Task 38644115

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>
07:13:56 (30912): wrapper (7.9.26016): starting
07:13:56 (30912): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A03_A13_0.pdb
QB_A03_A13_0.xml
QB_A03_A13.inpcrd
QB_A03_A13_input.yaml
QB_A03_A13.pdb
QB_A03_A13.prmtop
QB_A03_A13_sys.xml
run.bat
run.sh
07:13:59 (30912): Library/usr/bin/tar.exe exited; CPU time 0.000000
07:13:59 (30912): 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 'D:\Boinc\slots\13\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 'D:\Boinc\slots\13\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) : {3835412} normal block at 0x0000029EA6E0A140, 8 bytes long.
 Data: <  )     > 00 00 29 A7 9E 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833966} normal block at 0x0000029EA6E3BF10, 1080 bytes long.
 Data: < h              > C0 68 00 00 CD CD CD CD E8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {315} normal block at 0x0000029EA6E11B80, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
09:08:04 (35136): wrapper (7.9.26016): starting
09:08:04 (35136): 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 "D:\Boinc\slots\13\tmp" existiert bereits.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1754} normal block at 0x000001E6EC0E5430, 8 bytes long.
 Data: <        > 00 00 06 EC E6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x000001E6EC0E6510, 1080 bytes long.
 Data: <        D       > F4 8A 00 00 CD CD CD CD 44 01 00 00 00 00 00 00 
Object dump complete.
10:36:02 (29660): wrapper (7.9.26016): starting
10:36:02 (29660): 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 "D:\Boinc\slots\13\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 "D:\Boinc\slots\13\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc\slots\13\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc\slots\13\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
11:50:15 (29660): C:/Windows/system32/cmd.exe exited; CPU time 4130.531250
11:50:15 (29660): app exit status: 0x16
11:50:15 (29660): called boinc_finish(195)
0 bytes in 0 Free Blocks.
176 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: 85755735 bytes.
Dumping objects ->
{1842} normal block at 0x000001ED2C01F7E0, 48 bytes long.
 Data: <PATH=D:\Boinc\sl> 50 41 54 48 3D 44 3A 5C 42 6F 69 6E 63 5C 73 6C 
{1831} normal block at 0x000001ED2C01DF10, 32 bytes long.
 Data: <HOME=D:\Boinc\sl> 48 4F 4D 45 3D 44 3A 5C 42 6F 69 6E 63 5C 73 6C 
{1820} normal block at 0x000001ED2C01EA50, 32 bytes long.
 Data: <TMP=D:\Boinc\slo> 54 4D 50 3D 44 3A 5C 42 6F 69 6E 63 5C 73 6C 6F 
{1809} normal block at 0x000001ED2C01E330, 32 bytes long.
 Data: <TEMP=D:\Boinc\sl> 54 45 4D 50 3D 44 3A 5C 42 6F 69 6E 63 5C 73 6C 
{1798} normal block at 0x000001ED2C01E210, 32 bytes long.
 Data: <TMPDIR=D:\Boinc\> 54 4D 50 44 49 52 3D 44 3A 5C 42 6F 69 6E 63 5C 
{1767} normal block at 0x000001ED2C01FD20, 48 bytes long.
 Data: <PATH=D:\Boinc\sl> 50 41 54 48 3D 44 3A 5C 42 6F 69 6E 63 5C 73 6C 
..\api\boinc_api.cpp(309) : {1754} normal block at 0x000001ED2C025270, 8 bytes long.
 Data: <  O,    > 00 00 4F 2C ED 01 00 00 
{309} normal block at 0x000001ED2C025D60, 8 bytes long.
 Data: < c ,    > F0 63 02 2C ED 01 00 00 
{300} normal block at 0x000001ED2C015620, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{299} normal block at 0x000001ED2C0251D0, 16 bytes long.
 Data: < b ,            > F8 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x000001ED2C0253B0, 16 bytes long.
 Data: < b ,            > D0 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x000001ED2C01E870, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{296} normal block at 0x000001ED2C0258B0, 16 bytes long.
 Data: < b ,            > A8 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000001ED2C025C20, 16 bytes long.
 Data: < b ,            > 80 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000001ED2C025040, 16 bytes long.
 Data: <Xb ,            > 58 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001ED2C025DB0, 16 bytes long.
