Task 38643742

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>
14:22:51 (15280): wrapper (7.9.26016): starting
14:22:51 (15280): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A22_A13_0.pdb
QB_A22_A13_0.xml
QB_A22_A13.inpcrd
QB_A22_A13_input.yaml
QB_A22_A13.pdb
QB_A22_A13.prmtop
QB_A22_A13_sys.xml
run.bat
run.sh
14:22:53 (15280): Library/usr/bin/tar.exe exited; CPU time 0.000000
14:22:53 (15280): 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) : {3835339} normal block at 0x000001B9F3BBDFD0, 8 bytes long.
 Data: <  g     > 00 00 67 F5 B9 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x000001B9F59147C0, 1080 bytes long.
 Data: <                > F8 06 00 00 CD CD CD CD BC 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x000001B9F3BB12A0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
19:27:15 (2192): wrapper (7.9.26016): starting
19:27:15 (2192): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1684} normal block at 0x0000018656336360, 8 bytes long.
 Data: <  ~V    > 00 00 7E 56 86 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000018656337470, 1080 bytes long.
 Data: <                > D8 09 00 00 CD CD CD CD B0 01 00 00 00 00 00 00 
Object dump complete.
12:44:39 (28480): wrapper (7.9.26016): starting
12:44:39 (28480): 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) : {1684} normal block at 0x0000023159956730, 8 bytes long.
 Data: <   Y1   > 00 00 E5 59 31 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000023159957480, 1080 bytes long.
 Data: < N              > A0 4E 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
13:04:33 (34324): wrapper (7.9.26016): starting
13:04:33 (34324): 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
13:15:04 (34324): C:/Windows/system32/cmd.exe exited; CPU time 629.046875
13:15:04 (34324): app exit status: 0x16
13:15:04 (34324): 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: 10897084 bytes.
Dumping objects ->
{1772} normal block at 0x0000021B65925480, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1761} normal block at 0x0000021B659256B0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1750} normal block at 0x0000021B65925170, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1739} normal block at 0x0000021B65925870, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1728} normal block at 0x0000021B65925800, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1697} normal block at 0x0000021B659119F0, 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) : {1684} normal block at 0x0000021B65925EC0, 8 bytes long.
 Data: <   e    > 00 00 DB 65 1B 02 00 00 
{306} normal block at 0x0000021B65926BE0, 8 bytes long.
 Data: <`q e    > 60 71 92 65 1B 02 00 00 
{297} normal block at 0x0000021B6590FCD0, 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 0x0000021B659261E0, 16 bytes long.
 Data: <hp e            > 68 70 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000021B65926190, 16 bytes long.
 Data: <@p e            > 40 70 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000021B659202E0, 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 0x0000021B659263C0, 16 bytes long.
 Data: < p e            > 18 70 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000021B65926410, 16 bytes long.
 Data: < o e            > F0 6F 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000021B65926730, 16 bytes long.
 Data: < o e            > C8 6F 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000021B659265A0, 16 bytes long.
 Data: < o e            > A0 6F 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000021B659255D0, 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 0x0000021B65926A50, 16 bytes long.
 Data: <   e            > B8 F2 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000021B6591FD40, 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 0x0000021B659260F0, 16 bytes long.
 Data: <   e            > 90 F2 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000021B659260A0, 16 bytes long.
 Data: <h  e            > 68 F2 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000021B65926050, 16 bytes long.
 Data: <@  e            > 40 F2 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000021B65925E70, 16 bytes long.
 Data: <   e            > 18 F2 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000021B65925E20, 16 bytes long.
 Data: <   e            > F0 F1 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000021B65925FB0, 16 bytes long.
 Data: <   e            > C8 F1 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000021B659207C0, 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 0x0000021B65926B90, 16 bytes long.
 Data: <   e            > A0 F1 90 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000021B6590F1A0, 320 bytes long.
 Data: < k e       e    > 90 6B 92 65 1B 02 00 00 C0 07 92 65 1B 02 00 00 
{276} normal block at 0x0000021B65926C80, 16 bytes long.
 Data: < o e            > 80 6F 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000021B659262D0, 16 bytes long.
 Data: <Xo e            > 58 6F 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000021B659206A0, 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 0x0000021B65926B40, 16 bytes long.
 Data: <0o e            > 30 6F 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000021B6591FC80, 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 0x0000021B65926000, 16 bytes long.
 Data: <xn e            > 78 6E 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000021B659265F0, 16 bytes long.
 Data: <Pn e            > 50 6E 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000021B65925F10, 16 bytes long.
 Data: <(n e            > 28 6E 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000021B659264B0, 16 bytes long.
 Data: < n e            > 00 6E 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000021B65925F60, 16 bytes long.
 Data: < m e            > D8 6D 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000021B65926280, 16 bytes long.
 Data: < m e            > B0 6D 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000021B65926AA0, 16 bytes long.
 Data: < W e            > 90 57 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000021B65925790, 40 bytes long.
 Data: < j e       e    > A0 6A 92 65 1B 02 00 00 F0 19 91 65 1B 02 00 00 
{262} normal block at 0x0000021B659269B0, 16 bytes long.
 Data: < m e            > 90 6D 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000021B65926140, 16 bytes long.
 Data: <hm e            > 68 6D 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000021B6591FA40, 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 0x0000021B65926CD0, 16 bytes long.
 Data: <@m e            > 40 6D 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000021B65926D40, 992 bytes long.
 Data: < l e    @  e    > D0 6C 92 65 1B 02 00 00 40 FA 91 65 1B 02 00 00 
{94} normal block at 0x0000021B6591F9E0, 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 0x0000021B6591D9E0, 16 bytes long.
 Data: < S e            > A0 53 92 65 1B 02 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x0000021B659253A0, 40 bytes long.
 Data: <   e       e    > E0 D9 91 65 1B 02 00 00 E0 F9 91 65 1B 02 00 00 
{71} normal block at 0x0000021B6591E390, 16 bytes long.
 Data: <   $            > 80 EA 82 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x0000021B6591D940, 16 bytes long.
 Data: <@  $            > 40 E9 82 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000021B6591DAD0, 16 bytes long.
 Data: < W $            > F8 57 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000021B6591E2A0, 16 bytes long.
 Data: < W $            > D8 57 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000021B6591E340, 16 bytes long.
 Data: <P  $            > 50 04 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000021B6591E070, 16 bytes long.
 Data: <0  $            > 30 04 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000021B6591D990, 16 bytes long.
 Data: <   $            > E0 02 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000021B6591DB20, 16 bytes long.
 Data: <   $            > 10 04 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000021B6591E520, 16 bytes long.
 Data: <p  $            > 70 04 7F 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000021B6591E4D0, 16 bytes long.
 Data: <  }$            > 18 C0 7D 24 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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