Task 38596221

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
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 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
20:16:01 (23916): wrapper (7.9.26016): starting
20:16:01 (23916): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A04_A02_0.pdb
QB_A04_A02_0.xml
QB_A04_A02.inpcrd
QB_A04_A02_input.yaml
QB_A04_A02.pdb
QB_A04_A02.prmtop
QB_A04_A02_sys.xml
run.bat
run.sh
20:16:02 (23916): Library/usr/bin/tar.exe exited; CPU time 0.000000
20:16:02 (23916): 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\14\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\14\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\14\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\14\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\14\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\14\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
20:16:46 (23916): C:/Windows/system32/cmd.exe exited; CPU time 31.781250
20:16:46 (23916): app exit status: 0x16
20:16:46 (23916): 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: 981793 bytes.
Dumping objects ->
{3835293} normal block at 0x000001AE7F4A4B10, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835282} normal block at 0x000001AE7F4A4AA0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835271} normal block at 0x000001AE7F4A4A30, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835260} normal block at 0x000001AE7F4A4E90, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835249} normal block at 0x000001AE7F4A4950, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835218} normal block at 0x000001AE014F3700, 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) : {3835205} normal block at 0x000001AE7F49D6C0, 8 bytes long.
 Data: <        > 00 00 91 7F AE 01 00 00 
{3834057} normal block at 0x000001AE7F49DBC0, 8 bytes long.
 Data: <  H     > D0 D6 48 7F AE 01 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x000001AE7F491160, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x000001AE7F4925A0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{296} normal block at 0x000001AE7F4A6310, 16 bytes long.
 Data: < fJ             > F8 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000001AE7F4A5730, 16 bytes long.
 Data: < fJ             > D0 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000001AE7F4A0E80, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{293} normal block at 0x000001AE7F4A6270, 16 bytes long.
 Data: < fJ             > A8 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001AE7F4A5500, 16 bytes long.
 Data: < fJ             > 80 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001AE7F4A6090, 16 bytes long.
 Data: <XfJ             > 58 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001AE7F4A5960, 16 bytes long.
 Data: <0fJ             > 30 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001AE7F4A4D40, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{288} normal block at 0x000001AE7F4A5910, 16 bytes long.
 Data: <h H             > 68 B4 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001AE7F4A16C0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{286} normal block at 0x000001AE7F4A5B40, 16 bytes long.
 Data: <@ H             > 40 B4 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001AE7F4A5AF0, 16 bytes long.
 Data: <  H             > 18 B4 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001AE7F4A6220, 16 bytes long.
 Data: <  H             > F0 B3 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001AE7F4A5870, 16 bytes long.
 Data: <  H             > C8 B3 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001AE7F4A61D0, 16 bytes long.
 Data: <  H             > A0 B3 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001AE7F4A58C0, 16 bytes long.
 Data: <x H             > 78 B3 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001AE7F4A0B20, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{278} normal block at 0x000001AE7F4A5DC0, 16 bytes long.
 Data: <P H             > 50 B3 48 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001AE7F48B350, 320 bytes long.
 Data: < ]J       J     > C0 5D 4A 7F AE 01 00 00 20 0B 4A 7F AE 01 00 00 
{276} normal block at 0x000001AE7F4A54B0, 16 bytes long.
 Data: < fJ             > 10 66 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001AE7F4A5460, 16 bytes long.
 Data: < eJ             > E8 65 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001AE7F4A09A0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{273} normal block at 0x000001AE7F4A56E0, 16 bytes long.
 Data: < eJ             > C0 65 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001AE7F4A0D60, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{271} normal block at 0x000001AE7F4A5AA0, 16 bytes long.
 Data: < eJ             > 08 65 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001AE7F4A62C0, 16 bytes long.
 Data: < dJ             > E0 64 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001AE7F4A5EB0, 16 bytes long.
 Data: < dJ             > B8 64 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001AE7F4A5A50, 16 bytes long.
 Data: < dJ             > 90 64 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001AE7F4A5640, 16 bytes long.
 Data: <hdJ             > 68 64 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001AE7F4A5C30, 16 bytes long.
 Data: <@dJ             > 40 64 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001AE7F4A6180, 16 bytes long.
 Data: < LJ             > D0 4C 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001AE7F4A4CD0, 40 bytes long.
 Data: < aJ      7O     > 80 61 4A 7F AE 01 00 00 00 37 4F 01 AE 01 00 00 
{262} normal block at 0x000001AE7F4A5820, 16 bytes long.
 Data: < dJ             > 20 64 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001AE7F4A5A00, 16 bytes long.
 Data: < cJ             > F8 63 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001AE7F4A0A60, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{259} normal block at 0x000001AE7F4A5FA0, 16 bytes long.
 Data: < cJ             > D0 63 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001AE7F4A63D0, 992 bytes long.
 Data: < _J     ` J     > A0 5F 4A 7F AE 01 00 00 60 0A 4A 7F AE 01 00 00 
{94} normal block at 0x000001AE7F4A0940, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{93} normal block at 0x000001AE7F49DA30, 16 bytes long.
 Data: <  J             > E0 07 4A 7F AE 01 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x000001AE7F4A07E0, 40 bytes long.
 Data: <0 I     @	J     > 30 DA 49 7F AE 01 00 00 40 09 4A 7F AE 01 00 00 
{69} normal block at 0x000001AE7F49D300, 16 bytes long.
 Data: <  8~            > 80 EA 38 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001AE7F49D8A0, 16 bytes long.
 Data: <@ 8~            > 40 E9 38 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001AE7F49DF30, 16 bytes long.
 Data: < W5~            > F8 57 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001AE7F49DD50, 16 bytes long.
 Data: < W5~            > D8 57 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001AE7F49DB20, 16 bytes long.
 Data: <P 5~            > 50 04 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001AE7F49D670, 16 bytes long.
 Data: <0 5~            > 30 04 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001AE7F49D620, 16 bytes long.
 Data: <  5~            > E0 02 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001AE7F49DE40, 16 bytes long.
 Data: <  5~            > 10 04 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001AE7F49D5D0, 16 bytes long.
 Data: <p 5~            > 70 04 35 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001AE7F49DDA0, 16 bytes long.
 Data: <  3~            > 18 C0 33 7E F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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