Task 38643424

Stderr output

<core_client_version>7.24.1</core_client_version>
<![CDATA[
<message>
%1 nelze spustit.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
18:24:24 (34604): wrapper (7.9.26016): starting
18:24:24 (34604): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A03_A13_0.pdb
QB_A03_A13_0.xml
QB_A03_A13.inpcrd
QB_A03_A13_input.yaml
QB_A03_A13.pdb
QB_A03_A13.prmtop
QB_A03_A13_sys.xml
run.bat
run.sh
18:24:26 (34604): Library/usr/bin/tar.exe exited; CPU time 0.000000
18:24:26 (34604): 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:\Boinc_data\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 'D:\Boinc_data\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 "D:\Boinc_data\slots\14\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc_data\slots\14\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\Boinc_data\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
18:43:33 (34604): C:/Windows/system32/cmd.exe exited; CPU time 1117.421875
18:43:33 (34604): app exit status: 0x16
18:43:33 (34604): called boinc_finish(195)
0 bytes in 0 Free Blocks.
380 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: 23343697 bytes.
Dumping objects ->
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{3835296} normal block at 0x0000022174645A30, 32 bytes long.
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{3835285} normal block at 0x0000022174645130, 32 bytes long.
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{3835274} normal block at 0x0000022174645CD0, 32 bytes long.
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{3835263} normal block at 0x0000022174645370, 32 bytes long.
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{3835232} normal block at 0x00000221728B6640, 48 bytes long.
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{3835221} normal block at 0x000002217460E440, 102 bytes long.
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..\api\boinc_api.cpp(309) : {3835218} normal block at 0x0000022172887790, 8 bytes long.
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{282} normal block at 0x00000221728934C0, 16 bytes long.
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{281} normal block at 0x0000022172893420, 16 bytes long.
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{280} normal block at 0x0000022172893740, 16 bytes long.
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{279} normal block at 0x0000022172892FC0, 16 bytes long.
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{278} normal block at 0x0000022172893BF0, 16 bytes long.
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{277} normal block at 0x000002217288E510, 32 bytes long.
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{276} normal block at 0x0000022172893C40, 16 bytes long.
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{274} normal block at 0x0000022172893790, 16 bytes long.
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{273} normal block at 0x0000022172893E70, 16 bytes long.
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{272} normal block at 0x000002217288E030, 32 bytes long.
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{271} normal block at 0x0000022172893380, 16 bytes long.
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{270} normal block at 0x000002217288E6F0, 32 bytes long.
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{268} normal block at 0x00000221728932E0, 16 bytes long.
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{259} normal block at 0x0000022172893290, 16 bytes long.
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{258} normal block at 0x000002217288E270, 32 bytes long.
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{257} normal block at 0x0000022172893100, 16 bytes long.
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{92} normal block at 0x000002217288DFD0, 32 bytes long.
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{69} normal block at 0x00000221728875B0, 16 bytes long.
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{68} normal block at 0x0000022172887E20, 16 bytes long.
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{67} normal block at 0x0000022172887A10, 16 bytes long.
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{66} normal block at 0x0000022172887600, 16 bytes long.
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{65} normal block at 0x0000022172887290, 16 bytes long.
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{64} normal block at 0x0000022172887650, 16 bytes long.
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{63} normal block at 0x0000022172887470, 16 bytes long.
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{62} normal block at 0x00000221728873D0, 16 bytes long.
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{61} normal block at 0x00000221728876F0, 16 bytes long.
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{60} normal block at 0x0000022172887380, 16 bytes long.
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Object dump complete.

</stderr_txt>
]]>

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