Task 38620951

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
16:05:35 (12024): wrapper (7.9.26016): starting
16:05:35 (12024): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A32_A23_0.pdb
QB_A32_A23_0.xml
QB_A32_A23.inpcrd
QB_A32_A23_input.yaml
QB_A32_A23.pdb
QB_A32_A23.prmtop
QB_A32_A23_sys.xml
run.bat
run.sh
16:05:36 (12024): Library/usr/bin/tar.exe exited; CPU time 0.000000
16:05:36 (12024): 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
16:38:25 (12024): C:/Windows/system32/cmd.exe exited; CPU time 1891.265625
16:38:25 (12024): app exit status: 0x16
16:38:25 (12024): called boinc_finish(195)
0 bytes in 0 Free Blocks.
536 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: 34265645 bytes.
Dumping objects ->
{3835270} normal block at 0x00000223341FD880, 48 bytes long.
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{3835259} normal block at 0x0000022332564B30, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835248} normal block at 0x0000022332564A50, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835237} normal block at 0x0000022332564AC0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835226} normal block at 0x00000223325649E0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835195} normal block at 0x000002233424BC00, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835184} normal block at 0x00000223325C9B40, 140 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) : {3835181} normal block at 0x000002233255D340, 8 bytes long.
 Data: <  P2#   > 00 00 50 32 23 02 00 00 
{3834563} normal block at 0x00000223325CA9E0, 140 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 0x000002233255DB60, 8 bytes long.
 Data: <&#176;z)4#   > B0 7A 29 34 23 02 00 00 
..\zip\boinc_zip.cpp(122) : {310} normal block at 0x0000022332550540, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000223325517E0, 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 0x0000022332565C40, 16 bytes long.
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{293} normal block at 0x0000022332565920, 16 bytes long.
 Data: <&#160;eV2#           > A0 65 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000022332560C30, 32 bytes long.
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{291} normal block at 0x00000223325656F0, 16 bytes long.
 Data: <xeV2#           > 78 65 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000223325660F0, 16 bytes long.
 Data: <PeV2#           > 50 65 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000022332565600, 16 bytes long.
 Data: <(eV2#           > 28 65 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000022332565BA0, 16 bytes long.
 Data: < eV2#           > 00 65 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000022332564CF0, 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 0x00000223325656A0, 16 bytes long.
 Data: <&#168; U2#           > A8 16 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000223325616B0, 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 0x0000022332565B50, 16 bytes long.
 Data: <  U2#           > 80 16 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000022332565D80, 16 bytes long.
 Data: <X U2#           > 58 16 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000022332565560, 16 bytes long.
 Data: <0 U2#           > 30 16 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000022332565DD0, 16 bytes long.
 Data: <  U2#           > 08 16 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000022332565FB0, 16 bytes long.
 Data: <&#224; U2#           > E0 15 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000022332565420, 16 bytes long.
 Data: <&#184; U2#           > B8 15 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000022332560FF0, 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 0x0000022332565BF0, 16 bytes long.
 Data: <  U2#           > 90 15 55 32 23 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000022332551590, 320 bytes long.
 Data: <&#240;[V2#   &#240; V2#   > F0 5B 56 32 23 02 00 00 F0 0F 56 32 23 02 00 00 
{274} normal block at 0x0000022332565B00, 16 bytes long.
 Data: <&#224;dV2#           > E0 64 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000223325653D0, 16 bytes long.
 Data: <&#184;dV2#           > B8 64 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000022332560E10, 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 0x0000022332566140, 16 bytes long.
 Data: < dV2#           > 90 64 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000223325609F0, 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 0x0000022332565380, 16 bytes long.
 Data: <&#216;cV2#           > D8 63 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000022332565F10, 16 bytes long.
 Data: <&#176;cV2#           > B0 63 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000223325652E0, 16 bytes long.
 Data: < cV2#           > 88 63 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000022332566230, 16 bytes long.
 Data: <`cV2#           > 60 63 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000223325661E0, 16 bytes long.
 Data: <8cV2#           > 38 63 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000022332565470, 16 bytes long.
 Data: < cV2#           > 10 63 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000022332565830, 16 bytes long.
 Data: <&#208;FV2#           > D0 46 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000223325646D0, 40 bytes long.
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{260} normal block at 0x0000022332565A60, 16 bytes long.
 Data: <&#240;bV2#           > F0 62 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000022332565650, 16 bytes long.
 Data: <&#200;bV2#           > C8 62 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000022332561110, 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 0x00000223325655B0, 16 bytes long.
 Data: <&#160;bV2#           > A0 62 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x00000223325662A0, 992 bytes long.
 Data: <&#176;UV2#     V2#   > B0 55 56 32 23 02 00 00 10 11 56 32 23 02 00 00 
{92} normal block at 0x00000223325607B0, 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 0x000002233255DA20, 16 bytes long.
 Data: <&#224; V2#           > E0 06 56 32 23 02 00 00 00 00 00 00 00 00 00 00 
{90} normal block at 0x00000223325606E0, 40 bytes long.
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{69} normal block at 0x000002233255D8E0, 16 bytes long.
 Data: < &#234;&#254;V&#247;           > 80 EA FE 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002233255D570, 16 bytes long.
 Data: <@&#233;&#254;V&#247;           > 40 E9 FE 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002233255D070, 16 bytes long.
 Data: <&#248;W&#251;V&#247;           > F8 57 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002233255D700, 16 bytes long.
 Data: <&#216;W&#251;V&#247;           > D8 57 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002233255D2F0, 16 bytes long.
 Data: <P &#251;V&#247;           > 50 04 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002233255D6B0, 16 bytes long.
 Data: <0 &#251;V&#247;           > 30 04 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002233255D250, 16 bytes long.
 Data: <&#224; &#251;V&#247;           > E0 02 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002233255DA70, 16 bytes long.
 Data: <  &#251;V&#247;           > 10 04 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002233255DBB0, 16 bytes long.
 Data: <p &#251;V&#247;           > 70 04 FB 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002233255DE30, 16 bytes long.
 Data: < &#192;&#249;V&#247;           > 18 C0 F9 56 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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