Task 38643499

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>
14:17:34 (236424): wrapper (7.9.26016): starting
14:17:34 (236424): 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
14:17:36 (236424): Library/usr/bin/tar.exe exited; CPU time 0.031250
14:17:36 (236424): 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) : {3835159} normal block at 0x0000024D5A6E7F40, 8 bytes long.
 Data: <   ZM   > 00 00 D8 5A 4D 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833956} normal block at 0x0000024D5A7AE7D0, 1080 bytes long.
 Data: < z      l       > E4 7A 04 00 CD CD CD CD 6C 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {310} normal block at 0x0000024D5A6CA5A0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
16:37:40 (306436): wrapper (7.9.26016): starting
16:37:40 (306436): 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) : {1506} normal block at 0x000001F5B923C750, 8 bytes long.
 Data: <        > 00 00 1C B9 F5 01 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x000001F5B9241300, 1080 bytes long.
 Data: <        x       > 84 FC 03 00 CD CD CD CD 78 02 00 00 00 00 00 00 
Object dump complete.
17:24:02 (305948): wrapper (7.9.26016): starting
17:24:02 (305948): 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) : {1506} normal block at 0x000001F606E2AFB0, 8 bytes long.
 Data: <        > 00 00 D9 06 F6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x000001F606E2D110, 1080 bytes long.
 Data: <$               > 24 B1 04 00 CD CD CD CD E8 01 00 00 00 00 00 00 
Object dump complete.
18:49:02 (309336): wrapper (7.9.26016): starting
18:49:02 (309336): 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) : {1506} normal block at 0x000001C8A8EA7950, 8 bytes long.
 Data: <        > 00 00 E6 A8 C8 01 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x000001C8A8EB3380, 1080 bytes long.
 Data: <        d       > 18 B7 04 00 CD CD CD CD 64 02 00 00 00 00 00 00 
Object dump complete.
19:17:41 (306900): wrapper (7.9.26016): starting
19:17:41 (306900): 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) : {1506} normal block at 0x000001E28C75B6C0, 8 bytes long.
 Data: <  p     > 00 00 70 8C E2 01 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x000001E28C761300, 1080 bytes long.
 Data: <d               > 64 CC 04 00 CD CD CD CD 80 02 00 00 00 00 00 00 
Object dump complete.
20:02:19 (320264): wrapper (7.9.26016): starting
20:02:19 (320264): 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) : {1506} normal block at 0x00000240F184BF80, 8 bytes long.
 Data: <    @   > 00 00 D5 F1 40 02 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x00000240F184EA30, 1080 bytes long.
 Data: <        `       > BC 9F 04 00 CD CD CD CD 60 02 00 00 00 00 00 00 
Object dump complete.
20:13:26 (284868): wrapper (7.9.26016): starting
20:13:26 (284868): 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) : {1506} normal block at 0x0000020E88514D20, 8 bytes long.
 Data: <        > 00 00 B1 88 0E 02 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x0000020E8850CDE0, 1080 bytes long.
 Data: <                > C0 BF 04 00 CD CD CD CD 80 02 00 00 00 00 00 00 
Object dump complete.
20:58:12 (314556): wrapper (7.9.26016): starting
20:58:12 (314556): 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) : {1506} normal block at 0x000002C649C8C750, 8 bytes long.
 Data: <   J    > 00 00 10 4A C6 02 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x000002C649C91300, 1080 bytes long.
 Data: <        x       > 08 C4 04 00 CD CD CD CD 78 02 00 00 00 00 00 00 
Object dump complete.
22:16:23 (323964): wrapper (7.9.26016): starting
22:16:23 (323964): 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
22:34:52 (323964): C:/Windows/system32/cmd.exe exited; CPU time 1116.062500
22:34:52 (323964): app exit status: 0x16
22:34:52 (323964): 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: 23904948 bytes.
Dumping objects ->
{1594} normal block at 0x000001E1E9BB7410, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1583} normal block at 0x000001E1E9BB6F40, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1572} normal block at 0x000001E1E9BB6BC0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1561} normal block at 0x000001E1E9BB6CA0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1550} normal block at 0x000001E1E9BA6DD0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1519} normal block at 0x000001E1E9BAE320, 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) : {1506} normal block at 0x000001E1E9BB4000, 8 bytes long.
 Data: <        > 00 00 B4 E9 E1 01 00 00 
{304} normal block at 0x000001E1E9B983E0, 8 bytes long.
 Data: <@V      > 40 56 BB E9 E1 01 00 00 
{295} normal block at 0x000001E1E9B8D710, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{294} normal block at 0x000001E1E9BB4140, 16 bytes long.
