Task 38624555

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
02:49:38 (51800): wrapper (7.9.26016): starting
02:49:38 (51800): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A32_A26_0.pdb
QB_A32_A26_0.xml
QB_A32_A26.inpcrd
QB_A32_A26_input.yaml
QB_A32_A26.pdb
QB_A32_A26.prmtop
QB_A32_A26_sys.xml
run.bat
run.sh
02:49:41 (51800): Library/usr/bin/tar.exe exited; CPU time 0.000000
02:49:41 (51800): 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) : {3835179} normal block at 0x00000224053AD650, 8 bytes long.
 Data: <    $   > 00 00 9D 05 24 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833962} normal block at 0x00000224070D4800, 1080 bytes long.
 Data: < 0              > 10 30 00 00 CD CD CD CD 08 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x00000224053A1100, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
02:03:01 (6264): wrapper (7.9.26016): starting
02:03:01 (6264): 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
03:38:55 (6264): C:/Windows/system32/cmd.exe exited; CPU time 5764.296875
03:38:55 (6264): app exit status: 0x16
03:38:55 (6264): 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: 119797404 bytes.
Dumping objects ->
{1609} normal block at 0x0000026F4ADA5410, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1598} normal block at 0x0000026F4ADA53A0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1587} normal block at 0x0000026F4ADA5480, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1576} normal block at 0x0000026F4ADA5870, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1565} normal block at 0x0000026F4ADA56B0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1534} normal block at 0x0000026F4AD8F400, 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) : {1521} normal block at 0x0000026F4ADA6F00, 8 bytes long.
 Data: <   Ko   > 00 00 10 4B 6F 02 00 00 
{305} normal block at 0x0000026F4ADA67D0, 8 bytes long.
 Data: <@M Jo   > 40 4D DA 4A 6F 02 00 00 
{296} normal block at 0x0000026F4AD92730, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{295} normal block at 0x0000026F4ADA6B90, 16 bytes long.
 Data: < r Jo           > 98 72 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000026F4ADA64B0, 16 bytes long.
 Data: <pr Jo           > 70 72 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000026F4ADA0830, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{292} normal block at 0x0000026F4ADA6050, 16 bytes long.
 Data: <Hr Jo           > 48 72 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000026F4ADA63C0, 16 bytes long.
 Data: < r Jo           > 20 72 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000026F4ADA6460, 16 bytes long.
 Data: < q Jo           > F8 71 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000026F4ADA69B0, 16 bytes long.
 Data: < q Jo           > D0 71 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000026F4ADA54F0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{287} normal block at 0x0000026F4ADA6730, 16 bytes long.
 Data: <   Jo           > 88 CB D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000026F4ADA07D0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{285} normal block at 0x0000026F4ADA6370, 16 bytes long.
 Data: <`  Jo           > 60 CB D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000026F4ADA6960, 16 bytes long.
 Data: <8  Jo           > 38 CB D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000026F4ADA6C80, 16 bytes long.
 Data: <   Jo           > 10 CB D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000026F4ADA62D0, 16 bytes long.
 Data: <   Jo           > E8 CA D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000026F4ADA6140, 16 bytes long.
 Data: <   Jo           > C0 CA D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000026F4ADA6EB0, 16 bytes long.
 Data: <   Jo           > 98 CA D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000026F4AD9FCF0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{277} normal block at 0x0000026F4ADA6190, 16 bytes long.
 Data: <p  Jo           > 70 CA D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000026F4AD8CA70, 320 bytes long.
 Data: < a Jo      Jo   > 90 61 DA 4A 6F 02 00 00 F0 FC D9 4A 6F 02 00 00 
{275} normal block at 0x0000026F4ADA6D20, 16 bytes long.
 Data: < q Jo           > B0 71 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000026F4ADA6B40, 16 bytes long.
 Data: < q Jo           > 88 71 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000026F4AD9FF90, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{272} normal block at 0x0000026F4ADA6280, 16 bytes long.
 Data: <`q Jo           > 60 71 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000026F4ADA02F0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{270} normal block at 0x0000026F4ADA6410, 16 bytes long.
 Data: < p Jo           > A8 70 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000026F4ADA6E10, 16 bytes long.
 Data: < p Jo           > 80 70 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000026F4ADA60F0, 16 bytes long.
 Data: <Xp Jo           > 58 70 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000026F4ADA68C0, 16 bytes long.
 Data: <0p Jo           > 30 70 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000026F4ADA5FB0, 16 bytes long.
 Data: < p Jo           > 08 70 DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000026F4ADA6A50, 16 bytes long.
 Data: < o Jo           > E0 6F DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000026F4ADA6AA0, 16 bytes long.
 Data: < Z Jo           > A0 5A DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000026F4ADA5AA0, 40 bytes long.
 Data: < j Jo      Jo   > A0 6A DA 4A 6F 02 00 00 00 F4 D8 4A 6F 02 00 00 
{261} normal block at 0x0000026F4ADA60A0, 16 bytes long.
 Data: < o Jo           > C0 6F DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000026F4ADA6910, 16 bytes long.
 Data: < o Jo           > 98 6F DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000026F4ADA0710, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{258} normal block at 0x0000026F4ADA61E0, 16 bytes long.
 Data: <po Jo           > 70 6F DA 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000026F4ADA6F70, 992 bytes long.
 Data: < a Jo      Jo   > E0 61 DA 4A 6F 02 00 00 10 07 DA 4A 6F 02 00 00 
{93} normal block at 0x0000026F4ADA0590, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{92} normal block at 0x0000026F4AD9DE70, 16 bytes long.
 Data: <`  Jo           > 60 E2 D8 4A 6F 02 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x0000026F4AD8E260, 40 bytes long.
 Data: <p  Jo      Jo   > 70 DE D9 4A 6F 02 00 00 90 05 DA 4A 6F 02 00 00 
{70} normal block at 0x0000026F4AD9D920, 16 bytes long.
 Data: <                > 80 EA A1 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000026F4AD9DE20, 16 bytes long.
 Data: <@               > 40 E9 A1 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000026F4AD9E500, 16 bytes long.
 Data: < W              > F8 57 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000026F4AD9D9C0, 16 bytes long.
 Data: < W              > D8 57 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000026F4AD9E410, 16 bytes long.
 Data: <P               > 50 04 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000026F4AD9DF10, 16 bytes long.
 Data: <0               > 30 04 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000026F4AD9E2D0, 16 bytes long.
 Data: <                > E0 02 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000026F4AD9D970, 16 bytes long.
 Data: <                > 10 04 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000026F4AD9D790, 16 bytes long.
 Data: <p               > 70 04 9E 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000026F4AD9E4B0, 16 bytes long.
 Data: <                > 18 C0 9C 85 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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