Task 38644782

Stderr output

<core_client_version>8.0.2</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
07:59:38 (145032): wrapper (7.9.26016): starting
07:59:38 (145032): 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
07:59:40 (145032): Library/usr/bin/tar.exe exited; CPU time 0.031250
07:59:40 (145032): 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\15\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\15\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 "C:\ProgramData\BOINC\slots\15\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\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\15\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\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
15:25:25 (145032): C:/Windows/system32/cmd.exe exited; CPU time 23700.859375
15:25:25 (145032): app exit status: 0x16
15:25:25 (145032): called boinc_finish(195)
0 bytes in 0 Free Blocks.
576 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: 411607159 bytes.
Dumping objects ->
{3835327} normal block at 0x00000159F4F2D310, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835316} normal block at 0x00000159F3344DF0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835305} normal block at 0x00000159F3344D80, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835294} normal block at 0x00000159F3344B50, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835283} normal block at 0x00000159F3344AE0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835252} normal block at 0x00000159F4F78040, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835241} normal block at 0x00000159F4FD4370, 160 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) : {3835238} normal block at 0x00000159F333D270, 8 bytes long.
 Data: <  x&#243;Y   > 00 00 78 F3 59 01 00 00 
{3834593} normal block at 0x00000159F4FD4530, 160 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{3833963} normal block at 0x00000159F333DC70, 8 bytes long.
 Data: <&#208;&#214;2&#243;Y   > D0 D6 32 F3 59 01 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x00000159F3331110, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x00000159F3331CE0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{297} normal block at 0x00000159F3346100, 16 bytes long.
 Data: <&#200;f4&#243;Y           > C8 66 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x00000159F3345F70, 16 bytes long.
 Data: <&#160;f4&#243;Y           > A0 66 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000159F3340F10, 32 bytes long.
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{294} normal block at 0x00000159F3346010, 16 bytes long.
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{293} normal block at 0x00000159F33454D0, 16 bytes long.
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{292} normal block at 0x00000159F3345750, 16 bytes long.
 Data: <(f4&#243;Y           > 28 66 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000159F3345660, 16 bytes long.
 Data: < f4&#243;Y           > 00 66 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000159F3344990, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{289} normal block at 0x00000159F33461F0, 16 bytes long.
 Data: <(&#242;2&#243;Y           > 28 F2 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000159F3341330, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{287} normal block at 0x00000159F3345A20, 16 bytes long.
 Data: < &#242;2&#243;Y           > 00 F2 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000159F3345520, 16 bytes long.
 Data: <&#216;&#241;2&#243;Y           > D8 F1 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000159F3345FC0, 16 bytes long.
 Data: <&#176;&#241;2&#243;Y           > B0 F1 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000159F33459D0, 16 bytes long.
 Data: < &#241;2&#243;Y           > 88 F1 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000159F3345480, 16 bytes long.
 Data: <`&#241;2&#243;Y           > 60 F1 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000159F3345980, 16 bytes long.
 Data: <8&#241;2&#243;Y           > 38 F1 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000159F3341510, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{279} normal block at 0x00000159F33458E0, 16 bytes long.
 Data: < &#241;2&#243;Y           > 10 F1 32 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000159F332F110, 320 bytes long.
 Data: <&#224;X4&#243;Y     4&#243;Y   > E0 58 34 F3 59 01 00 00 10 15 34 F3 59 01 00 00 
{277} normal block at 0x00000159F3345F20, 16 bytes long.
 Data: <&#224;e4&#243;Y           > E0 65 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000159F3345610, 16 bytes long.
 Data: <&#184;e4&#243;Y           > B8 65 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000159F33414B0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{274} normal block at 0x00000159F3346330, 16 bytes long.
 Data: < e4&#243;Y           > 90 65 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000159F3341210, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{272} normal block at 0x00000159F3345930, 16 bytes long.
 Data: <&#216;d4&#243;Y           > D8 64 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000159F3345430, 16 bytes long.
 Data: <&#176;d4&#243;Y           > B0 64 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000159F3345ED0, 16 bytes long.
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{269} normal block at 0x00000159F33460B0, 16 bytes long.
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{268} normal block at 0x00000159F3345570, 16 bytes long.
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{267} normal block at 0x00000159F3345840, 16 bytes long.
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{265} normal block at 0x00000159F33457F0, 16 bytes long.
 Data: <&#160;L4&#243;Y           > A0 4C 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000159F3344CA0, 40 bytes long.
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{263} normal block at 0x00000159F3345BB0, 16 bytes long.
 Data: <&#240;c4&#243;Y           > F0 63 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x00000159F3346150, 16 bytes long.
 Data: <&#200;c4&#243;Y           > C8 63 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000159F3340AF0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{260} normal block at 0x00000159F3345890, 16 bytes long.
 Data: <&#160;c4&#243;Y           > A0 63 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000159F33463A0, 992 bytes long.
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{95} normal block at 0x00000159F3340FD0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{94} normal block at 0x00000159F333D680, 16 bytes long.
 Data: <&#160; 4&#243;Y           > A0 07 34 F3 59 01 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x00000159F33407A0, 40 bytes long.
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{72} normal block at 0x00000159F333D3B0, 16 bytes long.
 Data: < &#234; &#183;&#246;           > 80 EA 1B B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000159F333D6D0, 16 bytes long.
 Data: <@&#233; &#183;&#246;           > 40 E9 1B B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000159F333D220, 16 bytes long.
 Data: <&#248;W &#183;&#246;           > F8 57 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000159F333DC20, 16 bytes long.
 Data: <&#216;W &#183;&#246;           > D8 57 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000159F333DF40, 16 bytes long.
 Data: <P  &#183;&#246;           > 50 04 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000159F333DCC0, 16 bytes long.
 Data: <0  &#183;&#246;           > 30 04 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000159F333DE00, 16 bytes long.
 Data: <&#224;  &#183;&#246;           > E0 02 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000159F333D5E0, 16 bytes long.
 Data: <   &#183;&#246;           > 10 04 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000159F333D450, 16 bytes long.
 Data: <p  &#183;&#246;           > 70 04 18 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000159F333DA90, 16 bytes long.
 Data: < &#192; &#183;&#246;           > 18 C0 16 B7 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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