a number of atoms N=%d\n",plumed.getAtoms().getNatoms(),NumAtom_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/home/runner/opt/include/plumed/core/PlumedMain.h:106:9: note: declared here
106 | int getNatoms() const ;
| ^~~~~~~~~
Assembler messages:
Fatal error: can't create plumed_mklib.kC2e01/../codes/StructureFactor_sphericallyAveraged.o: No such file or directory
terminate called after throwing an instance of 'PLMD::Plumed::ExceptionError'
what():
(core/PlumedMain.cpp:1502) void PLMD::PlumedMain::load(const std::string&)
An error happened while executing command env PLUMED_ROOT='/home/runner/opt/lib/plumed' PLUMED_VERSION='2.10b' PLUMED_HTMLDIR='/home/runner/opt/share/doc/plumed' PLUMED_INCLUDEDIR='/home/runner/opt/include' PLUMED_PROGRAM_NAME='plumed' PLUMED_IS_INSTALLED='yes' "/home/runner/opt/lib/plumed"/scripts/mklib.sh -n -o ./../codes/StructureFactor_sphericallyAveraged.2.10b.so ../codes/StructureFactor_sphericallyAveraged.cpp
[pkrvmbietmlfzoi:11361] *** Process received signal ***
[pkrvmbietmlfzoi:11361] Signal: Aborted (6)
[pkrvmbietmlfzoi:11361] Signal code: (-6)
[pkrvmbietmlfzoi:11361] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7f07f5445330]
[pkrvmbietmlfzoi:11361] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7f07f549eb2c]
[pkrvmbietmlfzoi:11361] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7f07f544527e]
[pkrvmbietmlfzoi:11361] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7f07f54288ff]
[pkrvmbietmlfzoi:11361] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ff5)[0x7f07f58a5ff5]
[pkrvmbietmlfzoi:11361] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb0da)[0x7f07f58bb0da]
[pkrvmbietmlfzoi:11361] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x7f07f58a5a55]
[pkrvmbietmlfzoi:11361] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5a6f)[0x7f07f58a5a6f]
[pkrvmbietmlfzoi:11361] [ 8] plumed(+0x146dd)[0x5602564936dd]
[pkrvmbietmlfzoi:11361] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7f07f542a1ca]
[pkrvmbietmlfzoi:11361] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7f07f542a28b]
[pkrvmbietmlfzoi:11361] [11] plumed(+0x15365)[0x560256494365]
[pkrvmbietmlfzoi:11361] *** End of error message ***