Task 38643187

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
06:26:19 (19384): wrapper (7.9.26016): starting
06:26:19 (19384): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A21_A07_0.pdb
QB_A21_A07_0.xml
QB_A21_A07.inpcrd
QB_A21_A07_input.yaml
QB_A21_A07.pdb
QB_A21_A07.prmtop
QB_A21_A07_sys.xml
run.bat
run.sh
06:26:39 (19384): Library/usr/bin/tar.exe exited; CPU time 0.109375
06:26:39 (19384): 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\6\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\6\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\6\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\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\6\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\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
06:37:06 (19384): C:/Windows/system32/cmd.exe exited; CPU time 571.375000
06:37:06 (19384): app exit status: 0x16
06:37:06 (19384): called boinc_finish(195)
0 bytes in 0 Free Blocks.
256 bytes in 6 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: 9431573 bytes.
Dumping objects ->
{3835649} normal block at 0x0000017D646C4970, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835638} normal block at 0x0000017D646C4900, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835627} normal block at 0x0000017D646C4890, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835616} normal block at 0x0000017D646C47B0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835605} normal block at 0x0000017D646C46D0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835574} normal block at 0x0000017D662E7A80, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
..\api\boinc_api.cpp(309) : {3835561} normal block at 0x0000017D646BD720, 8 bytes long.
 Data: <  &#170;d}   > 00 00 AA 64 7D 01 00 00 
{3833955} normal block at 0x0000017D646BD2C0, 8 bytes long.
 Data: <&#192;&#213;jd}   > C0 D5 6A 64 7D 01 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x0000017D646B09B0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000017D646B25E0, 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 0x0000017D646C5CE0, 16 bytes long.
 Data: < cld}           > 98 63 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000017D646C5C90, 16 bytes long.
 Data: <pcld}           > 70 63 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000017D646C0560, 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 0x0000017D646C5BA0, 16 bytes long.
 Data: <Hcld}           > 48 63 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000017D646C5B00, 16 bytes long.
 Data: < cld}           > 20 63 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000017D646C5AB0, 16 bytes long.
 Data: <&#248;bld}           > F8 62 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000017D646C5FB0, 16 bytes long.
 Data: <&#208;bld}           > D0 62 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000017D646C4A50, 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 0x0000017D646C5970, 16 bytes long.
 Data: <&#248; kd}           > F8 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000017D646C0980, 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 0x0000017D646C5510, 16 bytes long.
 Data: <&#208; kd}           > D0 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000017D646C5650, 16 bytes long.
 Data: <&#168; kd}           > A8 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000017D646C53D0, 16 bytes long.
 Data: <  kd}           > 80 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000017D646C6000, 16 bytes long.
 Data: <X kd}           > 58 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000017D646C5740, 16 bytes long.
 Data: <0 kd}           > 30 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000017D646C5920, 16 bytes long.
 Data: <  kd}           > 08 05 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000017D646C1160, 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 0x0000017D646C5B50, 16 bytes long.
 Data: <&#224; kd}           > E0 04 6B 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000017D646B04E0, 320 bytes long.
 Data: <P[ld}   ` ld}   > 50 5B 6C 64 7D 01 00 00 60 11 6C 64 7D 01 00 00 
{273} normal block at 0x0000017D646C5A10, 16 bytes long.
 Data: <&#176;bld}           > B0 62 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000017D646C51A0, 16 bytes long.
 Data: < bld}           > 88 62 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000017D646C04A0, 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 0x0000017D646C54C0, 16 bytes long.
 Data: <`bld}           > 60 62 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000017D646C13A0, 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 0x0000017D646C5880, 16 bytes long.
 Data: <&#168;ald}           > A8 61 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000017D646C5150, 16 bytes long.
 Data: < ald}           > 80 61 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000017D646C59C0, 16 bytes long.
 Data: <Xald}           > 58 61 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000017D646C5380, 16 bytes long.
 Data: <0ald}           > 30 61 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000017D646C5830, 16 bytes long.
 Data: < ald}           > 08 61 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000017D646C5A60, 16 bytes long.
 Data: <&#224;`ld}           > E0 60 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000017D646C58D0, 16 bytes long.
 Data: <&#160;Kld}           > A0 4B 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000017D646C4BA0, 40 bytes long.
 Data: <&#208;Xld}    z.f}   > D0 58 6C 64 7D 01 00 00 80 7A 2E 66 7D 01 00 00 
{259} normal block at 0x0000017D646C5C40, 16 bytes long.
 Data: <&#192;`ld}           > C0 60 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000017D646C5470, 16 bytes long.
 Data: < `ld}           > 98 60 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000017D646C0C80, 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 0x0000017D646C57E0, 16 bytes long.
 Data: <p`ld}           > 70 60 6C 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000017D646C6070, 992 bytes long.
 Data: <&#224;Wld}     ld}   > E0 57 6C 64 7D 01 00 00 80 0C 6C 64 7D 01 00 00 
{91} normal block at 0x0000017D646C0D40, 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 0x0000017D646BD220, 16 bytes long.
 Data: <0&#197;jd}           > 30 C5 6A 64 7D 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x0000017D646AC530, 40 bytes long.
 Data: < &#210;kd}   @ ld}   > 20 D2 6B 64 7D 01 00 00 40 0D 6C 64 7D 01 00 00 
{68} normal block at 0x0000017D646BDA90, 16 bytes long.
 Data: < &#234;&#166; &#246;           > 80 EA A6 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000017D646BD9F0, 16 bytes long.
 Data: <@&#233;&#166; &#246;           > 40 E9 A6 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000017D646BD4F0, 16 bytes long.
 Data: <&#248;W&#163; &#246;           > F8 57 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000017D646BCFF0, 16 bytes long.
 Data: <&#216;W&#163; &#246;           > D8 57 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000017D646BD270, 16 bytes long.
 Data: <P &#163; &#246;           > 50 04 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000017D646BD0E0, 16 bytes long.
 Data: <0 &#163; &#246;           > 30 04 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000017D646BD1D0, 16 bytes long.
 Data: <&#224; &#163; &#246;           > E0 02 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000017D646BD450, 16 bytes long.
 Data: <  &#163; &#246;           > 10 04 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000017D646BD7C0, 16 bytes long.
 Data: <p &#163; &#246;           > 70 04 A3 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000017D646BD590, 16 bytes long.
 Data: < &#192;&#161; &#246;           > 18 C0 A1 04 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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