Task 38643600

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
(null) nelze spustit.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
18:07:19 (5196): wrapper (7.9.26016): starting
18:07:19 (5196): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A21_A06_0.pdb
QB_A21_A06_0.xml
QB_A21_A06.inpcrd
QB_A21_A06_input.yaml
QB_A21_A06.pdb
QB_A21_A06.prmtop
QB_A21_A06_sys.xml
run.bat
run.sh
18:07:20 (5196): Library/usr/bin/tar.exe exited; CPU time 0.000000
18:07:20 (5196): 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\1\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\1\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\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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\1\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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
18:10:07 (5196): C:/Windows/system32/cmd.exe exited; CPU time 154.015625
18:10:07 (5196): app exit status: 0x16
18:10:07 (5196): called boinc_finish(195)
0 bytes in 0 Free Blocks.
422 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: 2350576 bytes.
Dumping objects ->
{3835552} normal block at 0x0000025124524060, 48 bytes long.
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{3835541} normal block at 0x0000025122750950, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835530} normal block at 0x00000251227508E0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835519} normal block at 0x0000025122750720, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835508} normal block at 0x0000025122750560, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835477} normal block at 0x00000251244CA200, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835466} normal block at 0x00000251227426A0, 83 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) : {3835463} normal block at 0x000002512274DB50, 8 bytes long.
 Data: <  &#200;"Q   > 00 00 C8 22 51 02 00 00 
{3834682} normal block at 0x0000025122741FE0, 83 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{3833955} normal block at 0x000002512274DC90, 8 bytes long.
 Data: <&#160;&#215;s"Q   > A0 D7 73 22 51 02 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x0000025122740CD0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000025122742580, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{293} normal block at 0x0000025122755E90, 16 bytes long.
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{292} normal block at 0x00000251227558A0, 16 bytes long.
 Data: <Pgu"Q           > 50 67 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000025122751120, 32 bytes long.
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{290} normal block at 0x0000025122755850, 16 bytes long.
 Data: <(gu"Q           > 28 67 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000025122755E40, 16 bytes long.
 Data: < gu"Q           > 00 67 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000025122755DA0, 16 bytes long.
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{287} normal block at 0x00000251227561B0, 16 bytes long.
 Data: <&#176;fu"Q           > B0 66 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000025122750480, 48 bytes long.
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{285} normal block at 0x0000025122755800, 16 bytes long.
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{284} normal block at 0x0000025122750E80, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{283} normal block at 0x0000025122756110, 16 bytes long.
 Data: <&#208;&#242;s"Q           > D0 F2 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000251227560C0, 16 bytes long.
 Data: <&#168;&#242;s"Q           > A8 F2 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000025122755CB0, 16 bytes long.
 Data: < &#242;s"Q           > 80 F2 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000251227557B0, 16 bytes long.
 Data: <X&#242;s"Q           > 58 F2 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000025122755DF0, 16 bytes long.
 Data: <0&#242;s"Q           > 30 F2 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000025122756070, 16 bytes long.
 Data: < &#242;s"Q           > 08 F2 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000251227517E0, 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 0x0000025122755EE0, 16 bytes long.
 Data: <&#224;&#241;s"Q           > E0 F1 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002512273F1E0, 320 bytes long.
 Data: <&#224;^u"Q   &#224; u"Q   > E0 5E 75 22 51 02 00 00 E0 17 75 22 51 02 00 00 
{273} normal block at 0x0000025122755710, 16 bytes long.
 Data: < fu"Q           > 90 66 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000025122755620, 16 bytes long.
 Data: <hfu"Q           > 68 66 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000025122751660, 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 0x0000025122755FD0, 16 bytes long.
 Data: <@fu"Q           > 40 66 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000251227513C0, 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 0x0000025122755F80, 16 bytes long.
 Data: < eu"Q           > 88 65 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000025122755F30, 16 bytes long.
 Data: <`eu"Q           > 60 65 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000025122756020, 16 bytes long.
 Data: <8eu"Q           > 38 65 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000251227555D0, 16 bytes long.
 Data: < eu"Q           > 10 65 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000025122756390, 16 bytes long.
 Data: <&#232;du"Q           > E8 64 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000025122755D50, 16 bytes long.
 Data: <&#192;du"Q           > C0 64 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000025122755530, 16 bytes long.
 Data: <&#160; u"Q           > A0 03 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000251227503A0, 40 bytes long.
 Data: <0Uu"Q     L$Q   > 30 55 75 22 51 02 00 00 00 A2 4C 24 51 02 00 00 
{259} normal block at 0x00000251227556C0, 16 bytes long.
 Data: <&#160;du"Q           > A0 64 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000025122755760, 16 bytes long.
 Data: <xdu"Q           > 78 64 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000025122751240, 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 0x0000025122756160, 16 bytes long.
 Data: <Pdu"Q           > 50 64 75 22 51 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000025122756450, 992 bytes long.
 Data: <`au"Q   @ u"Q   > 60 61 75 22 51 02 00 00 40 12 75 22 51 02 00 00 
{91} normal block at 0x0000025122750CA0, 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 0x000002512274D9C0, 16 bytes long.
 Data: <&#224;&#238;s"Q           > E0 EE 73 22 51 02 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x000002512273EEE0, 40 bytes long.
 Data: <&#192;&#217;t"Q   &#160; u"Q   > C0 D9 74 22 51 02 00 00 A0 0C 75 22 51 02 00 00 
{68} normal block at 0x000002512274D920, 16 bytes long.
 Data: < &#234;[W&#246;           > 80 EA 5B 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002512274D830, 16 bytes long.
 Data: <@&#233;[W&#246;           > 40 E9 5B 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002512274D880, 16 bytes long.
 Data: <&#248;WXW&#246;           > F8 57 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002512274D560, 16 bytes long.
 Data: <&#216;WXW&#246;           > D8 57 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002512274DBF0, 16 bytes long.
 Data: <P XW&#246;           > 50 04 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002512274D1F0, 16 bytes long.
 Data: <0 XW&#246;           > 30 04 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002512274D740, 16 bytes long.
 Data: <&#224; XW&#246;           > E0 02 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002512274DA60, 16 bytes long.
 Data: <  XW&#246;           > 10 04 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002512274D650, 16 bytes long.
 Data: <p XW&#246;           > 70 04 58 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000002512274D970, 16 bytes long.
 Data: < &#192;VW&#246;           > 18 C0 56 57 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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