Task 38625283

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>
09:41:06 (9956): wrapper (7.9.26016): starting
09:41:06 (9956): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A07_A15_0.pdb
QB_A07_A15_0.xml
QB_A07_A15.inpcrd
QB_A07_A15_input.yaml
QB_A07_A15.pdb
QB_A07_A15.prmtop
QB_A07_A15_sys.xml
run.bat
run.sh
09:41:07 (9956): Library/usr/bin/tar.exe exited; CPU time 0.015625
09:41:07 (9956): 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\18\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\18\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\18\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\18\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\18\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\18\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\18\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\18\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\18\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\18\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\18\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
09:41:46 (9956): C:/Windows/system32/cmd.exe exited; CPU time 18.203125
09:41:46 (9956): app exit status: 0x16
09:41:46 (9956): called boinc_finish(195)
0 bytes in 0 Free Blocks.
460 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: 901237 bytes.
Dumping objects ->
{3835535} normal block at 0x0000027A563F73B0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835524} normal block at 0x0000027A563F6E70, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835513} normal block at 0x0000027A563F70A0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835502} normal block at 0x0000027A563F7030, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835491} normal block at 0x0000027A563F6D90, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835460} normal block at 0x0000027A58096500, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835449} normal block at 0x0000027A580AFA70, 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) : {3835446} normal block at 0x0000027A563EE4E0, 8 bytes long.
 Data: <  ~Vz   > 00 00 7E 56 7A 02 00 00 
{3834673} normal block at 0x0000027A580AF390, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{3833951} normal block at 0x0000027A563EE6C0, 8 bytes long.
 Data: <&#224;S Xz   > E0 53 0F 58 7A 02 00 00 
..\zip\boinc_zip.cpp(122) : {307} normal block at 0x0000027A563E1650, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000027A563E1FF0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{291} normal block at 0x0000027A563F5650, 16 bytes long.
 Data: <Hl?Vz           > 48 6C 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000027A563F5B00, 16 bytes long.
 Data: < l?Vz           > 20 6C 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000027A563EFD00, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{288} normal block at 0x0000027A563F60A0, 16 bytes long.
 Data: <&#248;k?Vz           > F8 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000027A563F6190, 16 bytes long.
 Data: <&#208;k?Vz           > D0 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000027A563F5A10, 16 bytes long.
 Data: <&#168;k?Vz           > A8 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000027A563F5790, 16 bytes long.
 Data: < k?Vz           > 80 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000027A563F72D0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{283} normal block at 0x0000027A563F64B0, 16 bytes long.
 Data: <&#216; >Vz           > D8 00 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000027A563F0420, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{281} normal block at 0x0000027A563F6050, 16 bytes long.
 Data: <&#176; >Vz           > B0 00 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000027A563F5E70, 16 bytes long.
 Data: <  >Vz           > 88 00 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000027A563F59C0, 16 bytes long.
 Data: <` >Vz           > 60 00 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000027A563F5970, 16 bytes long.
 Data: <8 >Vz           > 38 00 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000027A563F55B0, 16 bytes long.
 Data: <  >Vz           > 10 00 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000027A563F6320, 16 bytes long.
 Data: <&#232;&#255;=Vz           > E8 FF 3D 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000027A563F03C0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{273} normal block at 0x0000027A563F5740, 16 bytes long.
 Data: <&#192;&#255;=Vz           > C0 FF 3D 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000027A563DFFC0, 320 bytes long.
 Data: <@W?Vz   &#192; ?Vz   > 40 57 3F 56 7A 02 00 00 C0 03 3F 56 7A 02 00 00 
{271} normal block at 0x0000027A563F5BF0, 16 bytes long.
 Data: <`k?Vz           > 60 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000027A563F5920, 16 bytes long.
 Data: <8k?Vz           > 38 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000027A563F0300, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{268} normal block at 0x0000027A563F58D0, 16 bytes long.
 Data: < k?Vz           > 10 6B 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000027A563F0600, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{266} normal block at 0x0000027A563F5D80, 16 bytes long.
 Data: <Xj?Vz           > 58 6A 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000027A563F5600, 16 bytes long.
 Data: <0j?Vz           > 30 6A 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000027A563F6000, 16 bytes long.
 Data: < j?Vz           > 08 6A 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000027A563F5AB0, 16 bytes long.
 Data: <&#224;i?Vz           > E0 69 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000027A563F6410, 16 bytes long.
 Data: <&#184;i?Vz           > B8 69 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000027A563F5560, 16 bytes long.
 Data: < i?Vz           > 90 69 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000027A563F63C0, 16 bytes long.
 Data: <&#224; >Vz           > E0 03 3E 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000027A563E03E0, 40 bytes long.
 Data: <&#192;c?Vz    e	Xz   > C0 63 3F 56 7A 02 00 00 00 65 09 58 7A 02 00 00 
{257} normal block at 0x0000027A563F56F0, 16 bytes long.
 Data: <pi?Vz           > 70 69 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000027A563F5FB0, 16 bytes long.
 Data: <Hi?Vz           > 48 69 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000027A563F0540, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{254} normal block at 0x0000027A563F5D30, 16 bytes long.
 Data: < i?Vz           > 20 69 3F 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x0000027A563F6920, 992 bytes long.
 Data: <0]?Vz   @ ?Vz   > 30 5D 3F 56 7A 02 00 00 40 05 3F 56 7A 02 00 00 
{89} normal block at 0x0000027A563F0180, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{88} normal block at 0x0000027A563EDEF0, 16 bytes long.
 Data: <0&#200;=Vz           > 30 C8 3D 56 7A 02 00 00 00 00 00 00 00 00 00 00 
{87} normal block at 0x0000027A563DC830, 40 bytes long.
 Data: <&#240;&#222;>Vz     ?Vz   > F0 DE 3E 56 7A 02 00 00 80 01 3F 56 7A 02 00 00 
{66} normal block at 0x0000027A563EE490, 16 bytes long.
 Data: < &#234;YS&#247;           > 80 EA 59 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000027A563EE5D0, 16 bytes long.
 Data: <@&#233;YS&#247;           > 40 E9 59 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000027A563EE440, 16 bytes long.
 Data: <&#248;WVS&#247;           > F8 57 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000027A563EDA40, 16 bytes long.
 Data: <&#216;WVS&#247;           > D8 57 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000027A563EDA90, 16 bytes long.
 Data: <P VS&#247;           > 50 04 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000027A563EDEA0, 16 bytes long.
 Data: <0 VS&#247;           > 30 04 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000027A563EE0D0, 16 bytes long.
 Data: <&#224; VS&#247;           > E0 02 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000027A563EE260, 16 bytes long.
 Data: <  VS&#247;           > 10 04 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000027A563EDF90, 16 bytes long.
 Data: <p VS&#247;           > 70 04 56 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x0000027A563EE670, 16 bytes long.
 Data: < &#192;TS&#247;           > 18 C0 54 53 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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