Task 38643033

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>
05:48:19 (141892): wrapper (7.9.26016): starting
05:48:19 (141892): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A12_A04_0.pdb
QB_A12_A04_0.xml
QB_A12_A04.inpcrd
QB_A12_A04_input.yaml
QB_A12_A04.pdb
QB_A12_A04.prmtop
QB_A12_A04_sys.xml
run.bat
run.sh
05:48:23 (141892): Library/usr/bin/tar.exe exited; CPU time 0.015625
05:48:23 (141892): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835206} normal block at 0x0000017E8C7FBA50, 8 bytes long.
 Data: <  E ~   > 00 00 45 8E 7E 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833966} normal block at 0x0000017E8C7DE720, 1080 bytes long.
 Data: <        ,       > D4 1D 02 00 CD CD CD CD 2C 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {315} normal block at 0x0000017E8C7ED3F0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
09:12:43 (158600): wrapper (7.9.26016): starting
09:12:43 (158600): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1548} normal block at 0x000001733E1CB7C0, 8 bytes long.
 Data: <   ?s   > 00 00 CA 3F 73 01 00 00 
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x000001733E1CBC90, 1080 bytes long.
 Data: < a      l       > 08 61 02 00 CD CD CD CD 6C 01 00 00 00 00 00 00 
Object dump complete.
11:47:17 (164824): wrapper (7.9.26016): starting
11:47:17 (164824): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1548} normal block at 0x000001DF4AD3AE70, 8 bytes long.
 Data: <   J    > 00 00 D0 4A DF 01 00 00 
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x000001DF4AD3BC00, 1080 bytes long.
 Data: < x      l       > F0 78 02 00 CD CD CD CD 6C 01 00 00 00 00 00 00 
Object dump complete.
12:08:01 (140104): wrapper (7.9.26016): starting
12:08:01 (140104): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1548} normal block at 0x0000019EB56BBB80, 8 bytes long.
 Data: <  G     > 00 00 47 B7 9E 01 00 00 
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x0000019EB56BBC90, 1080 bytes long.
 Data: < ,      l       > 14 2C 01 00 CD CD CD CD 6C 01 00 00 00 00 00 00 
Object dump complete.
12:21:10 (162860): wrapper (7.9.26016): starting
12:21:10 (162860): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1548} normal block at 0x0000020287E2B3B0, 8 bytes long.
 Data: <  .     > 00 00 2E 88 02 02 00 00 
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x0000020287E2BC90, 1080 bytes long.
 Data: <        l       > D0 C2 00 00 CD CD CD CD 6C 01 00 00 00 00 00 00 
Object dump complete.
15:12:17 (93368): wrapper (7.9.26016): starting
15:12:17 (93368): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1548} normal block at 0x000001C0C22DB050, 8 bytes long.
 Data: <  v     > 00 00 76 C2 C0 01 00 00 
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x000001C0C22DBC00, 1080 bytes long.
 Data: <P,              > 50 2C 00 00 CD CD CD CD 84 01 00 00 00 00 00 00 
Object dump complete.
15:54:51 (165960): wrapper (7.9.26016): starting
15:54:51 (165960): 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\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 "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
17:42:00 (165960): C:/Windows/system32/cmd.exe exited; CPU time 6817.671875
17:42:00 (165960): app exit status: 0x16
17:42:00 (165960): called boinc_finish(195)
0 bytes in 0 Free Blocks.
426 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: 126946711 bytes.
Dumping objects ->
{1637} normal block at 0x000001A15CB836D0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1626} normal block at 0x000001A15CB835F0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1615} normal block at 0x000001A15CB83B30, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1604} normal block at 0x000001A15CB83660, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1593} normal block at 0x000001A15CB837B0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1562} normal block at 0x000001A15CB89EE0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1551} normal block at 0x000001A15CB89E40, 85 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) : {1548} normal block at 0x000001A15CB8B950, 8 bytes long.
 Data: <   ]    > 00 00 06 5D A1 01 00 00 
{926} normal block at 0x000001A15CB89F60, 85 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{309} normal block at 0x000001A15CB8B1D0, 8 bytes long.
 Data: <   \    > 90 BC B8 5C A1 01 00 00 
{300} normal block at 0x000001A15CB75FB0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{299} normal block at 0x000001A15CB8B540, 16 bytes long.
 Data: <   \            > 88 AB B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x000001A15CB8B5E0, 16 bytes long.
