Task 38643218

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
14:48:32 (24488): wrapper (7.9.26016): starting
14:48:32 (24488): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A18_0.pdb
QB_A20_A18_0.xml
QB_A20_A18.inpcrd
QB_A20_A18_input.yaml
QB_A20_A18.pdb
QB_A20_A18.prmtop
QB_A20_A18_sys.xml
run.bat
run.sh
14:48:36 (24488): Library/usr/bin/tar.exe exited; CPU time 0.015625
14:48:36 (24488): 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:\BoincData\slots\1\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:\BoincData\slots\1\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) : {3835359} normal block at 0x00000184C7109420, 8 bytes long.
 Data: <        > 00 00 0B C7 84 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833948} normal block at 0x00000184C8C6BE10, 1080 bytes long.
 Data: < ,              > 08 2C 00 00 CD CD CD CD CC 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {306} normal block at 0x00000184C7112E00, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
09:38:29 (24128): wrapper (7.9.26016): starting
09:38:29 (24128): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BoincData\slots\1\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 "D:\BoincData\slots\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BoincData\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BoincData\slots\1\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
10:54:00 (24128): C:/Windows/system32/cmd.exe exited; CPU time 4052.656250
10:54:00 (24128): app exit status: 0x16
10:54:00 (24128): called boinc_finish(195)
0 bytes in 0 Free Blocks.
458 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: 60808368 bytes.
Dumping objects ->
{1801} normal block at 0x000001663C3FD9B0, 48 bytes long.
 Data: <PATH=D:\BoincDat> 50 41 54 48 3D 44 3A 5C 42 6F 69 6E 63 44 61 74 
{1790} normal block at 0x000001663C3FBA70, 32 bytes long.
 Data: <HOME=D:\BoincDat> 48 4F 4D 45 3D 44 3A 5C 42 6F 69 6E 63 44 61 74 
{1779} normal block at 0x000001663C3FC010, 32 bytes long.
 Data: <TMP=D:\BoincData> 54 4D 50 3D 44 3A 5C 42 6F 69 6E 63 44 61 74 61 
{1768} normal block at 0x000001663C3FBCB0, 32 bytes long.
 Data: <TEMP=D:\BoincDat> 54 45 4D 50 3D 44 3A 5C 42 6F 69 6E 63 44 61 74 
{1757} normal block at 0x000001663C3FC550, 32 bytes long.
 Data: <TMPDIR=D:\BoincD> 54 4D 50 44 49 52 3D 44 3A 5C 42 6F 69 6E 63 44 
{1726} normal block at 0x000001663C3FD940, 48 bytes long.
 Data: <PATH=D:\BoincDat> 50 41 54 48 3D 44 3A 5C 42 6F 69 6E 63 44 61 74 
{1715} normal block at 0x000001663C3EB240, 141 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) : {1712} normal block at 0x000001663C4029E0, 8 bytes long.
 Data: <  :<f   > 00 00 3A 3C 66 01 00 00 
{991} normal block at 0x000001663C3EBE90, 141 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{302} normal block at 0x000001663C401F40, 8 bytes long.
 Data: < B@<f   > D0 42 40 3C 66 01 00 00 
{293} normal block at 0x000001663C3E5FB0, 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 0x000001663C402120, 16 bytes long.
 Data: < A@<f           > D8 41 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001663C401D10, 16 bytes long.
 Data: < A@<f           > B0 41 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001663C3FC490, 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 0x000001663C401C70, 16 bytes long.
 Data: < A@<f           > 88 41 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001663C4021C0, 16 bytes long.
 Data: <`A@<f           > 60 41 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001663C401EF0, 16 bytes long.
 Data: <8A@<f           > 38 41 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001663C402030, 16 bytes long.
 Data: < A@<f           > 10 41 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001663C3FDF60, 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 0x000001663C401E50, 16 bytes long.
 Data: <H_><f           > 48 5F 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001663C3FC250, 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 0x000001663C401C20, 16 bytes long.
 Data: < _><f           > 20 5F 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001663C402210, 16 bytes long.
 Data: < ^><f           > F8 5E 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001663C4026C0, 16 bytes long.
 Data: < ^><f           > D0 5E 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001663C401BD0, 16 bytes long.
 Data: < ^><f           > A8 5E 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001663C402440, 16 bytes long.
 Data: < ^><f           > 80 5E 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001663C401B80, 16 bytes long.
 Data: <X^><f           > 58 5E 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001663C3FC3D0, 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 0x000001663C401E00, 16 bytes long.
 Data: <0^><f           > 30 5E 3E 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001663C3E5E30, 320 bytes long.
 Data: <  @<f     ?<f   > 00 1E 40 3C 66 01 00 00 D0 C3 3F 3C 66 01 00 00 
{272} normal block at 0x000001663C402350, 16 bytes long.
 Data: < @@<f           > F0 40 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001663C401AE0, 16 bytes long.
 Data: < @@<f           > C8 40 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001663C3FC310, 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 0x000001663C402A30, 16 bytes long.
 Data: < @@<f           > A0 40 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001663C3FB8F0, 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 0x000001663C402850, 16 bytes long.
 Data: < ?@<f           > E8 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001663C402760, 16 bytes long.
 Data: < ?@<f           > C0 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001663C401F90, 16 bytes long.
 Data: < ?@<f           > 98 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001663C402170, 16 bytes long.
 Data: <p?@<f           > 70 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001663C402800, 16 bytes long.
 Data: <H?@<f           > 48 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001663C402990, 16 bytes long.
 Data: < ?@<f           > 20 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001663C402940, 16 bytes long.
 Data: <p ?<f           > 70 DB 3F 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001663C3FDB70, 40 bytes long.
 Data: <@)@<f   @ ?<f   > 40 29 40 3C 66 01 00 00 40 D9 3F 3C 66 01 00 00 
{258} normal block at 0x000001663C4028F0, 16 bytes long.
 Data: < ?@<f           > 00 3F 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000001663C4028A0, 16 bytes long.
 Data: < >@<f           > D8 3E 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000001663C3FC430, 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 0x000001663C401D60, 16 bytes long.
 Data: < >@<f           > B0 3E 40 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x000001663C403EB0, 992 bytes long.
 Data: <` @<f   0 ?<f   > 60 1D 40 3C 66 01 00 00 30 C4 3F 3C 66 01 00 00 
{90} normal block at 0x000001663C3FBDD0, 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 0x000001663C3F6E90, 16 bytes long.
 Data: <  ?<f           > D0 D8 3F 3C 66 01 00 00 00 00 00 00 00 00 00 00 
{88} normal block at 0x000001663C3FD8D0, 40 bytes long.
 Data: < n?<f     ?<f   > 90 6E 3F 3C 66 01 00 00 D0 BD 3F 3C 66 01 00 00 
{67} normal block at 0x000001663C3F7890, 16 bytes long.
 Data: <                > 80 EA D5 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001663C3F7840, 16 bytes long.
 Data: <@               > 40 E9 D5 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001663C3F76B0, 16 bytes long.
 Data: < W              > F8 57 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001663C3F7660, 16 bytes long.
 Data: < W              > D8 57 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001663C3F7750, 16 bytes long.
 Data: <P               > 50 04 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001663C3F6B20, 16 bytes long.
 Data: <0               > 30 04 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001663C3F77A0, 16 bytes long.
 Data: <                > E0 02 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001663C3F7700, 16 bytes long.
 Data: <                > 10 04 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001663C3F6AD0, 16 bytes long.
 Data: <p               > 70 04 D2 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000001663C3F6D50, 16 bytes long.
 Data: <                > 18 C0 D0 05 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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