Task 38643068

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
Das Betriebssystem kann (null) nicht ausf�hren.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
12:43:45 (40592): wrapper (7.9.26016): starting
12:43:45 (40592): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A03_0.pdb
QB_A20_A03_0.xml
QB_A20_A03.inpcrd
QB_A20_A03_input.yaml
QB_A20_A03.pdb
QB_A20_A03.prmtop
QB_A20_A03_sys.xml
run.bat
run.sh
12:43:46 (40592): Library/usr/bin/tar.exe exited; CPU time 0.000000
12:43:46 (40592): 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\0\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\0\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) : {3835140} normal block at 0x000001E3244CE540, 8 bytes long.
 Data: <   $    > 00 00 9B 24 E3 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833986} normal block at 0x000001E3245AE8D0, 1080 bytes long.
 Data: < !      x       > B0 21 01 00 CD CD CD CD 78 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {325} normal block at 0x000001E3244C8510, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
13:21:18 (74976): wrapper (7.9.26016): starting
13:21:18 (74976): 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\0\tmp" existiert bereits.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1472} normal block at 0x0000021CBFAC8C50, 8 bytes long.
 Data: <        > 00 00 06 C0 1C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {318} normal block at 0x0000021CBFAC9950, 1080 bytes long.
 Data: <\       P       > 5C 10 01 00 CD CD CD CD 50 01 00 00 00 00 00 00 
Object dump complete.
13:27:55 (49800): wrapper (7.9.26016): starting
13:27:55 (49800): 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\0\tmp" existiert bereits.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1472} normal block at 0x0000024BD8229F80, 8 bytes long.
 Data: <    K   > 00 00 8D D8 4B 02 00 00 
..\lib\diagnostics_win.cpp(417) : {318} normal block at 0x0000024BD822A860, 1080 bytes long.
 Data: <d       4       > 64 14 01 00 CD CD CD CD 34 01 00 00 00 00 00 00 
Object dump complete.
15:10:01 (69288): wrapper (7.9.26016): starting
15:10:01 (69288): 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\0\tmp" existiert bereits.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1472} normal block at 0x000002257F6B9A10, 8 bytes long.
 Data: <  g %   > 00 00 67 7F 25 02 00 00 
..\lib\diagnostics_win.cpp(417) : {318} normal block at 0x000002257F6B8FA0, 1080 bytes long.
 Data: <        T       > CC 08 01 00 CD CD CD CD 54 01 00 00 00 00 00 00 
Object dump complete.
15:16:38 (30628): wrapper (7.9.26016): starting
15:16:38 (30628): 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\0\tmp" existiert bereits.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1472} normal block at 0x000002783A6C80F0, 8 bytes long.
 Data: <   :x   > 00 00 CE 3A 78 02 00 00 
..\lib\diagnostics_win.cpp(417) : {318} normal block at 0x000002783A6C7750, 1080 bytes long.
 Data: <        8       > F8 94 00 00 CD CD CD CD 38 01 00 00 00 00 00 00 
Object dump complete.
15:27:49 (61320): wrapper (7.9.26016): starting
15:27:49 (61320): 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\0\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\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\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\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\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
15:35:18 (61320): C:/Windows/system32/cmd.exe exited; CPU time 429.281250
15:35:18 (61320): app exit status: 0x16
15:35:18 (61320): 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: 12281408 bytes.
Dumping objects ->
{1560} normal block at 0x0000027CAC856D90, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1549} normal block at 0x0000027CAC856D20, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1538} normal block at 0x0000027CAC8573B0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1527} normal block at 0x0000027CAC856EE0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1516} normal block at 0x0000027CAC857030, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1485} normal block at 0x0000027CAC8417F0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {1472} normal block at 0x0000027CAC858DE0, 8 bytes long.
 Data: <    |   > 00 00 82 AC 7C 02 00 00 
{319} normal block at 0x0000027CAC858F20, 8 bytes long.
 Data: <P   |   > 50 99 85 AC 7C 02 00 00 
{310} normal block at 0x0000027CAC849E70, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{309} normal block at 0x0000027CAC8587A0, 16 bytes long.
 Data: <X   |           > 58 98 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{308} normal block at 0x0000027CAC858CF0, 16 bytes long.
 Data: <0   |           > 30 98 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{307} normal block at 0x0000027CAC855A90, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{306} normal block at 0x0000027CAC859380, 16 bytes long.
 Data: <    |           > 08 98 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{305} normal block at 0x0000027CAC858CA0, 16 bytes long.
