Task 38643690

Stderr output

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
(unknown error) - exit code 195 (0xc3)</message>
<stderr_txt>
10:50:54 (34520): wrapper (7.9.26016): starting
10:50:54 (34520): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A11_0.pdb
QB_A20_A11_0.xml
QB_A20_A11.inpcrd
QB_A20_A11_input.yaml
QB_A20_A11.pdb
QB_A20_A11.prmtop
QB_A20_A11_sys.xml
run.bat
run.sh
10:50:56 (34520): Library/usr/bin/tar.exe exited; CPU time 0.015625
10:50:56 (34520): 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.
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
11:23:20 (34520): C:/Windows/system32/cmd.exe exited; CPU time 1972.531250
11:23:20 (34520): app exit status: 0x16
11:23:20 (34520): 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: 29241453 bytes.
Dumping objects ->
{3835251} normal block at 0x0000028050805210, 48 bytes long.
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{3835240} normal block at 0x0000028050804560, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835229} normal block at 0x0000028050804C60, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835218} normal block at 0x0000028050804720, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835207} normal block at 0x00000280508053D0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835176} normal block at 0x00000280524CCC10, 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) : {3835163} normal block at 0x00000280507D64B0, 8 bytes long.
 Data: <  wP    > 00 00 77 50 80 02 00 00 
{3833949} normal block at 0x00000280507D66E0, 8 bytes long.
 Data: <&#160; &#131;P    > A0 1B 83 50 80 02 00 00 
..\zip\boinc_zip.cpp(122) : {306} normal block at 0x00000280507E00F0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000280507C5DE0, 80 bytes long.
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{290} normal block at 0x00000280507E1720, 16 bytes long.
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{289} normal block at 0x00000280507E1590, 16 bytes long.
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{288} normal block at 0x00000280507D7860, 32 bytes long.
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{287} normal block at 0x00000280507E1E50, 16 bytes long.
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{286} normal block at 0x00000280507E16D0, 16 bytes long.
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{285} normal block at 0x00000280507E1E00, 16 bytes long.
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{284} normal block at 0x00000280507E10E0, 16 bytes long.
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{283} normal block at 0x00000280507DB890, 48 bytes long.
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{282} normal block at 0x00000280507E1770, 16 bytes long.
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{281} normal block at 0x00000280507D73E0, 32 bytes long.
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{280} normal block at 0x00000280507E1090, 16 bytes long.
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{278} normal block at 0x00000280507E1040, 16 bytes long.
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{277} normal block at 0x00000280507E1630, 16 bytes long.
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{276} normal block at 0x00000280507E17C0, 16 bytes long.
 Data: <&#216;\|P            > D8 5C 7C 50 80 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000280507E1270, 16 bytes long.
 Data: <&#176;\|P            > B0 5C 7C 50 80 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000280507E1130, 16 bytes long.
 Data: < \|P            > 88 5C 7C 50 80 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000280507D7380, 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 0x00000280507E0F50, 16 bytes long.
 Data: <`\|P            > 60 5C 7C 50 80 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000280507C5C60, 320 bytes long.
 Data: <P ~P     s}P    > 50 0F 7E 50 80 02 00 00 80 73 7D 50 80 02 00 00 
{270} normal block at 0x00000280507E12C0, 16 bytes long.
 Data: <&#176;"~P            > B0 22 7E 50 80 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000280507E1220, 16 bytes long.
 Data: < "~P            > 88 22 7E 50 80 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000280507D7320, 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 0x00000280507E1D10, 16 bytes long.
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{266} normal block at 0x00000280507D6CC0, 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 0x00000280507E0FF0, 16 bytes long.
 Data: <&#168;!~P            > A8 21 7E 50 80 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000280507E1C70, 16 bytes long.
 Data: < !~P            > 80 21 7E 50 80 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000280507E1400, 16 bytes long.
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{262} normal block at 0x00000280507E18B0, 16 bytes long.
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{261} normal block at 0x00000280507E1A90, 16 bytes long.
 Data: < !~P            > 08 21 7E 50 80 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000280507E1A40, 16 bytes long.
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{258} normal block at 0x00000280507E19A0, 16 bytes long.
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{257} normal block at 0x00000280507DB740, 40 bytes long.
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{256} normal block at 0x00000280507E0FA0, 16 bytes long.
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{255} normal block at 0x00000280507E1810, 16 bytes long.
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{254} normal block at 0x00000280507D6C00, 32 bytes long.
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{253} normal block at 0x00000280507E1540, 16 bytes long.
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{252} normal block at 0x00000280507E2070, 992 bytes long.
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{88} normal block at 0x00000280507D72C0, 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 0x00000280507D6960, 16 bytes long.
 Data: <&#240;&#188;}P            > F0 BC 7D 50 80 02 00 00 00 00 00 00 00 00 00 00 
{86} normal block at 0x00000280507DBCF0, 40 bytes long.
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{65} normal block at 0x00000280507D6280, 16 bytes long.
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{64} normal block at 0x00000280507D6910, 16 bytes long.
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{63} normal block at 0x00000280507D60A0, 16 bytes long.
 Data: <&#248;W&#179;&#205;&#246;           > F8 57 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000280507D6050, 16 bytes long.
 Data: <&#216;W&#179;&#205;&#246;           > D8 57 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000280507D5CE0, 16 bytes long.
 Data: <P &#179;&#205;&#246;           > 50 04 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000280507D68C0, 16 bytes long.
 Data: <0 &#179;&#205;&#246;           > 30 04 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x00000280507D5C90, 16 bytes long.
 Data: <&#224; &#179;&#205;&#246;           > E0 02 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x00000280507D6640, 16 bytes long.
 Data: <  &#179;&#205;&#246;           > 10 04 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x00000280507D5E70, 16 bytes long.
 Data: <p &#179;&#205;&#246;           > 70 04 B3 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x00000280507D6140, 16 bytes long.
 Data: < &#192;&#177;&#205;&#246;           > 18 C0 B1 CD F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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