Task 38614949

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>
09:07:10 (11008): wrapper (7.9.26016): starting
09:07:10 (11008): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A02_A11_0.pdb
QB_A02_A11_0.xml
QB_A02_A11.inpcrd
QB_A02_A11_input.yaml
QB_A02_A11.pdb
QB_A02_A11.prmtop
QB_A02_A11_sys.xml
run.bat
run.sh
09:07:11 (11008): Library/usr/bin/tar.exe exited; CPU time 0.000000
09:07:11 (11008): 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\0\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\0\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\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\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\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\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
11:44:39 (11008): C:/Windows/system32/cmd.exe exited; CPU time 8692.468750
11:44:39 (11008): app exit status: 0x16
11:44:39 (11008): 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: 186862729 bytes.
Dumping objects ->
{3835315} normal block at 0x000001346A1B5210, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835304} normal block at 0x0000013468516790, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835293} normal block at 0x0000013468516A30, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835282} normal block at 0x00000134685163A0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835271} normal block at 0x0000013468516720, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835240} normal block at 0x000001346A129D00, 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) : {3835227} normal block at 0x000001346850E710, 8 bytes long.
 Data: <  &#239;i4   > 00 00 EF 69 34 01 00 00 
{3833963} normal block at 0x000001346850F020, 8 bytes long.
 Data: <&#160;&#217;Oh4   > A0 D9 4F 68 34 01 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x0000013468501370, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x0000013468502720, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{297} normal block at 0x0000013468516C80, 16 bytes long.
 Data: <(~Qh4           > 28 7E 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000013468516FA0, 16 bytes long.
 Data: < ~Qh4           > 00 7E 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000013468512C40, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{294} normal block at 0x0000013468516B40, 16 bytes long.
 Data: <&#216;}Qh4           > D8 7D 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x00000134685179A0, 16 bytes long.
 Data: <&#176;}Qh4           > B0 7D 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000134685171D0, 16 bytes long.
 Data: < }Qh4           > 88 7D 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000013468517400, 16 bytes long.
 Data: <`}Qh4           > 60 7D 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000013468516410, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{289} normal block at 0x0000013468516D20, 16 bytes long.
 Data: <&#168;&#252;Oh4           > A8 FC 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000013468511F80, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{287} normal block at 0x0000013468517950, 16 bytes long.
 Data: < &#252;Oh4           > 80 FC 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000013468516FF0, 16 bytes long.
 Data: <X&#252;Oh4           > 58 FC 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000134685173B0, 16 bytes long.
 Data: <0&#252;Oh4           > 30 FC 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000013468516F00, 16 bytes long.
 Data: < &#252;Oh4           > 08 FC 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000013468517360, 16 bytes long.
 Data: <&#224;&#251;Oh4           > E0 FB 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000134685172C0, 16 bytes long.
 Data: <&#184;&#251;Oh4           > B8 FB 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000013468512AC0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{279} normal block at 0x0000013468516C30, 16 bytes long.
 Data: < &#251;Oh4           > 90 FB 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000134684FFB90, 320 bytes long.
 Data: <0lQh4   &#192;*Qh4   > 30 6C 51 68 34 01 00 00 C0 2A 51 68 34 01 00 00 
{277} normal block at 0x0000013468517130, 16 bytes long.
 Data: <@}Qh4           > 40 7D 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000013468517180, 16 bytes long.
 Data: < }Qh4           > 18 7D 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000013468512340, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{274} normal block at 0x0000013468517900, 16 bytes long.
 Data: <&#240;|Qh4           > F0 7C 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000013468512BE0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{272} normal block at 0x00000134685174A0, 16 bytes long.
 Data: <8|Qh4           > 38 7C 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000013468516DC0, 16 bytes long.
 Data: < |Qh4           > 10 7C 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000013468517310, 16 bytes long.
 Data: <&#232;{Qh4           > E8 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000134685179F0, 16 bytes long.
 Data: <&#192;{Qh4           > C0 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000013468516EB0, 16 bytes long.
 Data: < {Qh4           > 98 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000013468517A90, 16 bytes long.
 Data: <p{Qh4           > 70 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000013468516CD0, 16 bytes long.
 Data: <@fQh4           > 40 66 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000013468516640, 40 bytes long.
 Data: <&#208;lQh4      j4   > D0 6C 51 68 34 01 00 00 00 9D 12 6A 34 01 00 00 
{263} normal block at 0x0000013468517720, 16 bytes long.
 Data: <P{Qh4           > 50 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000013468517450, 16 bytes long.
 Data: <({Qh4           > 28 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000013468512700, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{260} normal block at 0x0000013468516E60, 16 bytes long.
 Data: < {Qh4           > 00 7B 51 68 34 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000013468517B00, 992 bytes long.
 Data: <`nQh4    'Qh4   > 60 6E 51 68 34 01 00 00 00 27 51 68 34 01 00 00 
{95} normal block at 0x0000013468512640, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{94} normal block at 0x000001346850EFD0, 16 bytes long.
 Data: <0&#230;Oh4           > 30 E6 4F 68 34 01 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x00000134684FE630, 40 bytes long.
 Data: <&#208;&#239;Ph4   @&Qh4   > D0 EF 50 68 34 01 00 00 40 26 51 68 34 01 00 00 
{72} normal block at 0x000001346850E760, 16 bytes long.
 Data: < &#234;2 &#246;           > 80 EA 32 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000001346850EE40, 16 bytes long.
 Data: <@&#233;2 &#246;           > 40 E9 32 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000001346850E670, 16 bytes long.
 Data: <&#248;W/ &#246;           > F8 57 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001346850E3A0, 16 bytes long.
 Data: <&#216;W/ &#246;           > D8 57 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001346850E800, 16 bytes long.
 Data: <P / &#246;           > 50 04 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001346850EF80, 16 bytes long.
 Data: <0 / &#246;           > 30 04 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001346850E350, 16 bytes long.
 Data: <&#224; / &#246;           > E0 02 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001346850E6C0, 16 bytes long.
 Data: <  / &#246;           > 10 04 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001346850ED50, 16 bytes long.
 Data: <p / &#246;           > 70 04 2F 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001346850EA80, 16 bytes long.
 Data: < &#192;- &#246;           > 18 C0 2D 06 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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