 Data: < i              > C8 69 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001E1E9BB42D0, 16 bytes long.
 Data: < i              > A0 69 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001E1E9BB3100, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{291} normal block at 0x000001E1E9BB3E70, 16 bytes long.
 Data: <xi              > 78 69 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001E1E9BA8A50, 16 bytes long.
 Data: <Pi              > 50 69 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001E1E9BA9090, 16 bytes long.
 Data: <(i              > 28 69 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001E1E9BA8B90, 16 bytes long.
 Data: < i              > 00 69 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001E1E9BA6E40, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{286} normal block at 0x000001E1E9BA90E0, 16 bytes long.
 Data: <h%              > 68 25 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001E1E9BB3A00, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{284} normal block at 0x000001E1E9BA8C30, 16 bytes long.
 Data: <@%              > 40 25 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001E1E9BA8B40, 16 bytes long.
 Data: < %              > 18 25 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001E1E9BA8AF0, 16 bytes long.
 Data: < $              > F0 24 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001E1E9BB0AE0, 16 bytes long.
 Data: < $              > C8 24 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001E1E9BB0720, 16 bytes long.
 Data: < $              > A0 24 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001E1E9BB0A40, 16 bytes long.
 Data: <x$              > 78 24 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001E1E9B92C20, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{276} normal block at 0x000001E1E9BB0630, 16 bytes long.
 Data: <P$              > 50 24 BB E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001E1E9BB2450, 320 bytes long.
 Data: <0        ,      > 30 06 BB E9 E1 01 00 00 20 2C B9 E9 E1 01 00 00 
{274} normal block at 0x000001E1E9BB0770, 16 bytes long.
 Data: < h              > E0 68 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001E1E9BB0C20, 16 bytes long.
 Data: < h              > B8 68 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001E1E9B92BC0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{271} normal block at 0x000001E1E9BB09A0, 16 bytes long.
 Data: < h              > 90 68 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001E1E9B93100, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{269} normal block at 0x000001E1E9BB0900, 16 bytes long.
 Data: < g              > D8 67 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001E1E9BB0680, 16 bytes long.
 Data: < g              > B0 67 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001E1E9BB0D60, 16 bytes long.
 Data: < g              > 88 67 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001E1E9BA9040, 16 bytes long.
 Data: <`g              > 60 67 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001E1E9BA8E60, 16 bytes long.
 Data: <8g              > 38 67 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001E1E9BA8E10, 16 bytes long.
 Data: < g              > 10 67 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001E1E9BA8FF0, 16 bytes long.
 Data: < p              > 00 70 BA E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001E1E9BA7000, 40 bytes long.
 Data: <                > F0 8F BA E9 E1 01 00 00 20 E3 BA E9 E1 01 00 00 
{260} normal block at 0x000001E1E9BA8D20, 16 bytes long.
 Data: < f              > F0 66 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001E1E9BA8DC0, 16 bytes long.
 Data: < f              > C8 66 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001E1E9B930A0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{257} normal block at 0x000001E1E9BA8CD0, 16 bytes long.
 Data: < f              > A0 66 B9 E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000001E1E9B966A0, 992 bytes long.
 Data: <         0      > D0 8C BA E9 E1 01 00 00 A0 30 B9 E9 E1 01 00 00 
{92} normal block at 0x000001E1E9B933A0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{91} normal block at 0x000001E1E9BA9180, 16 bytes long.
 Data: < i              > E0 69 BA E9 E1 01 00 00 00 00 00 00 00 00 00 00 
{90} normal block at 0x000001E1E9BA69E0, 40 bytes long.
 Data: <         3      > 80 91 BA E9 E1 01 00 00 A0 33 B9 E9 E1 01 00 00 
{69} normal block at 0x000001E1E9BA8FA0, 16 bytes long.
 Data: <   *            > 80 EA 96 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001E1E9BA8F00, 16 bytes long.
 Data: <@  *            > 40 E9 96 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001E1E9BA8D70, 16 bytes long.
 Data: < W *            > F8 57 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001E1E9BA8F50, 16 bytes long.
 Data: < W *            > D8 57 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001E1E9BA9130, 16 bytes long.
 Data: <P  *            > 50 04 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001E1E9BA8BE0, 16 bytes long.
 Data: <0  *            > 30 04 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001E1E9BAB120, 16 bytes long.
 Data: <   *            > E0 02 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001E1E9BAB030, 16 bytes long.
 Data: <   *            > 10 04 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001E1E9BAB350, 16 bytes long.
 Data: <p  *            > 70 04 93 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001E1E9BAB2B0, 16 bytes long.
 Data: <   *            > 18 C0 91 2A F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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