Task 38644910

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
Das Betriebssystem kann (null) nicht ausf�hren.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
15:03:35 (29604): wrapper (7.9.26016): starting
15:03:35 (29604): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A23_0.pdb
QB_A20_A23_0.xml
QB_A20_A23.inpcrd
QB_A20_A23_input.yaml
QB_A20_A23.pdb
QB_A20_A23.prmtop
QB_A20_A23_sys.xml
run.bat
run.sh
15:03:36 (29604): Library/usr/bin/tar.exe exited; CPU time 0.015625
15:03:36 (29604): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
  WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\7\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  WARNING: The scripts abfe_production.exe, abfe_structprep.exe, make_atm_system_from_amber.exe, make_atm_system_from_pdb.exe, make_atm_system_from_rcpt_lig.exe, rbfe_production.exe and rbfe_structprep.exe are installed in 'C:\ProgramData\BOINC\slots\7\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
08:26:35 (50736): wrapper (7.9.26016): starting
08:26:35 (50736): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
Ein Unterverzeichnis oder eine Datei mit dem Namen "C:\ProgramData\BOINC\slots\7\tmp" existiert bereits.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\ProgramData\BOINC\slots\7\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\7\Lib\site-packages\openmm\openmm.py", line 5022, in getState
    state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Particle coordinate is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan
10:17:36 (50736): C:/Windows/system32/cmd.exe exited; CPU time 6573.875000
10:17:36 (50736): app exit status: 0x16
10:17:36 (50736): called boinc_finish(195)
0 bytes in 0 Free Blocks.
536 bytes in 8 Normal Blocks.
1144 bytes in 1 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 123120918 bytes.
Dumping objects ->
{1953} normal block at 0x000002143EC84ED0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1942} normal block at 0x000002143EC84AE0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1931} normal block at 0x000002143EC84920, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1920} normal block at 0x000002143EC84B50, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1909} normal block at 0x000002143EC84E60, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1878} normal block at 0x000002143EC6F370, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1867} normal block at 0x000002143EC6B450, 140 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {1864} normal block at 0x000002143EC85DA0, 8 bytes long.
 Data: <   >    > 00 00 C0 3E 14 02 00 00 
{1064} normal block at 0x000002143EC6B550, 140 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{305} normal block at 0x000002143EC85A80, 8 bytes long.
 Data: < i >    > 10 69 C8 3E 14 02 00 00 
{296} normal block at 0x000002143EC762C0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{295} normal block at 0x000002143EC85990, 16 bytes long.
 Data: < h >            > 18 68 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000002143EC86160, 16 bytes long.
 Data: < g >            > F0 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000002143EC7FE70, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{292} normal block at 0x000002143EC85EE0, 16 bytes long.
 Data: < g >            > C8 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002143EC860C0, 16 bytes long.
 Data: < g >            > A0 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000002143EC85E90, 16 bytes long.
 Data: <xg >            > 78 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002143EC85620, 16 bytes long.
 Data: <Pg >            > 50 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000002143EC84CA0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{287} normal block at 0x000002143EC85D50, 16 bytes long.
 Data: <h  >            > 68 E8 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000002143EC7FA50, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{285} normal block at 0x000002143EC86340, 16 bytes long.
 Data: <@  >            > 40 E8 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000002143EC858F0, 16 bytes long.
 Data: <   >            > 18 E8 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000002143EC86020, 16 bytes long.
 Data: <   >            > F0 E7 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002143EC85A30, 16 bytes long.
 Data: <   >            > C8 E7 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002143EC862F0, 16 bytes long.
 Data: <   >            > A0 E7 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002143EC85D00, 16 bytes long.
 Data: <x  >            > 78 E7 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000002143EC801D0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{277} normal block at 0x000002143EC85DF0, 16 bytes long.
 Data: <P  >            > 50 E7 C7 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000002143EC7E750, 320 bytes long.
 Data: < ] >       >    > F0 5D C8 3E 14 02 00 00 D0 01 C8 3E 14 02 00 00 
{275} normal block at 0x000002143EC85CB0, 16 bytes long.
 Data: <0g >            > 30 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002143EC85800, 16 bytes long.
 Data: < g >            > 08 67 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000002143EC807D0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{272} normal block at 0x000002143EC85C10, 16 bytes long.
 Data: < f >            > E0 66 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000002143EC7FD50, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{270} normal block at 0x000002143EC86110, 16 bytes long.
 Data: <(f >            > 28 66 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002143EC858A0, 16 bytes long.
 Data: < f >            > 00 66 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002143EC85BC0, 16 bytes long.
 Data: < e >            > D8 65 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000002143EC86070, 16 bytes long.
 Data: < e >            > B0 65 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002143EC85B20, 16 bytes long.
 Data: < e >            > 88 65 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002143EC855D0, 16 bytes long.
 Data: <`e >            > 60 65 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002143EC85AD0, 16 bytes long.
 Data: < P >            > 20 50 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000002143EC85020, 40 bytes long.
 Data: < Z >    p  >    > D0 5A C8 3E 14 02 00 00 70 F3 C6 3E 14 02 00 00 
{261} normal block at 0x000002143EC862A0, 16 bytes long.
 Data: <@e >            > 40 65 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002143EC85580, 16 bytes long.
 Data: < e >            > 18 65 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000002143EC7FC90, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{258} normal block at 0x000002143EC85F80, 16 bytes long.
 Data: < d >            > F0 64 C8 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000002143EC864F0, 992 bytes long.
 Data: < _ >       >    > 80 5F C8 3E 14 02 00 00 90 FC C7 3E 14 02 00 00 
{93} normal block at 0x000002143EC7FDB0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{92} normal block at 0x000002143EC7EDF0, 16 bytes long.
 Data: <p  >            > 70 C1 C6 3E 14 02 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x000002143EC6C170, 40 bytes long.
 Data: <   >       >    > F0 ED C7 3E 14 02 00 00 B0 FD C7 3E 14 02 00 00 
{70} normal block at 0x000002143EC7ED00, 16 bytes long.
 Data: <                > 80 EA C2 A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002143EC7F480, 16 bytes long.
 Data: <@               > 40 E9 C2 A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002143EC7F610, 16 bytes long.
 Data: < W              > F8 57 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002143EC7F7A0, 16 bytes long.
 Data: < W              > D8 57 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002143EC7F520, 16 bytes long.
 Data: <P               > 50 04 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002143EC7F890, 16 bytes long.
 Data: <0               > 30 04 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002143EC7F700, 16 bytes long.
 Data: <                > E0 02 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002143EC7EFD0, 16 bytes long.
 Data: <                > 10 04 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002143EC7F6B0, 16 bytes long.
 Data: <p               > 70 04 BF A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002143EC7EEE0, 16 bytes long.
 Data: <                > 18 C0 BD A3 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra