Task 38643755

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>
20:39:06 (27976): wrapper (7.9.26016): starting
20:39:06 (27976): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A15_0.pdb
QB_A20_A15_0.xml
QB_A20_A15.inpcrd
QB_A20_A15_input.yaml
QB_A20_A15.pdb
QB_A20_A15.prmtop
QB_A20_A15_sys.xml
run.bat
run.sh
20:39:12 (27976): Library/usr/bin/tar.exe exited; CPU time 0.000000
20:39:12 (27976): 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\12\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\12\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) : {3835371} normal block at 0x0000016C92F2BD90, 8 bytes long.
 Data: <  4 l   > 00 00 34 93 6C 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833978} normal block at 0x0000016C94C956D0, 1080 bytes long.
 Data: <0i      $       > 30 69 00 00 CD CD CD CD 24 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {321} normal block at 0x0000016C92F21980, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
21:49:01 (13952): wrapper (7.9.26016): starting
21:49:01 (13952): 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\12\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\12\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\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\12\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\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
02:03:37 (13952): C:/Windows/system32/cmd.exe exited; CPU time 14344.406250
02:03:37 (13952): app exit status: 0x16
02:03:37 (13952): 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: 386112289 bytes.
Dumping objects ->
{1795} normal block at 0x0000025BF33D64F0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1784} normal block at 0x0000025BF33D6020, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1773} normal block at 0x0000025BF33D5F40, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1762} normal block at 0x0000025BF33D6480, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1751} normal block at 0x0000025BF33D62C0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1720} normal block at 0x0000025BF33BCD50, 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) : {1707} normal block at 0x0000025BF33D7720, 8 bytes long.
 Data: <    [   > 00 00 8F F3 5B 02 00 00 
{315} normal block at 0x0000025BF33D6BE0, 8 bytes long.
 Data: < W= [   > 90 57 3D F3 5B 02 00 00 
{306} normal block at 0x0000025BF33C2520, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{305} normal block at 0x0000025BF33D7680, 16 bytes long.
 Data: < |= [           > E8 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{304} normal block at 0x0000025BF33D6FA0, 16 bytes long.
 Data: < |= [           > C0 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{303} normal block at 0x0000025BF33D0480, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{302} normal block at 0x0000025BF33D73B0, 16 bytes long.
 Data: < |= [           > 98 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{301} normal block at 0x0000025BF33D7270, 16 bytes long.
 Data: <p|= [           > 70 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x0000025BF33D7900, 16 bytes long.
 Data: <H|= [           > 48 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x0000025BF33D6A00, 16 bytes long.
 Data: < |= [           > 20 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x0000025BF33D5ED0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{297} normal block at 0x0000025BF33D7630, 16 bytes long.
 Data: <  ; [           > E8 CC 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000025BF33D0600, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{295} normal block at 0x0000025BF33D7540, 16 bytes long.
 Data: <  ; [           > C0 CC 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000025BF33D6C30, 16 bytes long.
 Data: <  ; [           > 98 CC 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000025BF33D7360, 16 bytes long.
 Data: <p ; [           > 70 CC 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000025BF33D7860, 16 bytes long.
 Data: <H ; [           > 48 CC 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000025BF33D71D0, 16 bytes long.
 Data: <  ; [           > 20 CC 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000025BF33D74F0, 16 bytes long.
 Data: <  ; [           > F8 CB 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000025BF33D0420, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{287} normal block at 0x0000025BF33D72C0, 16 bytes long.
 Data: <  ; [           > D0 CB 3B F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000025BF33BCBD0, 320 bytes long.
 Data: < r= [     = [   > C0 72 3D F3 5B 02 00 00 20 04 3D F3 5B 02 00 00 
{285} normal block at 0x0000025BF33D74A0, 16 bytes long.
 Data: < |= [           > 00 7C 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000025BF33D7310, 16 bytes long.
 Data: < {= [           > D8 7B 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000025BF33D0D80, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{282} normal block at 0x0000025BF33D7950, 16 bytes long.
 Data: < {= [           > B0 7B 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000025BF33D07E0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{280} normal block at 0x0000025BF33D6FF0, 16 bytes long.
 Data: < z= [           > F8 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000025BF33D70E0, 16 bytes long.
 Data: < z= [           > D0 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000025BF33D7130, 16 bytes long.
 Data: < z= [           > A8 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000025BF33D6AA0, 16 bytes long.
 Data: < z= [           > 80 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000025BF33D75E0, 16 bytes long.
 Data: <Xz= [           > 58 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000025BF33D76D0, 16 bytes long.
 Data: <0z= [           > 30 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000025BF33D7590, 16 bytes long.
 Data: < d= [           > 10 64 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000025BF33D6410, 40 bytes long.
 Data: < u= [   P ; [   > 90 75 3D F3 5B 02 00 00 50 CD 3B F3 5B 02 00 00 
{271} normal block at 0x0000025BF33D7220, 16 bytes long.
 Data: < z= [           > 10 7A 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000025BF33D7770, 16 bytes long.
 Data: < y= [           > E8 79 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000025BF33D0C00, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{268} normal block at 0x0000025BF33D7450, 16 bytes long.
 Data: < y= [           > C0 79 3D F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000025BF33D79C0, 992 bytes long.
 Data: <Pt= [     = [   > 50 74 3D F3 5B 02 00 00 00 0C 3D F3 5B 02 00 00 
{103} normal block at 0x0000025BF33D0900, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{102} normal block at 0x0000025BF33CBF70, 16 bytes long.
 Data: <  < [           > 10 09 3C F3 5B 02 00 00 00 00 00 00 00 00 00 00 
{101} normal block at 0x0000025BF33C0910, 40 bytes long.
 Data: <p < [     = [   > 70 BF 3C F3 5B 02 00 00 00 09 3D F3 5B 02 00 00 
{80} normal block at 0x0000025BF33CBE80, 16 bytes long.
 Data: <                > 80 EA A1 A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{79} normal block at 0x0000025BF33CB840, 16 bytes long.
 Data: <@               > 40 E9 A1 A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{78} normal block at 0x0000025BF33CB480, 16 bytes long.
 Data: < W              > F8 57 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{77} normal block at 0x0000025BF33CC330, 16 bytes long.
 Data: < W              > D8 57 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x0000025BF33CB6B0, 16 bytes long.
 Data: <P               > 50 04 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x0000025BF33CBB10, 16 bytes long.
 Data: <0               > 30 04 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x0000025BF33CBE30, 16 bytes long.
 Data: <                > E0 02 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x0000025BF33CC3D0, 16 bytes long.
 Data: <                > 10 04 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x0000025BF33CBAC0, 16 bytes long.
 Data: <p               > 70 04 9E A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x0000025BF33CBED0, 16 bytes long.
 Data: <                > 18 C0 9C A9 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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