Task 38643241

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>
19:42:39 (20364): wrapper (7.9.26016): starting
19:42:39 (20364): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A03_A13_0.pdb
QB_A03_A13_0.xml
QB_A03_A13.inpcrd
QB_A03_A13_input.yaml
QB_A03_A13.pdb
QB_A03_A13.prmtop
QB_A03_A13_sys.xml
run.bat
run.sh
19:42:41 (20364): Library/usr/bin/tar.exe exited; CPU time 0.000000
19:42:41 (20364): 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 'D:\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 'D:\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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835199} normal block at 0x000002A98CABE220, 8 bytes long.
 Data: <        > 00 00 DF 8C A9 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x000002A98CAAE0C0, 1080 bytes long.
 Data: <                > F4 11 00 00 CD CD CD CD D8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x000002A98CAB1050, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
20:13:47 (45876): wrapper (7.9.26016): starting
20:13:47 (45876): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1544} normal block at 0x000002ABD6D27050, 8 bytes long.
 Data: <  $     > 00 00 24 D7 AB 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000002ABD6D27BC0, 1080 bytes long.
 Data: <,y              > 2C 79 00 00 CD CD CD CD AC 01 00 00 00 00 00 00 
Object dump complete.
20:33:42 (37392): wrapper (7.9.26016): starting
20:33:42 (37392): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\0\tmp already exists.
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 "D:\ProgramData\BOINC\slots\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\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 "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\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
20:36:12 (37392): C:/Windows/system32/cmd.exe exited; CPU time 135.250000
20:36:12 (37392): app exit status: 0x16
20:36:12 (37392): 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: 2937762 bytes.
Dumping objects ->
{1633} normal block at 0x000002F2061759D0, 48 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1622} normal block at 0x000002F206175D50, 48 bytes long.
 Data: <HOME=D:\ProgramD> 48 4F 4D 45 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1611} normal block at 0x000002F206175960, 48 bytes long.
 Data: <TMP=D:\ProgramDa> 54 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1600} normal block at 0x000002F206175F10, 48 bytes long.
 Data: <TEMP=D:\ProgramD> 54 45 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1589} normal block at 0x000002F206175E30, 48 bytes long.
 Data: <TMPDIR=D:\Progra> 54 4D 50 44 49 52 3D 44 3A 5C 50 72 6F 67 72 61 
{1558} normal block at 0x000002F2061603E0, 64 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1547} normal block at 0x000002F20615CA60, 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) : {1544} normal block at 0x000002F2061774B0, 8 bytes long.
 Data: <        > 00 00 14 06 F2 02 00 00 
{925} normal block at 0x000002F20615ECE0, 145 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{306} normal block at 0x000002F206177410, 8 bytes long.
 Data: <0z      > 30 7A 17 06 F2 02 00 00 
{297} normal block at 0x000002F206162850, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{296} normal block at 0x000002F206176C90, 16 bytes long.
 Data: <8y              > 38 79 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000002F2061773C0, 16 bytes long.
 Data: < y              > 10 79 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000002F206170D60, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{293} normal block at 0x000002F206176C40, 16 bytes long.
 Data: < x              > E8 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002F206176BA0, 16 bytes long.
 Data: < x              > C0 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002F206176DD0, 16 bytes long.
 Data: < x              > 98 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000002F206176B00, 16 bytes long.
 Data: <px              > 70 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002F206175C70, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{288} normal block at 0x000002F206176D80, 16 bytes long.
 Data: <                > 18 CF 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000002F2061706A0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{286} normal block at 0x000002F206176970, 16 bytes long.
 Data: <                > F0 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002F206176A10, 16 bytes long.
 Data: <                > C8 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000002F2061769C0, 16 bytes long.
 Data: <                > A0 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000002F206176BF0, 16 bytes long.
 Data: <x               > 78 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002F206176740, 16 bytes long.
 Data: <P               > 50 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002F2061766A0, 16 bytes long.
 Data: <(               > 28 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002F206170640, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{278} normal block at 0x000002F206177370, 16 bytes long.
 Data: <                > 00 CE 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002F20615CE00, 320 bytes long.
 Data: <ps      @       > 70 73 17 06 F2 02 00 00 40 06 17 06 F2 02 00 00 
{276} normal block at 0x000002F206176A60, 16 bytes long.
 Data: <Px              > 50 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000002F206177320, 16 bytes long.
 Data: <(x              > 28 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000002F206170BE0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{273} normal block at 0x000002F2061772D0, 16 bytes long.
 Data: < x              > 00 78 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002F2061704C0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{271} normal block at 0x000002F206176920, 16 bytes long.
 Data: <Hw              > 48 77 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000002F2061771E0, 16 bytes long.
 Data: < w              > 20 77 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000002F206176F60, 16 bytes long.
 Data: < v              > F8 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002F206177230, 16 bytes long.
 Data: < v              > D0 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000002F2061768D0, 16 bytes long.
 Data: < v              > A8 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002F2061770F0, 16 bytes long.
 Data: < v              > 80 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002F2061770A0, 16 bytes long.
 Data: < ^              > A0 5E 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000002F206175EA0, 40 bytes long.
 Data: < p              > A0 70 17 06 F2 02 00 00 E0 03 16 06 F2 02 00 00 
{262} normal block at 0x000002F206177500, 16 bytes long.
 Data: <`v              > 60 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000002F206176B50, 16 bytes long.
 Data: <8v              > 38 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000002F206170340, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{259} normal block at 0x000002F206176F10, 16 bytes long.
 Data: < v              > 10 76 17 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000002F206177610, 992 bytes long.
 Data: < o      @       > 10 6F 17 06 F2 02 00 00 40 03 17 06 F2 02 00 00 
{94} normal block at 0x000002F20616FFE0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{93} normal block at 0x000002F20616EAE0, 16 bytes long.
 Data: <                > F0 E5 15 06 F2 02 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x000002F20615E5F0, 40 bytes long.
 Data: <                > E0 EA 16 06 F2 02 00 00 E0 FF 16 06 F2 02 00 00 
{71} normal block at 0x000002F20616E400, 16 bytes long.
 Data: <                > 80 EA A0 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002F20616DF50, 16 bytes long.
 Data: <@               > 40 E9 A0 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002F20616E630, 16 bytes long.
 Data: < W              > F8 57 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002F20616E2C0, 16 bytes long.
 Data: < W              > D8 57 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002F20616E360, 16 bytes long.
 Data: <P               > 50 04 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002F20616DF00, 16 bytes long.
 Data: <0               > 30 04 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002F20616E900, 16 bytes long.
 Data: <                > E0 02 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002F20616E090, 16 bytes long.
 Data: <                > 10 04 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002F20616DFF0, 16 bytes long.
 Data: <p               > 70 04 9D 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002F20616E270, 16 bytes long.
 Data: <                > 18 C0 9B 86 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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