 Data: <0b ,            > 30 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001ED2C01FAF0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{291} normal block at 0x000001ED2C0259A0, 16 bytes long.
 Data: <   ,            > E8 F4 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001ED2C01E7B0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{289} normal block at 0x000001ED2C025770, 16 bytes long.
 Data: <   ,            > C0 F4 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001ED2C025A40, 16 bytes long.
 Data: <   ,            > 98 F4 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001ED2C024F00, 16 bytes long.
 Data: <p  ,            > 70 F4 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001ED2C025180, 16 bytes long.
 Data: <H  ,            > 48 F4 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001ED2C025630, 16 bytes long.
 Data: <   ,            > 20 F4 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001ED2C024F50, 16 bytes long.
 Data: <   ,            > F8 F3 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001ED2C01E630, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{281} normal block at 0x000001ED2C025130, 16 bytes long.
 Data: <   ,            > D0 F3 00 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001ED2C00F3D0, 320 bytes long.
 Data: <0Q ,    0  ,    > 30 51 02 2C ED 01 00 00 30 E6 01 2C ED 01 00 00 
{279} normal block at 0x000001ED2C025900, 16 bytes long.
 Data: < b ,            > 10 62 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001ED2C0250E0, 16 bytes long.
 Data: < a ,            > E8 61 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001ED2C01E0F0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{276} normal block at 0x000001ED2C024FF0, 16 bytes long.
 Data: < a ,            > C0 61 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001ED2C01EAB0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{274} normal block at 0x000001ED2C0255E0, 16 bytes long.
 Data: < a ,            > 08 61 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001ED2C025D10, 16 bytes long.
 Data: < ` ,            > E0 60 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001ED2C025860, 16 bytes long.
 Data: < ` ,            > B8 60 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001ED2C025360, 16 bytes long.
 Data: < ` ,            > 90 60 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001ED2C0254F0, 16 bytes long.
 Data: <h` ,            > 68 60 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001ED2C024EB0, 16 bytes long.
 Data: <@` ,            > 40 60 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001ED2C025400, 16 bytes long.
 Data: <   ,            > 10 FA 01 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001ED2C01FA10, 40 bytes long.
 Data: < T ,       ,    > 00 54 02 2C ED 01 00 00 20 FD 01 2C ED 01 00 00 
{265} normal block at 0x000001ED2C024FA0, 16 bytes long.
 Data: < ` ,            > 20 60 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001ED2C024E60, 16 bytes long.
 Data: < _ ,            > F8 5F 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001ED2C01E270, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{262} normal block at 0x000001ED2C025540, 16 bytes long.
 Data: < _ ,            > D0 5F 02 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001ED2C025FD0, 992 bytes long.
 Data: <@U ,    p  ,    > 40 55 02 2C ED 01 00 00 70 E2 01 2C ED 01 00 00 
{97} normal block at 0x000001ED2C01DDF0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{96} normal block at 0x000001ED2C01A840, 16 bytes long.
 Data: <p  ,            > 70 F7 01 2C ED 01 00 00 00 00 00 00 00 00 00 00 
{95} normal block at 0x000001ED2C01F770, 40 bytes long.
 Data: <@  ,       ,    > 40 A8 01 2C ED 01 00 00 F0 DD 01 2C ED 01 00 00 
{74} normal block at 0x000001ED2C019FD0, 16 bytes long.
 Data: <  ap            > 80 EA 61 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000001ED2C01A480, 16 bytes long.
 Data: <@ ap            > 40 E9 61 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000001ED2C01AA70, 16 bytes long.
 Data: < W^p            > F8 57 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000001ED2C019F80, 16 bytes long.
 Data: < W^p            > D8 57 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000001ED2C01A1B0, 16 bytes long.
 Data: <P ^p            > 50 04 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001ED2C019F30, 16 bytes long.
 Data: <0 ^p            > 30 04 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001ED2C01A020, 16 bytes long.
 Data: <  ^p            > E0 02 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001ED2C019E40, 16 bytes long.
 Data: <  ^p            > 10 04 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001ED2C01A9D0, 16 bytes long.
 Data: <p ^p            > 70 04 5E 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001ED2C019DA0, 16 bytes long.
 Data: <  \p            > 18 C0 5C 70 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra