Task 38596160

Stderr output

<core_client_version>8.0.4</core_client_version>
<![CDATA[
<message>
Das Betriebssystem kann (null) nicht ausf�hren.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
12:09:57 (18628): wrapper (7.9.26016): starting
12:09:57 (18628): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A08_A03_0.pdb
QB_A08_A03_0.xml
QB_A08_A03.inpcrd
QB_A08_A03_input.yaml
QB_A08_A03.pdb
QB_A08_A03.prmtop
QB_A08_A03_sys.xml
run.bat
run.sh
12:09:58 (18628): Library/usr/bin/tar.exe exited; CPU time 0.000000
12:09:58 (18628): 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 'X:\BOINC_Data\02_9002\slots\2\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 'X:\BOINC_Data\02_9002\slots\2\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.
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "X:\BOINC_Data\02_9002\slots\2\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "X:\BOINC_Data\02_9002\slots\2\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "X:\BOINC_Data\02_9002\slots\2\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
12:10:30 (18628): C:/Windows/system32/cmd.exe exited; CPU time 24.906250
12:10:30 (18628): app exit status: 0x16
12:10:30 (18628): called boinc_finish(195)
0 bytes in 0 Free Blocks.
646 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: 1019275 bytes.
Dumping objects ->
{3835681} normal block at 0x0000025053EBDF30, 48 bytes long.
 Data: <PATH=X:\BOINC_DA> 50 41 54 48 3D 58 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835670} normal block at 0x0000025053EBDFA0, 48 bytes long.
 Data: <HOME=X:\BOINC_DA> 48 4F 4D 45 3D 58 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835659} normal block at 0x0000025052286860, 48 bytes long.
 Data: <TMP=X:\BOINC_DAT> 54 4D 50 3D 58 3A 5C 42 4F 49 4E 43 5F 44 41 54 
{3835648} normal block at 0x0000025052286240, 48 bytes long.
 Data: <TEMP=X:\BOINC_DA> 54 45 4D 50 3D 58 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835637} normal block at 0x0000025052286630, 48 bytes long.
 Data: <TMPDIR=X:\BOINC_> 54 4D 50 44 49 52 3D 58 3A 5C 42 4F 49 4E 43 5F 
{3835606} normal block at 0x0000025053F08B40, 64 bytes long.
 Data: <PATH=X:\BOINC_DA> 50 41 54 48 3D 58 3A 5C 42 4F 49 4E 43 5F 44 41 
{3835595} normal block at 0x0000025053F19BA0, 195 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) : {3835592} normal block at 0x000002505227EAA0, 8 bytes long.
 Data: <  $RP   > 00 00 24 52 50 02 00 00 
{3834752} normal block at 0x0000025053F1A7A0, 195 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{3833953} normal block at 0x000002505227E7D0, 8 bytes long.
 Data: <p &#233;SP   > 70 05 E9 53 50 02 00 00 
..\zip\boinc_zip.cpp(122) : {308} normal block at 0x0000025052272190, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000025052272DF0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{292} normal block at 0x0000025052287190, 16 bytes long.
 Data: <X|(RP           > 58 7C 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000025052287780, 16 bytes long.
 Data: <0|(RP           > 30 7C 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000025052281F40, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{289} normal block at 0x0000025052287140, 16 bytes long.
 Data: < |(RP           > 08 7C 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000025052286C90, 16 bytes long.
 Data: <&#224;{(RP           > E0 7B 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000250522870A0, 16 bytes long.
 Data: <&#184;{(RP           > B8 7B 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000025052287690, 16 bytes long.
 Data: < {(RP           > 90 7B 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000025052286400, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{284} normal block at 0x0000025052286BF0, 16 bytes long.
 Data: <&#216; 'RP           > D8 03 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000025052281EE0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{282} normal block at 0x0000025052287410, 16 bytes long.
 Data: <&#176; 'RP           > B0 03 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000250522877D0, 16 bytes long.
 Data: <  'RP           > 88 03 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000025052286BA0, 16 bytes long.
 Data: <` 'RP           > 60 03 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000250522874B0, 16 bytes long.
 Data: <8 'RP           > 38 03 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000250522870F0, 16 bytes long.
 Data: <  'RP           > 10 03 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000025052286A10, 16 bytes long.
 Data: <&#232; 'RP           > E8 02 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000025052282840, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{274} normal block at 0x0000025052286C40, 16 bytes long.
 Data: <&#192; 'RP           > C0 02 27 52 50 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000250522702C0, 320 bytes long.
 Data: <@l(RP   @((RP   > 40 6C 28 52 50 02 00 00 40 28 28 52 50 02 00 00 
{272} normal block at 0x00000250522873C0, 16 bytes long.
 Data: <p{(RP           > 70 7B 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000025052286D80, 16 bytes long.
 Data: <H{(RP           > 48 7B 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000025052282180, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{269} normal block at 0x0000025052287370, 16 bytes long.
 Data: < {(RP           > 20 7B 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000025052282960, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{267} normal block at 0x0000025052286F60, 16 bytes long.
 Data: <hz(RP           > 68 7A 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000025052287050, 16 bytes long.
 Data: <@z(RP           > 40 7A 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000025052286D30, 16 bytes long.
 Data: < z(RP           > 18 7A 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000025052287730, 16 bytes long.
 Data: <&#240;y(RP           > F0 79 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000025052286F10, 16 bytes long.
 Data: <&#200;y(RP           > C8 79 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000025052286E70, 16 bytes long.
 Data: <&#160;y(RP           > A0 79 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000025052286AB0, 16 bytes long.
 Data: <&#176;b(RP           > B0 62 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000250522862B0, 40 bytes long.
 Data: <&#176;j(RP   @&#139;&#240;SP   > B0 6A 28 52 50 02 00 00 40 8B F0 53 50 02 00 00 
{258} normal block at 0x0000025052286B50, 16 bytes long.
 Data: < y(RP           > 80 79 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000025052286E20, 16 bytes long.
 Data: <Xy(RP           > 58 79 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000025052282BA0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{255} normal block at 0x0000025052286DD0, 16 bytes long.
 Data: <0y(RP           > 30 79 28 52 50 02 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x0000025052287930, 992 bytes long.
 Data: <&#208;m(RP   &#160;+(RP   > D0 6D 28 52 50 02 00 00 A0 2B 28 52 50 02 00 00 
{90} normal block at 0x0000025052281E20, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{89} normal block at 0x000002505227EB90, 16 bytes long.
 Data: <&#240;&#212;&RP           > F0 D4 26 52 50 02 00 00 00 00 00 00 00 00 00 00 
{88} normal block at 0x000002505226D4F0, 40 bytes long.
 Data: < &#235;'RP     (RP   > 90 EB 27 52 50 02 00 00 20 1E 28 52 50 02 00 00 
{67} normal block at 0x000002505227E190, 16 bytes long.
 Data: < &#234;&#208;&#219;&#247;           > 80 EA D0 DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002505227E690, 16 bytes long.
 Data: <@&#233;&#208;&#219;&#247;           > 40 E9 D0 DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002505227EF50, 16 bytes long.
 Data: <&#248;W&#205;&#219;&#247;           > F8 57 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002505227E9B0, 16 bytes long.
 Data: <&#216;W&#205;&#219;&#247;           > D8 57 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002505227ED70, 16 bytes long.
 Data: <P &#205;&#219;&#247;           > 50 04 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002505227E780, 16 bytes long.
 Data: <0 &#205;&#219;&#247;           > 30 04 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002505227EEB0, 16 bytes long.
 Data: <&#224; &#205;&#219;&#247;           > E0 02 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002505227E730, 16 bytes long.
 Data: <  &#205;&#219;&#247;           > 10 04 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000002505227E2D0, 16 bytes long.
 Data: <p &#205;&#219;&#247;           > 70 04 CD DB F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000002505227EA00, 16 bytes long.
 Data: < &#192;&#203;&#219;&#247;           > 18 C0 CB DB F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra