Task 38645119

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>
19:40:38 (24356): wrapper (7.9.26016): starting
19:40:38 (24356): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A26_A23_0.pdb
QB_A26_A23_0.xml
QB_A26_A23.inpcrd
QB_A26_A23_input.yaml
QB_A26_A23.pdb
QB_A26_A23.prmtop
QB_A26_A23_sys.xml
run.bat
run.sh
19:40:47 (24356): Library/usr/bin/tar.exe exited; CPU time 0.015625
19:40:47 (24356): 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) : {3835167} normal block at 0x0000024A9F37BA30, 8 bytes long.
 Data: <    J   > 00 00 9C 9F 4A 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833956} normal block at 0x0000024AA11C4A10, 1080 bytes long.
 Data: <        D       > F8 9B 00 00 CD CD CD CD 44 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {310} normal block at 0x0000024A9F382510, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
06:56:22 (34956): wrapper (7.9.26016): starting
06:56:22 (34956): 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
07:31:40 (34956): C:/Windows/system32/cmd.exe exited; CPU time 2143.296875
07:31:40 (34956): app exit status: 0x16
07:31:40 (34956): 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: 40195332 bytes.
Dumping objects ->
{1602} normal block at 0x00000165F67E6D30, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1591} normal block at 0x00000165F67E6A20, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1580} normal block at 0x00000165F67E6EF0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1569} normal block at 0x00000165F67E6DA0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1558} normal block at 0x00000165F67E6C50, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1527} normal block at 0x00000165F67CE420, 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) : {1514} normal block at 0x00000165F67E8110, 8 bytes long.
 Data: <  n e   > 00 00 6E F6 65 01 00 00 
{304} normal block at 0x00000165F67E8340, 8 bytes long.
 Data: <  ~ e   > F0 8C 7E F6 65 01 00 00 
{295} normal block at 0x00000165F67CF420, 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 0x00000165F67E8610, 16 bytes long.
 Data: <  ~ e           > F8 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x00000165F67E82F0, 16 bytes long.
 Data: <  ~ e           > D0 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000165F67DF420, 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 0x00000165F67E8480, 16 bytes long.
 Data: <  ~ e           > A8 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000165F67E82A0, 16 bytes long.
 Data: <  ~ e           > 80 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000165F67E8200, 16 bytes long.
 Data: <X ~ e           > 58 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000165F67E7E90, 16 bytes long.
 Data: <0 ~ e           > 30 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000165F67E6E10, 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 0x00000165F67E86B0, 16 bytes long.
 Data: < h~ e           > B8 68 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000165F67DEBE0, 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 0x00000165F67E7FD0, 16 bytes long.
 Data: < h~ e           > 90 68 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000165F67E8390, 16 bytes long.
 Data: <hh~ e           > 68 68 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000165F67E84D0, 16 bytes long.
 Data: <@h~ e           > 40 68 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000165F67E81B0, 16 bytes long.
 Data: < h~ e           > 18 68 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000165F67E7990, 16 bytes long.
 Data: < g~ e           > F0 67 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000165F67E8160, 16 bytes long.
 Data: < g~ e           > C8 67 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000165F67DF000, 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 0x00000165F67E7C60, 16 bytes long.
 Data: < g~ e           > A0 67 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000165F67E67A0, 320 bytes long.
 Data: <`|~ e     } e   > 60 7C 7E F6 65 01 00 00 00 F0 7D F6 65 01 00 00 
{274} normal block at 0x00000165F67E7940, 16 bytes long.
 Data: <  ~ e           > 10 8B 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000165F67E8250, 16 bytes long.
 Data: <  ~ e           > E8 8A 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000165F67DEEE0, 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 0x00000165F67E8430, 16 bytes long.
 Data: <  ~ e           > C0 8A 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000165F67DEB80, 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 0x00000165F67E7F80, 16 bytes long.
 Data: <  ~ e           > 08 8A 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000165F67E7BC0, 16 bytes long.
 Data: <  ~ e           > E0 89 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000165F67E78A0, 16 bytes long.
 Data: <  ~ e           > B8 89 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000165F67E7F30, 16 bytes long.
 Data: <  ~ e           > 90 89 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000165F67E80C0, 16 bytes long.
 Data: <h ~ e           > 68 89 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000165F67E8570, 16 bytes long.
 Data: <@ ~ e           > 40 89 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x00000165F67E7B70, 16 bytes long.
 Data: < p~ e           > B0 70 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000165F67E70B0, 40 bytes long.
 Data: <p{~ e     | e   > 70 7B 7E F6 65 01 00 00 20 E4 7C F6 65 01 00 00 
{260} normal block at 0x00000165F67E7D00, 16 bytes long.
 Data: <  ~ e           > 20 89 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000165F67E7CB0, 16 bytes long.
 Data: <  ~ e           > F8 88 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x00000165F67DF180, 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 0x00000165F67E8020, 16 bytes long.
 Data: <  ~ e           > D0 88 7E F6 65 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x00000165F67E88D0, 992 bytes long.
 Data: <  ~ e     } e   > 20 80 7E F6 65 01 00 00 80 F1 7D F6 65 01 00 00 
{92} normal block at 0x00000165F67DE8E0, 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 0x00000165F67DAF40, 16 bytes long.
 Data: <P } e           > 50 8F 7D F6 65 01 00 00 00 00 00 00 00 00 00 00 
{90} normal block at 0x00000165F67D8F50, 40 bytes long.
 Data: <@ } e     } e   > 40 AF 7D F6 65 01 00 00 E0 E8 7D F6 65 01 00 00 
{69} normal block at 0x00000165F67DA9F0, 16 bytes long.
 Data: <                > 80 EA 8A D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000165F67DB210, 16 bytes long.
 Data: <@               > 40 E9 8A D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000165F67DB7B0, 16 bytes long.
 Data: < W              > F8 57 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000165F67DB1C0, 16 bytes long.
 Data: < W              > D8 57 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000165F67DB030, 16 bytes long.
 Data: <P               > 50 04 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000165F67DB760, 16 bytes long.
 Data: <0               > 30 04 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000165F67DAEA0, 16 bytes long.
 Data: <                > E0 02 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000165F67DB6C0, 16 bytes long.
 Data: <                > 10 04 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000165F67DB580, 16 bytes long.
 Data: <p               > 70 04 87 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000165F67DB710, 16 bytes long.
 Data: <                > 18 C0 85 D2 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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