Task 38611667

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>
16:01:01 (7196): wrapper (7.9.26016): starting
16:01:01 (7196): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A13_A31_0.pdb
QB_A13_A31_0.xml
QB_A13_A31.inpcrd
QB_A13_A31_input.yaml
QB_A13_A31.pdb
QB_A13_A31.prmtop
QB_A13_A31_sys.xml
run.bat
run.sh
16:01:04 (7196): Library/usr/bin/tar.exe exited; CPU time 0.015625
16:01:04 (7196): 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\2\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\2\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) : {3835181} normal block at 0x00000237CC76DE30, 8 bytes long.
 Data: <  s 7   > 00 00 73 CC 37 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x00000237CE2E4600, 1080 bytes long.
 Data: <                > F4 1A 00 00 CD CD CD CD A4 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x00000237CC761800, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
21:09:25 (22868): wrapper (7.9.26016): starting
21:09:25 (22868): 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\2\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1526} normal block at 0x0000021BD40C79B0, 8 bytes long.
 Data: <        > 00 00 09 D4 1B 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000021BD40C8AC0, 1080 bytes long.
 Data: < 6              > A0 36 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
01:41:00 (22876): wrapper (7.9.26016): starting
01:41:00 (22876): 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\2\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1526} normal block at 0x00000264BB357120, 8 bytes long.
 Data: <    d   > 00 00 8D BB 64 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x00000264BB357600, 1080 bytes long.
 Data: < V              > E4 56 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
07:53:40 (14592): wrapper (7.9.26016): starting
07:53:40 (14592): 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\2\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1526} normal block at 0x00000190DB766670, 8 bytes long.
 Data: <        > 00 00 C0 DB 90 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x00000190DB7675A0, 1080 bytes long.
 Data: <                > BC 20 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
04:36:28 (20916): wrapper (7.9.26016): starting
04:36:28 (20916): 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\2\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\2\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\2\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\2\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\2\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\2\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\2\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\2\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\2\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
08:04:24 (20916): C:/Windows/system32/cmd.exe exited; CPU time 11555.265625
08:04:24 (20916): app exit status: 0x16
08:04:24 (20916): 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: 182336092 bytes.
Dumping objects ->
{1615} normal block at 0x0000020C29765610, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1604} normal block at 0x0000020C29765680, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1593} normal block at 0x0000020C29765A70, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1582} normal block at 0x0000020C29765760, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1571} normal block at 0x0000020C29765AE0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1540} normal block at 0x0000020C29750F00, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1529} normal block at 0x0000020C2974BC40, 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) : {1526} normal block at 0x0000020C29767030, 8 bytes long.
 Data: <   )    > 00 00 B7 29 0C 02 00 00 
{912} normal block at 0x0000020C2974EBE0, 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 0x0000020C29766450, 8 bytes long.
 Data: < vv)    > 00 76 76 29 0C 02 00 00 
{297} normal block at 0x0000020C29752970, 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 0x0000020C29766A40, 16 bytes long.
 Data: < uv)            > 08 75 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000020C29766630, 16 bytes long.
 Data: < tv)            > E0 74 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000020C29760950, 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 0x0000020C297668B0, 16 bytes long.
 Data: < tv)            > B8 74 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000020C297665E0, 16 bytes long.
 Data: < tv)            > 90 74 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000020C29766B30, 16 bytes long.
 Data: <htv)            > 68 74 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000020C29766AE0, 16 bytes long.
 Data: <@tv)            > 40 74 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000020C29765BC0, 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 0x0000020C297670D0, 16 bytes long.
 Data: <  u)            > 98 0E 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000020C297610D0, 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 0x0000020C29766F90, 16 bytes long.
 Data: <p u)            > 70 0E 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000020C29766360, 16 bytes long.
 Data: <H u)            > 48 0E 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000020C29766950, 16 bytes long.
 Data: <  u)            > 20 0E 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000020C297662C0, 16 bytes long.
 Data: <  u)            > F8 0D 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000020C29766E00, 16 bytes long.
 Data: <  u)            > D0 0D 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000020C29766270, 16 bytes long.
 Data: <  u)            > A8 0D 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000020C29760A70, 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 0x0000020C29766590, 16 bytes long.
 Data: <  u)            > 80 0D 75 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000020C29750D80, 320 bytes long.
 Data: < ev)    p v)    > 90 65 76 29 0C 02 00 00 70 0A 76 29 0C 02 00 00 
{276} normal block at 0x0000020C29766770, 16 bytes long.
 Data: < tv)            > 20 74 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000020C29766540, 16 bytes long.
 Data: < sv)            > F8 73 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000020C297609B0, 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 0x0000020C29766EF0, 16 bytes long.
 Data: < sv)            > D0 73 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000020C29760DD0, 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 0x0000020C29766EA0, 16 bytes long.
 Data: < sv)            > 18 73 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000020C297663B0, 16 bytes long.
 Data: < rv)            > F0 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000020C297666D0, 16 bytes long.
 Data: < rv)            > C8 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000020C297669F0, 16 bytes long.
 Data: < rv)            > A0 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000020C29766F40, 16 bytes long.
 Data: <xrv)            > 78 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000020C29766310, 16 bytes long.
 Data: <Prv)            > 50 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000020C29767080, 16 bytes long.
 Data: < ]v)            > 10 5D 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000020C29765D10, 40 bytes long.
 Data: < pv)      u)    > 80 70 76 29 0C 02 00 00 00 0F 75 29 0C 02 00 00 
{262} normal block at 0x0000020C29766400, 16 bytes long.
 Data: <0rv)            > 30 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000020C29766720, 16 bytes long.
 Data: < rv)            > 08 72 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000020C29761070, 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 0x0000020C297669A0, 16 bytes long.
 Data: < qv)            > E0 71 76 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000020C297671E0, 992 bytes long.
 Data: < iv)    p v)    > A0 69 76 29 0C 02 00 00 70 10 76 29 0C 02 00 00 
{94} normal block at 0x0000020C297604D0, 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 0x0000020C2975DD10, 16 bytes long.
 Data: <` t)            > 60 CD 74 29 0C 02 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x0000020C2974CD60, 40 bytes long.
 Data: <  u)      v)    > 10 DD 75 29 0C 02 00 00 D0 04 76 29 0C 02 00 00 
{71} normal block at 0x0000020C2975E620, 16 bytes long.
 Data: <                > 80 EA CF 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x0000020C2975E6C0, 16 bytes long.
 Data: <@               > 40 E9 CF 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000020C2975DCC0, 16 bytes long.
 Data: < W              > F8 57 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000020C2975E080, 16 bytes long.
 Data: < W              > D8 57 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000020C2975E9E0, 16 bytes long.
 Data: <P               > 50 04 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000020C2975E030, 16 bytes long.
 Data: <0               > 30 04 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000020C2975E940, 16 bytes long.
 Data: <                > E0 02 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000020C2975E580, 16 bytes long.
 Data: <                > 10 04 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000020C2975E530, 16 bytes long.
 Data: <p               > 70 04 CC 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000020C2975DB80, 16 bytes long.
 Data: <                > 18 C0 CA 0D F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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