Task 38643077

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>
06:44:16 (15072): wrapper (7.9.26016): starting
06:44:16 (15072): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A10_0.pdb
QB_A20_A10_0.xml
QB_A20_A10.inpcrd
QB_A20_A10_input.yaml
QB_A20_A10.pdb
QB_A20_A10.prmtop
QB_A20_A10_sys.xml
run.bat
run.sh
06:44:18 (15072): Library/usr/bin/tar.exe exited; CPU time 0.000000
06:44:18 (15072): 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\5\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\5\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) : {3835403} normal block at 0x0000016CCEC5B2A0, 8 bytes long.
 Data: <    l   > 00 00 15 CF 6C 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833970} normal block at 0x0000016CCEC64550, 1080 bytes long.
 Data: <LT              > 4C 54 00 00 CD CD CD CD E8 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {317} normal block at 0x0000016CCEC60FF0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
14:59:03 (1772): wrapper (7.9.26016): starting
14:59:03 (1772): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\5\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1743} normal block at 0x0000018E0AD46EC0, 8 bytes long.
 Data: <  -     > 00 00 2D 0B 8E 01 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x0000018E0AD47CB0, 1080 bytes long.
 Data: < H      L       > FC 48 00 00 CD CD CD CD 4C 01 00 00 00 00 00 00 
Object dump complete.
00:34:31 (1760): wrapper (7.9.26016): starting
00:34:31 (1760): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\5\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 "C:\ProgramData\BOINC\slots\5\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\5\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\5\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\5\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\5\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\5\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\5\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\5\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\5\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
12:18:30 (1760): C:/Windows/system32/cmd.exe exited; CPU time 42662.515625
12:18:30 (1760): app exit status: 0x16
12:18:30 (1760): called boinc_finish(195)
0 bytes in 0 Free Blocks.
656 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: 635307256 bytes.
Dumping objects ->
{1832} normal block at 0x00000147251B4B80, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1821} normal block at 0x00000147251B4BF0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1810} normal block at 0x00000147251B4A30, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1799} normal block at 0x00000147251B4B10, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1788} normal block at 0x00000147251B49C0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1757} normal block at 0x00000147251A0FD0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1746} normal block at 0x00000147251ACD00, 200 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) : {1743} normal block at 0x00000147251B6490, 8 bytes long.
 Data: <  s%G   > 00 00 73 25 47 01 00 00 
{1026} normal block at 0x00000147251AC480, 200 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{311} normal block at 0x00000147251B63A0, 8 bytes long.
 Data: < k %G   > 00 6B 1B 25 47 01 00 00 
{302} normal block at 0x000001472519F310, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{301} normal block at 0x00000147251B58B0, 16 bytes long.
 Data: < j %G           > 08 6A 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x00000147251B5F40, 16 bytes long.
 Data: < i %G           > E0 69 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x00000147251AEB00, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{298} normal block at 0x00000147251B5CC0, 16 bytes long.
 Data: < i %G           > B8 69 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x00000147251B5EF0, 16 bytes long.
 Data: < i %G           > 90 69 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x00000147251B5E50, 16 bytes long.
 Data: <hi %G           > 68 69 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000147251B5860, 16 bytes long.
 Data: <@i %G           > 40 69 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000147251B4AA0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{293} normal block at 0x00000147251B5810, 16 bytes long.
 Data: <X  %G           > 58 04 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000147251AE9E0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{291} normal block at 0x00000147251B63F0, 16 bytes long.
 Data: <0  %G           > 30 04 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000147251B5D60, 16 bytes long.
 Data: <   %G           > 08 04 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000147251B6300, 16 bytes long.
 Data: <   %G           > E0 03 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000147251B6350, 16 bytes long.
 Data: <   %G           > B8 03 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x00000147251B5900, 16 bytes long.
 Data: <   %G           > 90 03 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000147251B5A90, 16 bytes long.
 Data: <h  %G           > 68 03 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000147251AE5C0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{283} normal block at 0x00000147251B62B0, 16 bytes long.
 Data: <@  %G           > 40 03 1A 25 47 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000147251A0340, 320 bytes long.
 Data: < b %G      %G   > B0 62 1B 25 47 01 00 00 C0 E5 1A 25 47 01 00 00 
{281} normal block at 0x00000147251B57C0, 16 bytes long.
 Data: < i %G           > 20 69 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000147251B6030, 16 bytes long.
 Data: < h %G           > F8 68 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000147251AEBC0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{278} normal block at 0x00000147251B6670, 16 bytes long.
 Data: < h %G           > D0 68 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000147251AE620, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{276} normal block at 0x00000147251B65D0, 16 bytes long.
 Data: < h %G           > 18 68 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000147251B6580, 16 bytes long.
 Data: < g %G           > F0 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000147251B5770, 16 bytes long.
 Data: < g %G           > C8 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000147251B6260, 16 bytes long.
 Data: < g %G           > A0 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000147251B6210, 16 bytes long.
 Data: <xg %G           > 78 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000147251B59F0, 16 bytes long.
 Data: <Pg %G           > 50 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000147251B6620, 16 bytes long.
 Data: < N %G           > 20 4E 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000147251B4E20, 40 bytes long.
 Data: < f %G      %G   > 20 66 1B 25 47 01 00 00 D0 0F 1A 25 47 01 00 00 
{267} normal block at 0x00000147251B61C0, 16 bytes long.
 Data: <0g %G           > 30 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000147251B6530, 16 bytes long.
 Data: < g %G           > 08 67 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000147251AED40, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{264} normal block at 0x00000147251B64E0, 16 bytes long.
 Data: < f %G           > E0 66 1B 25 47 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000147251B66E0, 992 bytes long.
 Data: < d %G   @  %G   > E0 64 1B 25 47 01 00 00 40 ED 1A 25 47 01 00 00 
{99} normal block at 0x00000147251AEF20, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{98} normal block at 0x00000147251AAC90, 16 bytes long.
 Data: <   %G           > A0 E6 19 25 47 01 00 00 00 00 00 00 00 00 00 00 
{97} normal block at 0x000001472519E6A0, 40 bytes long.
 Data: <   %G      %G   > 90 AC 1A 25 47 01 00 00 20 EF 1A 25 47 01 00 00 
{76} normal block at 0x00000147251AA9C0, 16 bytes long.
 Data: <                > 80 EA F2 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x00000147251AAA60, 16 bytes long.
 Data: <@               > 40 E9 F2 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x00000147251AB5A0, 16 bytes long.
 Data: < W              > F8 57 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x00000147251AAEC0, 16 bytes long.
 Data: < W              > D8 57 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x00000147251AB550, 16 bytes long.
 Data: <P               > 50 04 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000147251AA920, 16 bytes long.
 Data: <0               > 30 04 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000147251AB370, 16 bytes long.
 Data: <                > E0 02 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000147251AAE70, 16 bytes long.
 Data: <                > 10 04 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000147251AB050, 16 bytes long.
 Data: <p               > 70 04 EF 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000147251AB320, 16 bytes long.
 Data: <                > 18 C0 ED 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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