Task 38686291

Stderr output

<core_client_version>8.0.2</core_client_version>
<![CDATA[
<message>
(unknown error) (0) - exit code 195 (0xc3)</message>
<stderr_txt>
07:00:47 (3196): wrapper (7.9.26016): starting
07:00:47 (3196): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A34_A12_0.pdb
QB_A34_A12_0.xml
QB_A34_A12_input.yaml
QB_A34_A12.pdb
QB_A34_A12.prmtop
QB_A34_A12_sys.xml
run.bat
run.sh
07:00:50 (3196): Library/usr/bin/tar.exe exited; CPU time 0.000000
07:00:50 (3196): 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
07:16:06 (3196): C:/Windows/system32/cmd.exe exited; CPU time 836.718750
07:16:06 (3196): app exit status: 0x16
07:16:06 (3196): called boinc_finish(195)
0 bytes in 0 Free Blocks.
546 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: 9659657 bytes.
Dumping objects ->
{3835132} normal block at 0x00000179335D0E90, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835121} normal block at 0x00000179335D1440, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835110} normal block at 0x00000179335D1670, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835099} normal block at 0x00000179335D1600, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835088} normal block at 0x00000179335D1520, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835057} normal block at 0x00000179336E4610, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835046} normal block at 0x0000017931C6D000, 145 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) : {3835043} normal block at 0x0000017931C171C0, 8 bytes long.
 Data: <  &#190;1y   > 00 00 BE 31 79 01 00 00 
{3834495} normal block at 0x0000017931C6E5F0, 145 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 0x0000017931C173A0, 8 bytes long.
 Data: <&#176;#t3y   > B0 23 74 33 79 01 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x0000017931C218C0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000017931C060D0, 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 0x0000017931C22A40, 16 bytes long.
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{292} normal block at 0x0000017931C22860, 16 bytes long.
 Data: <&#208;>&#194;1y           > D0 3E C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000017931C1B820, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{290} normal block at 0x0000017931C23620, 16 bytes long.
 Data: <&#168;>&#194;1y           > A8 3E C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000017931C229A0, 16 bytes long.
 Data: < >&#194;1y           > 80 3E C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000017931C235D0, 16 bytes long.
 Data: <X>&#194;1y           > 58 3E C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000017931C23260, 16 bytes long.
 Data: <0>&#194;1y           > 30 3E C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000017931C1D890, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x0000017931C23440, 16 bytes long.
 Data: <h`&#192;1y           > 68 60 C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000017931C1C000, 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 0x0000017931C228B0, 16 bytes long.
 Data: <@`&#192;1y           > 40 60 C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000017931C23210, 16 bytes long.
 Data: < `&#192;1y           > 18 60 C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000017931C23120, 16 bytes long.
 Data: <&#240;_&#192;1y           > F0 5F C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000017931C22F40, 16 bytes long.
 Data: <&#200;_&#192;1y           > C8 5F C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000017931C231C0, 16 bytes long.
 Data: <&#160;_&#192;1y           > A0 5F C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000017931C22E50, 16 bytes long.
 Data: <x_&#192;1y           > 78 5F C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000017931C1C0C0, 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 0x0000017931C22CC0, 16 bytes long.
 Data: <P_&#192;1y           > 50 5F C0 31 79 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000017931C05F50, 320 bytes long.
 Data: <&#192;,&#194;1y   &#192;&#192;&#193;1y   > C0 2C C2 31 79 01 00 00 C0 C0 C1 31 79 01 00 00 
{273} normal block at 0x0000017931C22C70, 16 bytes long.
 Data: < >&#194;1y           > 10 3E C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000017931C229F0, 16 bytes long.
 Data: <&#232;=&#194;1y           > E8 3D C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000017931C1BFA0, 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 0x0000017931C233A0, 16 bytes long.
 Data: <&#192;=&#194;1y           > C0 3D C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000017931C1B7C0, 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 0x0000017931C22B30, 16 bytes long.
 Data: < =&#194;1y           > 08 3D C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000017931C230D0, 16 bytes long.
 Data: <&#224;<&#194;1y           > E0 3C C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000017931C23580, 16 bytes long.
 Data: <&#184;<&#194;1y           > B8 3C C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000017931C22A90, 16 bytes long.
 Data: < <&#194;1y           > 90 3C C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000017931C23530, 16 bytes long.
 Data: <h<&#194;1y           > 68 3C C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000017931C22E00, 16 bytes long.
 Data: <@<&#194;1y           > 40 3C C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000017931C22DB0, 16 bytes long.
 Data: < &#217;&#193;1y           > 00 D9 C1 31 79 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000017931C1D900, 40 bytes long.
 Data: <&#176;-&#194;1y    Fn3y   > B0 2D C2 31 79 01 00 00 10 46 6E 33 79 01 00 00 
{259} normal block at 0x0000017931C22EF0, 16 bytes long.
 Data: < <&#194;1y           > 20 3C C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000017931C22C20, 16 bytes long.
 Data: <&#248;;&#194;1y           > F8 3B C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000017931C1C6C0, 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 0x0000017931C23490, 16 bytes long.
 Data: <&#208;;&#194;1y           > D0 3B C2 31 79 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000017931C23BD0, 992 bytes long.
 Data: < 4&#194;1y   &#192;&#198;&#193;1y   > 90 34 C2 31 79 01 00 00 C0 C6 C1 31 79 01 00 00 
{91} normal block at 0x0000017931C1BB80, 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 0x0000017931C16D10, 16 bytes long.
 Data: < &#216;&#193;1y           > 20 D8 C1 31 79 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x0000017931C1D820, 40 bytes long.
 Data: < m&#193;1y    &#187;&#193;1y   > 10 6D C1 31 79 01 00 00 80 BB C1 31 79 01 00 00 
{68} normal block at 0x0000017931C170D0, 16 bytes long.
 Data: < &#234;Jd&#247;           > 80 EA 4A 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000017931C16EA0, 16 bytes long.
 Data: <@&#233;Jd&#247;           > 40 E9 4A 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000017931C169A0, 16 bytes long.
 Data: <&#248;WGd&#247;           > F8 57 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000017931C16E50, 16 bytes long.
 Data: <&#216;WGd&#247;           > D8 57 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000017931C176C0, 16 bytes long.
 Data: <P Gd&#247;           > 50 04 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000017931C17080, 16 bytes long.
 Data: <0 Gd&#247;           > 30 04 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000017931C17030, 16 bytes long.
 Data: <&#224; Gd&#247;           > E0 02 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000017931C16950, 16 bytes long.
 Data: <  Gd&#247;           > 10 04 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000017931C16DB0, 16 bytes long.
 Data: <p Gd&#247;           > 70 04 47 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000017931C16900, 16 bytes long.
 Data: < &#192;Ed&#247;           > 18 C0 45 64 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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