 Data: <`  \            > 60 AB B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x000001A15CB849B0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{296} normal block at 0x000001A15CB872B0, 16 bytes long.
 Data: <8  \            > 38 AB B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000001A15CB87260, 16 bytes long.
 Data: <   \            > 10 AB B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x000001A15CB870D0, 16 bytes long.
 Data: <   \            > E8 AA B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001A15CB87080, 16 bytes long.
 Data: <   \            > C0 AA B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001A15CB83970, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{291} normal block at 0x000001A15CB87030, 16 bytes long.
 Data: <   \            > C8 A2 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001A15CB84DD0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{289} normal block at 0x000001A15CB869F0, 16 bytes long.
 Data: <   \            > A0 A2 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001A15CB86C20, 16 bytes long.
 Data: <x  \            > 78 A2 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001A15CB87710, 16 bytes long.
 Data: <P  \            > 50 A2 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001A15CB87210, 16 bytes long.
 Data: <(  \            > 28 A2 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001A15CB86FE0, 16 bytes long.
 Data: <   \            > 00 A2 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001A15CB86F40, 16 bytes long.
 Data: <   \            > D8 A1 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001A15CB84FB0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{281} normal block at 0x000001A15CB876C0, 16 bytes long.
 Data: <   \            > B0 A1 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001A15CB8A1B0, 320 bytes long.
 Data: < v \     O \    > C0 76 B8 5C A1 01 00 00 B0 4F B8 5C A1 01 00 00 
{279} normal block at 0x000001A15CB87530, 16 bytes long.
 Data: <   \            > A0 AA B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001A15CB86EF0, 16 bytes long.
 Data: <x  \            > 78 AA B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001A15CB84770, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{276} normal block at 0x000001A15CB86810, 16 bytes long.
 Data: <P  \            > 50 AA B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001A15CB855B0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{274} normal block at 0x000001A15CB873A0, 16 bytes long.
 Data: <   \            > 98 A9 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001A15CB86E50, 16 bytes long.
 Data: <p  \            > 70 A9 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001A15CB87670, 16 bytes long.
 Data: <H  \            > 48 A9 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001A15CB86D10, 16 bytes long.
 Data: <   \            > 20 A9 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001A15CB87620, 16 bytes long.
 Data: <   \            > F8 A8 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001A15CB86CC0, 16 bytes long.
 Data: <   \            > D0 A8 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001A15CB86A40, 16 bytes long.
 Data: < 5 \            > 10 35 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001A15CB83510, 40 bytes long.
 Data: <@j \       \    > 40 6A B8 5C A1 01 00 00 E0 9E B8 5C A1 01 00 00 
{265} normal block at 0x000001A15CB86C70, 16 bytes long.
 Data: <   \            > B0 A8 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001A15CB875D0, 16 bytes long.
 Data: <   \            > 88 A8 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001A15CB854F0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{262} normal block at 0x000001A15CB87350, 16 bytes long.
 Data: <`  \            > 60 A8 B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001A15CB8A860, 992 bytes long.
 Data: <Ps \     T \    > 50 73 B8 5C A1 01 00 00 F0 54 B8 5C A1 01 00 00 
{97} normal block at 0x000001A15CB848F0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{96} normal block at 0x000001A15CB87120, 16 bytes long.
 Data: <P: \            > 50 3A B8 5C A1 01 00 00 00 00 00 00 00 00 00 00 
{95} normal block at 0x000001A15CB83A50, 40 bytes long.
 Data: < q \     H \    > 20 71 B8 5C A1 01 00 00 F0 48 B8 5C A1 01 00 00 
{74} normal block at 0x000001A15CB86E00, 16 bytes long.
 Data: <                > 80 EA 83 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000001A15CB86B80, 16 bytes long.
 Data: <@               > 40 E9 83 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000001A15CB87440, 16 bytes long.
 Data: < W              > F8 57 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000001A15CB86BD0, 16 bytes long.
 Data: < W              > D8 57 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000001A15CB86950, 16 bytes long.
 Data: <P               > 50 04 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001A15CB7DB10, 16 bytes long.
 Data: <0               > 30 04 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001A15CB7DA20, 16 bytes long.
 Data: <                > E0 02 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001A15CB7D980, 16 bytes long.
 Data: <                > 10 04 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001A15CB7D930, 16 bytes long.
 Data: <p               > 70 04 80 E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001A15CB7D610, 16 bytes long.
 Data: <  ~             > 18 C0 7E E6 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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