Task 38623469

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
The operating system cannot run <sporadic_ac>.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
11:09:26 (34732): wrapper (7.9.26016): starting
11:09:26 (34732): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A32_A07_0.pdb
QB_A32_A07_0.xml
QB_A32_A07.inpcrd
QB_A32_A07_input.yaml
QB_A32_A07.pdb
QB_A32_A07.prmtop
QB_A32_A07_sys.xml
run.bat
run.sh
11:09:27 (34732): Library/usr/bin/tar.exe exited; CPU time 0.015625
11:09:27 (34732): 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 'M:\BOINC\slots\4\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 'M:\BOINC\slots\4\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.
11:52:00 (5480): wrapper (7.9.26016): starting
11:52:00 (5480): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file M:\BOINC\slots\4\tmp already exists.
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 "M:\BOINC\slots\4\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "M:\BOINC\slots\4\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "M:\BOINC\slots\4\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
14:13:07 (5480): C:/Windows/system32/cmd.exe exited; CPU time 8143.843750
14:13:07 (5480): app exit status: 0x16
14:13:07 (5480): called boinc_finish(195)
0 bytes in 0 Free Blocks.
456 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: 134452804 bytes.
Dumping objects ->
{1968} normal block at 0x000002412CC86350, 48 bytes long.
 Data: <PATH=M:\BOINC\sl> 50 41 54 48 3D 4D 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1957} normal block at 0x000002412CC81170, 32 bytes long.
 Data: <HOME=M:\BOINC\sl> 48 4F 4D 45 3D 4D 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1946} normal block at 0x000002412CC80E70, 32 bytes long.
 Data: <TMP=M:\BOINC\slo> 54 4D 50 3D 4D 3A 5C 42 4F 49 4E 43 5C 73 6C 6F 
{1935} normal block at 0x000002412CC80FF0, 32 bytes long.
 Data: <TEMP=M:\BOINC\sl> 54 45 4D 50 3D 4D 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1924} normal block at 0x000002412CC81410, 32 bytes long.
 Data: <TMPDIR=M:\BOINC\> 54 4D 50 44 49 52 3D 4D 3A 5C 42 4F 49 4E 43 5C 
{1893} normal block at 0x000002412CC867B0, 48 bytes long.
 Data: <PATH=M:\BOINC\sl> 50 41 54 48 3D 4D 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1882} normal block at 0x000002412CC89700, 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) : {1879} normal block at 0x000002412CC86B20, 8 bytes long.
 Data: <   ,A   > 00 00 C0 2C 41 02 00 00 
{1079} normal block at 0x000002412CC72130, 140 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{308} normal block at 0x000002412CC87160, 8 bytes long.
 Data: <`~ ,A   > 60 7E C8 2C 41 02 00 00 
{299} normal block at 0x000002412CC73970, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{298} normal block at 0x000002412CC86A80, 16 bytes long.
 Data: <h} ,A           > 68 7D C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x000002412CC87520, 16 bytes long.
 Data: <@} ,A           > 40 7D C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x000002412CC81110, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{295} normal block at 0x000002412CC87110, 16 bytes long.
 Data: < } ,A           > 18 7D C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000002412CC877A0, 16 bytes long.
 Data: < | ,A           > F0 7C C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000002412CC86B70, 16 bytes long.
 Data: < | ,A           > C8 7C C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002412CC874D0, 16 bytes long.
 Data: < | ,A           > A0 7C C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002412CC86430, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{290} normal block at 0x000002412CC86C60, 16 bytes long.
 Data: <H  ,A           > 48 08 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002412CC80DB0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{288} normal block at 0x000002412CC86D50, 16 bytes long.
 Data: <   ,A           > 20 08 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000002412CC87430, 16 bytes long.
 Data: <   ,A           > F8 07 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000002412CC873E0, 16 bytes long.
 Data: <   ,A           > D0 07 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002412CC87750, 16 bytes long.
 Data: <   ,A           > A8 07 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000002412CC872F0, 16 bytes long.
 Data: <   ,A           > 80 07 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000002412CC870C0, 16 bytes long.
 Data: <X  ,A           > 58 07 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002412CC818F0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{280} normal block at 0x000002412CC87070, 16 bytes long.
 Data: <0  ,A           > 30 07 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002412CC70730, 320 bytes long.
 Data: <pp ,A      ,A   > 70 70 C8 2C 41 02 00 00 F0 18 C8 2C 41 02 00 00 
{278} normal block at 0x000002412CC87890, 16 bytes long.
 Data: < | ,A           > 80 7C C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002412CC87020, 16 bytes long.
 Data: <X| ,A           > 58 7C C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000002412CC812F0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{275} normal block at 0x000002412CC87700, 16 bytes long.
 Data: <0| ,A           > 30 7C C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002412CC80E10, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{273} normal block at 0x000002412CC87390, 16 bytes long.
 Data: <x{ ,A           > 78 7B C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002412CC87660, 16 bytes long.
 Data: <P{ ,A           > 50 7B C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000002412CC878E0, 16 bytes long.
 Data: <({ ,A           > 28 7B C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000002412CC876B0, 16 bytes long.
 Data: < { ,A           > 00 7B C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002412CC87840, 16 bytes long.
 Data: < z ,A           > D8 7A C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002412CC86F30, 16 bytes long.
 Data: < z ,A           > B0 7A C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002412CC879D0, 16 bytes long.
 Data: < b ,A           > E0 62 C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002412CC862E0, 40 bytes long.
 Data: < y ,A    g ,A   > D0 79 C8 2C 41 02 00 00 B0 67 C8 2C 41 02 00 00 
{264} normal block at 0x000002412CC877F0, 16 bytes long.
 Data: < z ,A           > 90 7A C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002412CC86FD0, 16 bytes long.
 Data: <hz ,A           > 68 7A C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000002412CC81290, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{261} normal block at 0x000002412CC87610, 16 bytes long.
 Data: <@z ,A           > 40 7A C8 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002412CC87A40, 992 bytes long.
 Data: < v ,A      ,A   > 10 76 C8 2C 41 02 00 00 90 12 C8 2C 41 02 00 00 
{96} normal block at 0x000002412CC817D0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{95} normal block at 0x000002412CC7EFC0, 16 bytes long.
 Data: <pB ,A           > 70 42 C7 2C 41 02 00 00 00 00 00 00 00 00 00 00 
{94} normal block at 0x000002412CC74270, 40 bytes long.
 Data: <   ,A      ,A   > C0 EF C7 2C 41 02 00 00 D0 17 C8 2C 41 02 00 00 
{73} normal block at 0x000002412CC7F290, 16 bytes long.
 Data: <                > 80 EA 03 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000002412CC7EE80, 16 bytes long.
 Data: <@               > 40 E9 03 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000002412CC7F650, 16 bytes long.
 Data: < W              > F8 57 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002412CC7EF70, 16 bytes long.
 Data: < W              > D8 57 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002412CC7F150, 16 bytes long.
 Data: <P               > 50 04 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002412CC7EE30, 16 bytes long.
 Data: <0               > 30 04 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002412CC7F2E0, 16 bytes long.
 Data: <                > E0 02 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002412CC7E980, 16 bytes long.
 Data: <                > 10 04 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002412CC7ED40, 16 bytes long.
 Data: <p               > 70 04 00 91 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002412CC7E930, 16 bytes long.
 Data: <                > 18 C0 FE 90 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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