Task 38643422

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
09:48:53 (13516): wrapper (7.9.26016): starting
09:48:53 (13516): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A12_A04_0.pdb
QB_A12_A04_0.xml
QB_A12_A04.inpcrd
QB_A12_A04_input.yaml
QB_A12_A04.pdb
QB_A12_A04.prmtop
QB_A12_A04_sys.xml
run.bat
run.sh
09:48:56 (13516): Library/usr/bin/tar.exe exited; CPU time 0.000000
09:48:56 (13516): 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 'F:\ProgramData\BOINC\slots\26\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 'F:\ProgramData\BOINC\slots\26\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 "F:\ProgramData\BOINC\slots\26\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "F:\ProgramData\BOINC\slots\26\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "F:\ProgramData\BOINC\slots\26\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
10:10:37 (13516): C:/Windows/system32/cmd.exe exited; CPU time 1199.562500
10:10:37 (13516): app exit status: 0x16
10:10:37 (13516): 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: 21092463 bytes.
Dumping objects ->
{3835192} normal block at 0x00000129792E0140, 48 bytes long.
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{3835181} normal block at 0x00000129792DF9D0, 48 bytes long.
 Data: <HOME=F:\ProgramD> 48 4F 4D 45 3D 46 3A 5C 50 72 6F 67 72 61 6D 44 
{3835170} normal block at 0x00000129792DF6C0, 48 bytes long.
 Data: <TMP=F:\ProgramDa> 54 4D 50 3D 46 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835159} normal block at 0x00000129792E03E0, 48 bytes long.
 Data: <TEMP=F:\ProgramD> 54 45 4D 50 3D 46 3A 5C 50 72 6F 67 72 61 6D 44 
{3835148} normal block at 0x00000129792DFEA0, 48 bytes long.
 Data: <TMPDIR=F:\Progra> 54 4D 50 44 49 52 3D 46 3A 5C 50 72 6F 67 72 61 
{3835117} normal block at 0x000001297923CD80, 64 bytes long.
 Data: <PATH=F:\ProgramD> 50 41 54 48 3D 46 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {3835104} normal block at 0x00000129775D8880, 8 bytes long.
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{3833955} normal block at 0x00000129775D8650, 8 bytes long.
 Data: <&#160;&#212;-y)   > A0 D4 2D 79 29 01 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x00000129775E1F30, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000129775C5DE0, 80 bytes long.
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{293} normal block at 0x00000129775E2D40, 16 bytes long.
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{292} normal block at 0x00000129775E3C90, 16 bytes long.
 Data: < P^w)           > 10 50 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000129775DD810, 32 bytes long.
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{290} normal block at 0x00000129775E3150, 16 bytes long.
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{289} normal block at 0x00000129775E3C40, 16 bytes long.
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{288} normal block at 0x00000129775E3BF0, 16 bytes long.
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{287} normal block at 0x00000129775E3BA0, 16 bytes long.
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{286} normal block at 0x00000129775DE980, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x00000129775E3970, 16 bytes long.
 Data: <x]\w)           > 78 5D 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000129775DCEB0, 32 bytes long.
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{283} normal block at 0x00000129775E2E80, 16 bytes long.
 Data: <P]\w)           > 50 5D 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000129775E3920, 16 bytes long.
 Data: <(]\w)           > 28 5D 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000129775E3880, 16 bytes long.
 Data: < ]\w)           > 00 5D 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000129775E3830, 16 bytes long.
 Data: <&#216;\\w)           > D8 5C 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000129775E2F70, 16 bytes long.
 Data: <&#176;\\w)           > B0 5C 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000129775E3B50, 16 bytes long.
 Data: < \\w)           > 88 5C 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000129775DDB10, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{275} normal block at 0x00000129775E3B00, 16 bytes long.
 Data: <`\\w)           > 60 5C 5C 77 29 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000129775C5C60, 320 bytes long.
 Data: < ;^w)    &#219;]w)   > 00 3B 5E 77 29 01 00 00 10 DB 5D 77 29 01 00 00 
{273} normal block at 0x00000129775E3AB0, 16 bytes long.
 Data: <PO^w)           > 50 4F 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000129775E3740, 16 bytes long.
 Data: <(O^w)           > 28 4F 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000129775DD750, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{270} normal block at 0x00000129775E3330, 16 bytes long.
 Data: < O^w)           > 00 4F 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000129775DDC30, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{268} normal block at 0x00000129775E37E0, 16 bytes long.
 Data: <HN^w)           > 48 4E 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000129775E35B0, 16 bytes long.
 Data: < N^w)           > 20 4E 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000129775E3240, 16 bytes long.
 Data: <&#248;M^w)           > F8 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000129775E2D90, 16 bytes long.
 Data: <&#208;M^w)           > D0 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000129775E3A60, 16 bytes long.
 Data: <&#168;M^w)           > A8 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000129775E30B0, 16 bytes long.
 Data: < M^w)           > 80 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000129775E34C0, 16 bytes long.
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{260} normal block at 0x00000129775DEC20, 40 bytes long.
 Data: <&#192;4^w)    &#205;#y)   > C0 34 5E 77 29 01 00 00 80 CD 23 79 29 01 00 00 
{259} normal block at 0x00000129775E3010, 16 bytes long.
 Data: <`M^w)           > 60 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x00000129775E3100, 16 bytes long.
 Data: <8M^w)           > 38 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x00000129775DD3F0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{256} normal block at 0x00000129775E36F0, 16 bytes long.
 Data: < M^w)           > 10 4D 5E 77 29 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x00000129775E4D10, 992 bytes long.
 Data: <&#240;6^w)   &#240;&#211;]w)   > F0 36 5E 77 29 01 00 00 F0 D3 5D 77 29 01 00 00 
{91} normal block at 0x00000129775DD870, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{90} normal block at 0x00000129775D8420, 16 bytes long.
 Data: <@&#235;]w)           > 40 EB 5D 77 29 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x00000129775DEB40, 40 bytes long.
 Data: < &#132;]w)   p&#216;]w)   > 20 84 5D 77 29 01 00 00 70 D8 5D 77 29 01 00 00 
{68} normal block at 0x00000129775D8BF0, 16 bytes long.
 Data: < &#234;&#235; &#247;           > 80 EA EB 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000129775D8AB0, 16 bytes long.
 Data: <@&#233;&#235; &#247;           > 40 E9 EB 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000129775D8E70, 16 bytes long.
 Data: <&#248;W&#232; &#247;           > F8 57 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000129775D85B0, 16 bytes long.
 Data: <&#216;W&#232; &#247;           > D8 57 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000129775D8470, 16 bytes long.
 Data: <P &#232; &#247;           > 50 04 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000129775D8510, 16 bytes long.
 Data: <0 &#232; &#247;           > 30 04 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000129775D81A0, 16 bytes long.
 Data: <&#224; &#232; &#247;           > E0 02 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000129775D8E20, 16 bytes long.
 Data: <  &#232; &#247;           > 10 04 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000129775D8DD0, 16 bytes long.
 Data: <p &#232; &#247;           > 70 04 E8 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x00000129775D8D80, 16 bytes long.
 Data: < &#192;&#230; &#247;           > 18 C0 E6 1F F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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