Task 38611046

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
15:21:05 (3660): wrapper (7.9.26016): starting
15:21:05 (3660): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A40_A25_0.pdb
QB_A40_A25_0.xml
QB_A40_A25.inpcrd
QB_A40_A25_input.yaml
QB_A40_A25.pdb
QB_A40_A25.prmtop
QB_A40_A25_sys.xml
run.bat
run.sh
15:21:06 (3660): Library/usr/bin/tar.exe exited; CPU time 0.000000
15:21:06 (3660): 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) : {3835102} normal block at 0x00000182207556D0, 8 bytes long.
 Data: <   "    > 00 00 03 22 82 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833948} normal block at 0x000001822223FD00, 1080 bytes long.
 Data: <        L       > CC 11 00 00 CD CD CD CD 4C 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {306} normal block at 0x00000182207608B0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
12:26:25 (7664): wrapper (7.9.26016): starting
12:26:25 (7664): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\0\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 "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
13:16:09 (7664): C:/Windows/system32/cmd.exe exited; CPU time 2733.859375
13:16:09 (7664): app exit status: 0x16
13:16:09 (7664): 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: 30071912 bytes.
Dumping objects ->
{1541} normal block at 0x000002A16506A350, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1530} normal block at 0x000002A16506A2E0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1519} normal block at 0x000002A165069FD0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1508} normal block at 0x000002A16506A120, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1497} normal block at 0x000002A165069EF0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1466} normal block at 0x000002A16505A940, 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) : {1453} normal block at 0x000002A1650722F0, 8 bytes long.
 Data: <   f    > 00 00 9C 66 A1 02 00 00 
{300} normal block at 0x000002A1650727F0, 8 bytes long.
 Data: <p- e    > 70 2D 07 65 A1 02 00 00 
{291} normal block at 0x000002A165055A50, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{290} normal block at 0x000002A1650722A0, 16 bytes long.
 Data: <x, e            > 78 2C 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002A165072520, 16 bytes long.
 Data: <P, e            > 50 2C 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000002A16506C9C0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{287} normal block at 0x000002A1650728E0, 16 bytes long.
 Data: <(, e            > 28 2C 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000002A165071CB0, 16 bytes long.
 Data: < , e            > 00 2C 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000002A165071A30, 16 bytes long.
 Data: < + e            > D8 2B 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002A1650724D0, 16 bytes long.
 Data: < + e            > B0 2B 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000002A16506A270, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{282} normal block at 0x000002A165071B20, 16 bytes long.
 Data: < Y e            > E8 59 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002A16506CBA0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{280} normal block at 0x000002A165072110, 16 bytes long.
 Data: < Y e            > C0 59 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000002A165072070, 16 bytes long.
 Data: < Y e            > 98 59 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002A165072020, 16 bytes long.
 Data: <pY e            > 70 59 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000002A1650720C0, 16 bytes long.
 Data: <HY e            > 48 59 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000002A165071B70, 16 bytes long.
 Data: < Y e            > 20 59 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002A165071F30, 16 bytes long.
 Data: < X e            > F8 58 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000002A16506D200, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{272} normal block at 0x000002A165072250, 16 bytes long.
 Data: < X e            > D0 58 05 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000002A1650558D0, 320 bytes long.
 Data: <P" e       e    > 50 22 07 65 A1 02 00 00 00 D2 06 65 A1 02 00 00 
{270} normal block at 0x000002A165072890, 16 bytes long.
 Data: < + e            > 90 2B 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002A165071990, 16 bytes long.
 Data: <h+ e            > 68 2B 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002A16506CA20, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{267} normal block at 0x000002A165072200, 16 bytes long.
 Data: <@+ e            > 40 2B 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002A16506C900, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{265} normal block at 0x000002A165072700, 16 bytes long.
 Data: < * e            > 88 2A 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002A1650721B0, 16 bytes long.
 Data: <`* e            > 60 2A 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002A165072160, 16 bytes long.
 Data: <8* e            > 38 2A 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000002A165072840, 16 bytes long.
 Data: < * e            > 10 2A 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000002A165072480, 16 bytes long.
 Data: < ) e            > E8 29 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002A165072430, 16 bytes long.
 Data: < ) e            > C0 29 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000002A1650723E0, 16 bytes long.
 Data: <   e            > B0 A0 06 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000002A16506A0B0, 40 bytes long.
 Data: < # e    @  e    > E0 23 07 65 A1 02 00 00 40 A9 05 65 A1 02 00 00 
{256} normal block at 0x000002A1650726B0, 16 bytes long.
 Data: < ) e            > A0 29 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000002A165071A80, 16 bytes long.
 Data: <x) e            > 78 29 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x000002A16506C840, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{253} normal block at 0x000002A1650727A0, 16 bytes long.
 Data: <P) e            > 50 29 07 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{252} normal block at 0x000002A165072950, 992 bytes long.
 Data: < ' e    @  e    > A0 27 07 65 A1 02 00 00 40 C8 06 65 A1 02 00 00 
{88} normal block at 0x000002A16506CEA0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{87} normal block at 0x000002A165065390, 16 bytes long.
 Data: <@  e            > 40 A0 06 65 A1 02 00 00 00 00 00 00 00 00 00 00 
{86} normal block at 0x000002A16506A040, 40 bytes long.
 Data: < S e       e    > 90 53 06 65 A1 02 00 00 A0 CE 06 65 A1 02 00 00 
{65} normal block at 0x000002A165065A20, 16 bytes long.
 Data: <                > 80 EA 86 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002A1650652A0, 16 bytes long.
 Data: <@               > 40 E9 86 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002A165065F70, 16 bytes long.
 Data: < W              > F8 57 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002A1650655C0, 16 bytes long.
 Data: < W              > D8 57 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002A165065DE0, 16 bytes long.
 Data: <P               > 50 04 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002A165065340, 16 bytes long.
 Data: <0               > 30 04 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000002A165065D40, 16 bytes long.
 Data: <                > E0 02 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000002A165065570, 16 bytes long.
 Data: <                > 10 04 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x000002A165065CA0, 16 bytes long.
 Data: <p               > 70 04 83 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x000002A165065930, 16 bytes long.
 Data: <                > 18 C0 81 BA F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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