Project ID: plumID:21.035
Stderr for source: CmuMD-NaCl/flat-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">> In file included from /home/runner/opt/include/plumed_master/colvar/../core/../tools/Tools.h:27, from /home/runner/opt/include/plumed_master/colvar/../core/Action.h:28, 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 Cmumd.4pSXPf.cpp:22: /home/runner/opt/include/plumed_master/colvar/../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/colvar/../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/colvar/../core/ActionAtomistic.h:27: /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:94: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 94 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:100: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 100 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:102: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 102 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:108: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 108 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:112: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 112 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:116: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 116 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../core/../tools/Pbc.h:120: warning: ignoring ‘#pragma acc routine’ [-Wunknown-pragmas] 120 | #pragma acc routine seq | /home/runner/opt/include/plumed_master/colvar/../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/colvar/../core/Colvar.h:27: /home/runner/opt/include/plumed_master/colvar/../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/colvar/../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/colvar/../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/colvar/../core/../tools/Matrix.h:123: warning: ignoring ‘#pragma acc exit’ [-Wunknown-pragmas] 123 | #pragma acc exit data delete( this[0:1]) | Cmumd.4pSXPf.cpp: In member function ‘virtual void PLMD::colvar::CmuMD::calculate()’: Cmumd.4pSXPf.cpp:290:14: error: invalid use of incomplete type ‘class PLMD::Communicator’ 290 | stride=comm.Get_size(); //Number of processes | ^~~~ 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: /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ Cmumd.4pSXPf.cpp:291:12: error: invalid use of incomplete type ‘class PLMD::Communicator’ 291 | rank=comm.Get_rank(); //Rank of present process | ^~~~ /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ Cmumd.4pSXPf.cpp:392:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 392 | comm.Sum(histz); | ^~~~ /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ Cmumd.4pSXPf.cpp:393:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 393 | comm.Sum(com_solv); | ^~~~ /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ Cmumd.4pSXPf.cpp:644:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 644 | comm.Sum(deriv); | ^~~~ /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ Cmumd.4pSXPf.cpp:645:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 645 | comm.Sum(n_CR); | ^~~~ /home/runner/opt/include/plumed_master/colvar/../core/../tools/FileBase.h:29:7: note: forward declaration of ‘class PLMD::Communicator’ 29 | class Communicator; | ^~~~~~~~~~~~ Cmumd.4pSXPf.cpp:646:7: error: invalid use of incomplete type ‘class PLMD::Communicator’ 646 | comm.Sum(virial); | ^~~~ /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:1502) void PLMD::PlumedMain::load(const std::string&) An error happened while executing command env PLUMED_ROOT='/home/runner/opt/lib/plumed_master' PLUMED_VERSION='2.11.0-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 ./Cmumd.2.11.0-dev.so Cmumd.cpp [pkrvmbietmlfzoi:09984] *** Process received signal *** [pkrvmbietmlfzoi:09984] Signal: Aborted (6) [pkrvmbietmlfzoi:09984] Signal code: (-6) [pkrvmbietmlfzoi:09984] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x7f73a7245330] [pkrvmbietmlfzoi:09984] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11c)[0x7f73a729eb2c] [pkrvmbietmlfzoi:09984] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x1e)[0x7f73a724527e] [pkrvmbietmlfzoi:09984] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xdf)[0x7f73a72288ff] [pkrvmbietmlfzoi:09984] [ 4] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5ff5)[0x7f73a76a5ff5] [pkrvmbietmlfzoi:09984] [ 5] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xbb0da)[0x7f73a76bb0da] [pkrvmbietmlfzoi:09984] [ 6] /lib/x86_64-linux-gnu/libstdc++.so.6(_ZSt10unexpectedv+0x0)[0x7f73a76a5a55] [pkrvmbietmlfzoi:09984] [ 7] /lib/x86_64-linux-gnu/libstdc++.so.6(+0xa5a6f)[0x7f73a76a5a6f] [pkrvmbietmlfzoi:09984] [ 8] plumed_master(+0x146dd)[0x559d130dc6dd] [pkrvmbietmlfzoi:09984] [ 9] /lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x7f73a722a1ca] [pkrvmbietmlfzoi:09984] [10] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7f73a722a28b] [pkrvmbietmlfzoi:09984] [11] plumed_master(+0x15365)[0x559d130dd365] [pkrvmbietmlfzoi:09984] *** End of error message ***