Task 38643840

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
08:52:47 (41452): wrapper (7.9.26016): starting
08:52:47 (41452): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A23_0.pdb
QB_A20_A23_0.xml
QB_A20_A23.inpcrd
QB_A20_A23_input.yaml
QB_A20_A23.pdb
QB_A20_A23.prmtop
QB_A20_A23_sys.xml
run.bat
run.sh
08:52:49 (41452): Library/usr/bin/tar.exe exited; CPU time 0.000000
08:52:49 (41452): 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) : {3835348} normal block at 0x000001FD917CEDC0, 8 bytes long.
 Data: <        > 00 00 D4 91 FD 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833962} normal block at 0x000001FD935A54B0, 1080 bytes long.
 Data: <0       0       > 30 9D 00 00 CD CD CD CD 30 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x000001FD917C6690, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
09:53:09 (16684): wrapper (7.9.26016): starting
09:53:09 (16684): 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
10:08:16 (16684): C:/Windows/system32/cmd.exe exited; CPU time 897.906250
10:08:16 (16684): app exit status: 0x16
10:08:16 (16684): 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: 17939754 bytes.
Dumping objects ->
{1780} normal block at 0x00000240975C54C0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1769} normal block at 0x00000240975C5220, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1758} normal block at 0x00000240975C5300, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1747} normal block at 0x00000240975C5140, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1736} normal block at 0x00000240975C5680, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1705} normal block at 0x00000240975C05A0, 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) : {1692} normal block at 0x00000240975C6550, 8 bytes long.
 Data: <    @   > 00 00 B6 97 40 02 00 00 
{307} normal block at 0x00000240975C6140, 8 bytes long.
 Data: < p\ @   > C0 70 5C 97 40 02 00 00 
{298} normal block at 0x00000240975B7E40, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{297} normal block at 0x00000240975C5DD0, 16 bytes long.
 Data: < o\ @           > C8 6F 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x00000240975C6A50, 16 bytes long.
 Data: < o\ @           > A0 6F 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000240975C1120, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{294} normal block at 0x00000240975C69B0, 16 bytes long.
 Data: <xo\ @           > 78 6F 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x00000240975C6960, 16 bytes long.
 Data: <Po\ @           > 50 6F 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000240975C68C0, 16 bytes long.
 Data: <(o\ @           > 28 6F 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000240975C6370, 16 bytes long.
 Data: < o\ @           > 00 6F 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000240975C5450, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{289} normal block at 0x00000240975C64B0, 16 bytes long.
 Data: <h [ @           > 68 01 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000240975C0CA0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{287} normal block at 0x00000240975C6870, 16 bytes long.
 Data: <@ [ @           > 40 01 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000240975C6730, 16 bytes long.
 Data: <  [ @           > 18 01 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000240975C6050, 16 bytes long.
 Data: <  [ @           > F0 00 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000240975C60F0, 16 bytes long.
 Data: <  [ @           > C8 00 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000240975C66E0, 16 bytes long.
 Data: <  [ @           > A0 00 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000240975C5F10, 16 bytes long.
 Data: <x [ @           > 78 00 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000240975C10C0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{279} normal block at 0x00000240975C62D0, 16 bytes long.
 Data: <P [ @           > 50 00 5B 97 40 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000240975B0050, 320 bytes long.
 Data: < b\ @     \ @   > D0 62 5C 97 40 02 00 00 C0 10 5C 97 40 02 00 00 
{277} normal block at 0x00000240975C65A0, 16 bytes long.
 Data: < n\ @           > E0 6E 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000240975C5E70, 16 bytes long.
 Data: < n\ @           > B8 6E 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000240975C12A0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{274} normal block at 0x00000240975C6A00, 16 bytes long.
 Data: < n\ @           > 90 6E 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000240975C0820, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{272} normal block at 0x00000240975C5E20, 16 bytes long.
 Data: < m\ @           > D8 6D 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000240975C5D80, 16 bytes long.
 Data: < m\ @           > B0 6D 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000240975C60A0, 16 bytes long.
 Data: < m\ @           > 88 6D 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000240975C6230, 16 bytes long.
 Data: <`m\ @           > 60 6D 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000240975C6C30, 16 bytes long.
 Data: <8m\ @           > 38 6D 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000240975C6B40, 16 bytes long.
 Data: < m\ @           > 10 6D 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000240975C6910, 16 bytes long.
 Data: < Q\ @           > B0 51 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000240975C51B0, 40 bytes long.
 Data: < i\ @     \ @   > 10 69 5C 97 40 02 00 00 A0 05 5C 97 40 02 00 00 
{263} normal block at 0x00000240975C61E0, 16 bytes long.
 Data: < l\ @           > F0 6C 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x00000240975C6320, 16 bytes long.
 Data: < l\ @           > C8 6C 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000240975C0D60, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{260} normal block at 0x00000240975C6780, 16 bytes long.
 Data: < l\ @           > A0 6C 5C 97 40 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000240975C6CA0, 992 bytes long.
 Data: < g\ @   ` \ @   > 80 67 5C 97 40 02 00 00 60 0D 5C 97 40 02 00 00 
{95} normal block at 0x00000240975C1000, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{94} normal block at 0x00000240975BF630, 16 bytes long.
 Data: <` Z @           > 60 C8 5A 97 40 02 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x00000240975AC860, 40 bytes long.
 Data: <0 [ @     \ @   > 30 F6 5B 97 40 02 00 00 00 10 5C 97 40 02 00 00 
{72} normal block at 0x00000240975BF770, 16 bytes long.
 Data: <                > 80 EA DD 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000240975BF360, 16 bytes long.
 Data: <@               > 40 E9 DD 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000240975BEA00, 16 bytes long.
 Data: < W              > F8 57 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000240975BF6D0, 16 bytes long.
 Data: < W              > D8 57 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000240975BF5E0, 16 bytes long.
 Data: <P               > 50 04 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000240975BECD0, 16 bytes long.
 Data: <0               > 30 04 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000240975BF590, 16 bytes long.
 Data: <                > E0 02 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000240975BEF00, 16 bytes long.
 Data: <                > 10 04 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000240975BF7C0, 16 bytes long.
 Data: <p               > 70 04 DA 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000240975BEB90, 16 bytes long.
 Data: <                > 18 C0 D8 7F F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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