Task 38644444

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>
18:48:31 (33464): wrapper (7.9.26016): starting
18:48:31 (33464): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A26_A17_0.pdb
QB_A26_A17_0.xml
QB_A26_A17.inpcrd
QB_A26_A17_input.yaml
QB_A26_A17.pdb
QB_A26_A17.prmtop
QB_A26_A17_sys.xml
run.bat
run.sh
18:48:33 (33464): Library/usr/bin/tar.exe exited; CPU time 0.000000
18:48:33 (33464): 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) : {3835129} normal block at 0x00000177EE44AF60, 8 bytes long.
 Data: <    w   > 00 00 8F EE 77 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833970} normal block at 0x00000177F01BE9C0, 1080 bytes long.
 Data: <Pv      @       > 50 76 00 00 CD CD CD CD 40 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {317} normal block at 0x00000177EE452450, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
19:04:31 (17904): wrapper (7.9.26016): starting
19:04:31 (17904): 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) : {1469} normal block at 0x0000021F95547C80, 8 bytes long.
 Data: <  P     > 00 00 50 95 1F 02 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x0000021F955489D0, 1080 bytes long.
 Data: <        H       > C0 A3 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
19:09:45 (41636): wrapper (7.9.26016): starting
19:09:45 (41636): 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) : {1469} normal block at 0x00000138FAAF7D60, 8 bytes long.
 Data: <    8   > 00 00 F0 FA 38 01 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x00000138FAAF8BE0, 1080 bytes long.
 Data: < n      ,       > F4 6E 00 00 CD CD CD CD 2C 01 00 00 00 00 00 00 
Object dump complete.
19:44:13 (30648): wrapper (7.9.26016): starting
19:44:13 (30648): 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) : {1469} normal block at 0x0000015CDBB27940, 8 bytes long.
 Data: <    \   > 00 00 F4 DB 5C 01 00 00 
..\lib\diagnostics_win.cpp(417) : {310} normal block at 0x0000015CDBB28190, 1080 bytes long.
 Data: <        \       > C0 A1 00 00 CD CD CD CD 5C 01 00 00 00 00 00 00 
Object dump complete.
19:49:29 (24620): wrapper (7.9.26016): starting
19:49:29 (24620): 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
20:02:18 (24620): C:/Windows/system32/cmd.exe exited; CPU time 801.312500
20:02:18 (24620): app exit status: 0x16
20:02:18 (24620): 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: 14587426 bytes.
Dumping objects ->
{1557} normal block at 0x00000216525A58C0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1546} normal block at 0x00000216525A5380, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1535} normal block at 0x00000216525A55B0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1524} normal block at 0x00000216525A5620, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1513} normal block at 0x00000216525A59A0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1482} normal block at 0x000002165258F870, 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) : {1469} normal block at 0x00000216525A6260, 8 bytes long.
 Data: <  VR    > 00 00 56 52 16 02 00 00 
{311} normal block at 0x00000216525A6530, 8 bytes long.
 Data: <psZR    > 70 73 5A 52 16 02 00 00 
{302} normal block at 0x0000021652596D50, 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 0x00000216525A6DF0, 16 bytes long.
 Data: <xrZR            > 78 72 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x00000216525A68A0, 16 bytes long.
 Data: <PrZR            > 50 72 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x000002165259F700, 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 0x00000216525A6AD0, 16 bytes long.
 Data: <(rZR            > 28 72 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x00000216525A6DA0, 16 bytes long.
 Data: < rZR            > 00 72 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x00000216525A67B0, 16 bytes long.
 Data: < qZR            > D8 71 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000216525A65D0, 16 bytes long.
 Data: < qZR            > B0 71 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000216525A54D0, 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 0x00000216525A6A80, 16 bytes long.
 Data: <  YR            > E8 03 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002165259F340, 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 0x00000216525A6990, 16 bytes long.
 Data: <  YR            > C0 03 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000216525A6760, 16 bytes long.
 Data: <  YR            > 98 03 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000216525A6A30, 16 bytes long.
 Data: <p YR            > 70 03 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000216525A6580, 16 bytes long.
 Data: <H YR            > 48 03 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x00000216525A68F0, 16 bytes long.
 Data: <  YR            > 20 03 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000216525A6670, 16 bytes long.
 Data: <  YR            > F8 02 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000002165259F7C0, 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 0x00000216525A6170, 16 bytes long.
 Data: <  YR            > D0 02 59 52 16 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000216525902D0, 320 bytes long.
 Data: <paZR      YR    > 70 61 5A 52 16 02 00 00 C0 F7 59 52 16 02 00 00 
{281} normal block at 0x00000216525A6210, 16 bytes long.
 Data: < qZR            > 90 71 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000216525A6440, 16 bytes long.
 Data: <hqZR            > 68 71 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002165259F5E0, 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 0x00000216525A6490, 16 bytes long.
 Data: <@qZR            > 40 71 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002165259EDA0, 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 0x00000216525A6D00, 16 bytes long.
 Data: < pZR            > 88 70 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000216525A6850, 16 bytes long.
 Data: <`pZR            > 60 70 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000216525A60D0, 16 bytes long.
 Data: <8pZR            > 38 70 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000216525A6710, 16 bytes long.
 Data: < pZR            > 10 70 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000216525A66C0, 16 bytes long.
 Data: < oZR            > E8 6F 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000216525A6800, 16 bytes long.
 Data: < oZR            > C0 6F 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000216525A6620, 16 bytes long.
 Data: < VZR            > 90 56 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000216525A5690, 40 bytes long.
 Data: < fZR    p XR    > 20 66 5A 52 16 02 00 00 70 F8 58 52 16 02 00 00 
{267} normal block at 0x00000216525A6EE0, 16 bytes long.
 Data: < oZR            > A0 6F 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000216525A69E0, 16 bytes long.
 Data: <xoZR            > 78 6F 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002165259F580, 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 0x00000216525A6CB0, 16 bytes long.
 Data: <PoZR            > 50 6F 5A 52 16 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000216525A6F50, 992 bytes long.
 Data: < lZR      YR    > B0 6C 5A 52 16 02 00 00 80 F5 59 52 16 02 00 00 
{99} normal block at 0x000002165259EEC0, 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 0x000002165259AE80, 16 bytes long.
 Data: <0 XR            > 30 D8 58 52 16 02 00 00 00 00 00 00 00 00 00 00 
{97} normal block at 0x000002165258D830, 40 bytes long.
 Data: <  YR      YR    > 80 AE 59 52 16 02 00 00 C0 EE 59 52 16 02 00 00 
{76} normal block at 0x000002165259B420, 16 bytes long.
 Data: <  9             > 80 EA 39 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x000002165259B790, 16 bytes long.
 Data: <@ 9             > 40 E9 39 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x000002165259B880, 16 bytes long.
 Data: < W6             > F8 57 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000002165259AA20, 16 bytes long.
 Data: < W6             > D8 57 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000002165259B510, 16 bytes long.
 Data: <P 6             > 50 04 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000002165259B240, 16 bytes long.
 Data: <0 6             > 30 04 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002165259B8D0, 16 bytes long.
 Data: <  6             > E0 02 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002165259B100, 16 bytes long.
 Data: <  6             > 10 04 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002165259AF20, 16 bytes long.
 Data: <p 6             > 70 04 36 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002165259AC50, 16 bytes long.
 Data: <  4             > 18 C0 34 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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