Task 38643711

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>
23:31:13 (45844): wrapper (7.9.26016): starting
23:31:13 (45844): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A04_A02_0.pdb
QB_A04_A02_0.xml
QB_A04_A02.inpcrd
QB_A04_A02_input.yaml
QB_A04_A02.pdb
QB_A04_A02.prmtop
QB_A04_A02_sys.xml
run.bat
run.sh
23:31:15 (45844): Library/usr/bin/tar.exe exited; CPU time 0.015625
23:31:15 (45844): 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 'E:\ProgramData\BOINC\slots\6\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 'E:\ProgramData\BOINC\slots\6\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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835162} normal block at 0x000001A127707FF0, 8 bytes long.
 Data: <  F)    > 00 00 46 29 A1 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x000001A1293E9060, 1080 bytes long.
 Data: <T               > 54 18 00 00 CD CD CD CD B8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x000001A1277137A0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
03:09:11 (42948): wrapper (7.9.26016): starting
03:09:11 (42948): 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 "E:\ProgramData\BOINC\slots\6\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 "E:\ProgramData\BOINC\slots\6\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\ProgramData\BOINC\slots\6\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
04:44:19 (42948): C:/Windows/system32/cmd.exe exited; CPU time 5934.234375
04:44:19 (42948): app exit status: 0x16
04:44:19 (42948): called boinc_finish(195)
0 bytes in 0 Free Blocks.
256 bytes in 6 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: 101234308 bytes.
Dumping objects ->
{1598} normal block at 0x00000229791EE910, 48 bytes long.
 Data: <PATH=E:\ProgramD> 50 41 54 48 3D 45 3A 5C 50 72 6F 67 72 61 6D 44 
{1587} normal block at 0x00000229791EE6E0, 48 bytes long.
 Data: <HOME=E:\ProgramD> 48 4F 4D 45 3D 45 3A 5C 50 72 6F 67 72 61 6D 44 
{1576} normal block at 0x00000229791EE670, 48 bytes long.
 Data: <TMP=E:\ProgramDa> 54 4D 50 3D 45 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1565} normal block at 0x00000229791EE520, 48 bytes long.
 Data: <TEMP=E:\ProgramD> 54 45 4D 50 3D 45 3A 5C 50 72 6F 67 72 61 6D 44 
{1554} normal block at 0x00000229791EEC20, 48 bytes long.
 Data: <TMPDIR=E:\Progra> 54 4D 50 44 49 52 3D 45 3A 5C 50 72 6F 67 72 61 
{1523} normal block at 0x00000229791D6C00, 64 bytes long.
 Data: <PATH=E:\ProgramD> 50 41 54 48 3D 45 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {1510} normal block at 0x00000229791F4C40, 8 bytes long.
 Data: <   y)   > 00 00 1C 79 29 02 00 00 
{303} normal block at 0x00000229791F4A10, 8 bytes long.
 Data: < Y y)   > 90 59 1F 79 29 02 00 00 
{294} normal block at 0x00000229791D6500, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{293} normal block at 0x00000229791F47E0, 16 bytes long.
 Data: < X y)           > 98 58 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000229791F5050, 16 bytes long.
 Data: <pX y)           > 70 58 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000229791ECD00, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{290} normal block at 0x00000229791F4790, 16 bytes long.
 Data: <HX y)           > 48 58 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000229791F5230, 16 bytes long.
 Data: < X y)           > 20 58 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000229791F4D80, 16 bytes long.
 Data: < W y)           > F8 57 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000229791F48D0, 16 bytes long.
 Data: < W y)           > D0 57 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x00000229791EEBB0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x00000229791F5500, 16 bytes long.
 Data: < d y)           > 98 64 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000229791EC0A0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{283} normal block at 0x00000229791F4B50, 16 bytes long.
 Data: <pd y)           > 70 64 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000229791F4BF0, 16 bytes long.
 Data: <Hd y)           > 48 64 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000229791F5000, 16 bytes long.
 Data: < d y)           > 20 64 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000229791F4AB0, 16 bytes long.
 Data: < c y)           > F8 63 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000229791F46F0, 16 bytes long.
 Data: < c y)           > D0 63 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000229791F4A60, 16 bytes long.
 Data: < c y)           > A8 63 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000229791EC880, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{275} normal block at 0x00000229791F46A0, 16 bytes long.
 Data: < c y)           > 80 63 1D 79 29 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000229791D6380, 320 bytes long.
 Data: < F y)      y)   > A0 46 1F 79 29 02 00 00 80 C8 1E 79 29 02 00 00 
{273} normal block at 0x00000229791F5320, 16 bytes long.
 Data: < W y)           > B0 57 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000229791F5460, 16 bytes long.
 Data: < W y)           > 88 57 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000229791ECBE0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{270} normal block at 0x00000229791F4BA0, 16 bytes long.
 Data: <`W y)           > 60 57 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000229791EC280, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{268} normal block at 0x00000229791F4CE0, 16 bytes long.
 Data: < V y)           > A8 56 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000229791F5190, 16 bytes long.
 Data: < V y)           > 80 56 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000229791F4830, 16 bytes long.
 Data: <XV y)           > 58 56 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000229791F5140, 16 bytes long.
 Data: <0V y)           > 30 56 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000229791F4E20, 16 bytes long.
 Data: < V y)           > 08 56 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000229791F5370, 16 bytes long.
 Data: < U y)           > E0 55 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000229791F51E0, 16 bytes long.
 Data: <   y)           > D0 EA 1E 79 29 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000229791EEAD0, 40 bytes long.
 Data: < Q y)    l y)   > E0 51 1F 79 29 02 00 00 00 6C 1D 79 29 02 00 00 
{259} normal block at 0x00000229791F5410, 16 bytes long.
 Data: < U y)           > C0 55 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x00000229791F4FB0, 16 bytes long.
 Data: < U y)           > 98 55 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x00000229791ECCA0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{256} normal block at 0x00000229791F50F0, 16 bytes long.
 Data: <pU y)           > 70 55 1F 79 29 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x00000229791F5570, 992 bytes long.
 Data: < P y)      y)   > F0 50 1F 79 29 02 00 00 A0 CC 1E 79 29 02 00 00 
{91} normal block at 0x00000229791EC820, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{90} normal block at 0x00000229791E8090, 16 bytes long.
 Data: <P  y)           > 50 E7 1E 79 29 02 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x00000229791EE750, 40 bytes long.
 Data: <   y)      y)   > 90 80 1E 79 29 02 00 00 20 C8 1E 79 29 02 00 00 
{68} normal block at 0x00000229791E7AF0, 16 bytes long.
 Data: <  ?C            > 80 EA 3F 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000229791E7370, 16 bytes long.
 Data: <@ ?C            > 40 E9 3F 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000229791E7AA0, 16 bytes long.
 Data: < W<C            > F8 57 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000229791E7C30, 16 bytes long.
 Data: < W<C            > D8 57 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000229791E80E0, 16 bytes long.
 Data: <P <C            > 50 04 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000229791E8130, 16 bytes long.
 Data: <0 <C            > 30 04 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000229791E7FA0, 16 bytes long.
 Data: <  <C            > E0 02 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000229791E7F00, 16 bytes long.
 Data: <  <C            > 10 04 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000229791E8180, 16 bytes long.
 Data: <p <C            > 70 04 3C 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x00000229791E7CD0, 16 bytes long.
 Data: <  :C            > 18 C0 3A 43 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra