Task 38643097

Stderr output

<core_client_version>7.24.1</core_client_version>
<![CDATA[
<message>
%1 nelze spustit.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
14:36:28 (17940): wrapper (7.9.26016): starting
14:36:28 (17940): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A18_0.pdb
QB_A20_A18_0.xml
QB_A20_A18.inpcrd
QB_A20_A18_input.yaml
QB_A20_A18.pdb
QB_A20_A18.prmtop
QB_A20_A18_sys.xml
run.bat
run.sh
14:36:30 (17940): Library/usr/bin/tar.exe exited; CPU time 0.000000
14:36:30 (17940): 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
15:17:34 (17940): C:/Windows/system32/cmd.exe exited; CPU time 2412.765625
15:17:34 (17940): app exit status: 0x16
15:17:34 (17940): 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: 49207261 bytes.
Dumping objects ->
{3835307} normal block at 0x000001BD325B6920, 48 bytes long.
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{3835296} normal block at 0x000001BD34245770, 32 bytes long.
 Data: <HOME=D:\Boinc_da> 48 4F 4D 45 3D 44 3A 5C 42 6F 69 6E 63 5F 64 61 
{3835285} normal block at 0x000001BD342460D0, 32 bytes long.
 Data: <TMP=D:\Boinc_dat> 54 4D 50 3D 44 3A 5C 42 6F 69 6E 63 5F 64 61 74 
{3835274} normal block at 0x000001BD34245710, 32 bytes long.
 Data: <TEMP=D:\Boinc_da> 54 45 4D 50 3D 44 3A 5C 42 6F 69 6E 63 5F 64 61 
{3835263} normal block at 0x000001BD34246130, 32 bytes long.
 Data: <TMPDIR=D:\Boinc_> 54 4D 50 44 49 52 3D 44 3A 5C 42 6F 69 6E 63 5F 
{3835232} normal block at 0x000001BD325B6530, 48 bytes long.
 Data: <PATH=D:\Boinc_da> 50 41 54 48 3D 44 3A 5C 42 6F 69 6E 63 5F 64 61 
{3835221} normal block at 0x000001BD3420DED0, 102 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) : {3835218} normal block at 0x000001BD325876B0, 8 bytes long.
 Data: <  U2    > 00 00 55 32 BD 01 00 00 
{3834570} normal block at 0x000001BD3420DCC0, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{3833957} normal block at 0x000001BD32586C60, 8 bytes long.
 Data: <&#192;&#138;$4    > C0 8A 24 34 BD 01 00 00 
..\zip\boinc_zip.cpp(122) : {310} normal block at 0x000001BD32591A80, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000001BD3258D660, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{294} normal block at 0x000001BD325933D0, 16 bytes long.
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{293} normal block at 0x000001BD32593380, 16 bytes long.
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{292} normal block at 0x000001BD3258C0C0, 32 bytes long.
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{291} normal block at 0x000001BD32593290, 16 bytes long.
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{290} normal block at 0x000001BD325931F0, 16 bytes long.
 Data: <0AY2            > 30 41 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001BD325939C0, 16 bytes long.
 Data: < AY2            > 08 41 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001BD325930B0, 16 bytes long.
 Data: <&#224;@Y2            > E0 40 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001BD3258DB60, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{286} normal block at 0x000001BD325936F0, 16 bytes long.
 Data: <X)Y2            > 58 29 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001BD3258BFA0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{284} normal block at 0x000001BD32593150, 16 bytes long.
 Data: <0)Y2            > 30 29 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001BD32593880, 16 bytes long.
 Data: < )Y2            > 08 29 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001BD32592FC0, 16 bytes long.
 Data: <&#224;(Y2            > E0 28 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001BD32593240, 16 bytes long.
 Data: <&#184;(Y2            > B8 28 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001BD325938D0, 16 bytes long.
 Data: < (Y2            > 90 28 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001BD325936A0, 16 bytes long.
 Data: <h(Y2            > 68 28 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001BD3258BEE0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{276} normal block at 0x000001BD32592F70, 16 bytes long.
 Data: <@(Y2            > 40 28 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001BD32592840, 320 bytes long.
 Data: <p/Y2    &#224;&#190;X2    > 70 2F 59 32 BD 01 00 00 E0 BE 58 32 BD 01 00 00 
{274} normal block at 0x000001BD32592DE0, 16 bytes long.
 Data: <&#192;@Y2            > C0 40 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001BD325932E0, 16 bytes long.
 Data: < @Y2            > 98 40 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001BD3258BE20, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{271} normal block at 0x000001BD325935B0, 16 bytes long.
 Data: <p@Y2            > 70 40 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001BD3258BDC0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{269} normal block at 0x000001BD32592D90, 16 bytes long.
 Data: <&#184;?Y2            > B8 3F 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001BD32593650, 16 bytes long.
 Data: < ?Y2            > 90 3F 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001BD32592F20, 16 bytes long.
 Data: <h?Y2            > 68 3F 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001BD325937E0, 16 bytes long.
 Data: <@?Y2            > 40 3F 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001BD32593600, 16 bytes long.
 Data: < ?Y2            > 18 3F 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001BD32593970, 16 bytes long.
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{262} normal block at 0x000001BD32592E80, 16 bytes long.
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{261} normal block at 0x000001BD3258DFC0, 40 bytes long.
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{260} normal block at 0x000001BD32593330, 16 bytes long.
 Data: <&#208;>Y2            > D0 3E 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001BD32592ED0, 16 bytes long.
 Data: <&#168;>Y2            > A8 3E 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001BD3258BC40, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{257} normal block at 0x000001BD32593830, 16 bytes long.
 Data: < >Y2            > 80 3E 59 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000001BD32593E80, 992 bytes long.
 Data: <08Y2    @&#188;X2    > 30 38 59 32 BD 01 00 00 40 BC 58 32 BD 01 00 00 
{92} normal block at 0x000001BD3258C540, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{91} normal block at 0x000001BD325878E0, 16 bytes long.
 Data: < &#218;X2            > 80 DA 58 32 BD 01 00 00 00 00 00 00 00 00 00 00 
{90} normal block at 0x000001BD3258DA80, 40 bytes long.
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{69} normal block at 0x000001BD32587160, 16 bytes long.
 Data: < &#234;&#229;h&#246;           > 80 EA E5 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001BD32587570, 16 bytes long.
 Data: <@&#233;&#229;h&#246;           > 40 E9 E5 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001BD32586D00, 16 bytes long.
 Data: <&#248;W&#226;h&#246;           > F8 57 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001BD32587840, 16 bytes long.
 Data: <&#216;W&#226;h&#246;           > D8 57 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001BD32587520, 16 bytes long.
 Data: <P &#226;h&#246;           > 50 04 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001BD32586FD0, 16 bytes long.
 Data: <0 &#226;h&#246;           > 30 04 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001BD325874D0, 16 bytes long.
 Data: <&#224; &#226;h&#246;           > E0 02 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001BD32587B60, 16 bytes long.
 Data: <  &#226;h&#246;           > 10 04 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001BD32586CB0, 16 bytes long.
 Data: <p &#226;h&#246;           > 70 04 E2 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001BD32587200, 16 bytes long.
 Data: < &#192;&#224;h&#246;           > 18 C0 E0 68 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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