 Data: <    |           > E0 97 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{304} normal block at 0x0000027CAC8591A0, 16 bytes long.
 Data: <    |           > B8 97 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{303} normal block at 0x0000027CAC858700, 16 bytes long.
 Data: <    |           > 90 97 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{302} normal block at 0x0000027CAC856FC0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{301} normal block at 0x0000027CAC858980, 16 bytes long.
 Data: <    |           > F8 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x0000027CAC855EB0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{299} normal block at 0x0000027CAC859150, 16 bytes long.
 Data: <    |           > D0 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x0000027CAC858660, 16 bytes long.
 Data: <    |           > A8 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000027CAC859330, 16 bytes long.
 Data: <    |           > 80 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000027CAC858C50, 16 bytes long.
 Data: <X   |           > 58 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000027CAC858570, 16 bytes long.
 Data: <0   |           > 30 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000027CAC858C00, 16 bytes long.
 Data: <    |           > 08 13 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000027CAC855A30, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{291} normal block at 0x0000027CAC858BB0, 16 bytes long.
 Data: <    |           > E0 12 84 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000027CAC8412E0, 320 bytes long.
 Data: <    |   0Z  |   > B0 8B 85 AC 7C 02 00 00 30 5A 85 AC 7C 02 00 00 
{289} normal block at 0x0000027CAC858FC0, 16 bytes long.
 Data: <p   |           > 70 97 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000027CAC858F70, 16 bytes long.
 Data: <H   |           > 48 97 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000027CAC855430, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{286} normal block at 0x0000027CAC858D90, 16 bytes long.
 Data: <    |           > 20 97 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000027CAC855610, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{284} normal block at 0x0000027CAC858AC0, 16 bytes long.
 Data: <h   |           > 68 96 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000027CAC858930, 16 bytes long.
 Data: <@   |           > 40 96 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000027CAC858D40, 16 bytes long.
 Data: <    |           > 18 96 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000027CAC858ED0, 16 bytes long.
 Data: <    |           > F0 95 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000027CAC8592E0, 16 bytes long.
 Data: <    |           > C8 95 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000027CAC8591F0, 16 bytes long.
 Data: <    |           > A0 95 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000027CAC858A70, 16 bytes long.
 Data: < r  |           > D0 72 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000027CAC8572D0, 40 bytes long.
 Data: <p   |       |   > 70 8A 85 AC 7C 02 00 00 F0 17 84 AC 7C 02 00 00 
{275} normal block at 0x0000027CAC858890, 16 bytes long.
 Data: <    |           > 80 95 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000027CAC858E80, 16 bytes long.
 Data: <X   |           > 58 95 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000027CAC856030, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{272} normal block at 0x0000027CAC858B60, 16 bytes long.
 Data: <0   |           > 30 95 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000027CAC859530, 992 bytes long.
 Data: <`   |   0`  |   > 60 8B 85 AC 7C 02 00 00 30 60 85 AC 7C 02 00 00 
{107} normal block at 0x0000027CAC856090, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{106} normal block at 0x0000027CAC84DB80, 16 bytes long.
 Data: <@s  |           > 40 73 85 AC 7C 02 00 00 00 00 00 00 00 00 00 00 
{105} normal block at 0x0000027CAC857340, 40 bytes long.
 Data: <    |    `  |   > 80 DB 84 AC 7C 02 00 00 90 60 85 AC 7C 02 00 00 
{84} normal block at 0x0000027CAC84E2B0, 16 bytes long.
 Data: <                > 80 EA 81 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{83} normal block at 0x0000027CAC84D9F0, 16 bytes long.
 Data: <@               > 40 E9 81 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{82} normal block at 0x0000027CAC84E260, 16 bytes long.
 Data: < W~             > F8 57 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{81} normal block at 0x0000027CAC84DC70, 16 bytes long.
 Data: < W~             > D8 57 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{80} normal block at 0x0000027CAC84E490, 16 bytes long.
 Data: <P ~             > 50 04 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{79} normal block at 0x0000027CAC84D810, 16 bytes long.
 Data: <0 ~             > 30 04 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{78} normal block at 0x0000027CAC84D770, 16 bytes long.
 Data: <  ~             > E0 02 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{77} normal block at 0x0000027CAC84DB30, 16 bytes long.
 Data: <  ~             > 10 04 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x0000027CAC84D8B0, 16 bytes long.
 Data: <p ~             > 70 04 7E 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x0000027CAC84E580, 16 bytes long.
 Data: <  |             > 18 C0 7C 11 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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