Task 38591012

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>
10:23:37 (17068): wrapper (7.9.26016): starting
10:23:37 (17068): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A19_0.pdb
QB_A20_A19_0.xml
QB_A20_A19_equil.pdb
QB_A20_A19.inpcrd
QB_A20_A19_input.yaml
QB_A20_A19_mdlambda.pdb
QB_A20_A19_min.pdb
QB_A20_A19_npt.pdb
QB_A20_A19.pdb
QB_A20_A19.prmtop
QB_A20_A19_sys.xml
QB_A20_A19_therm.pdb
run.bat
run.sh
10:23:40 (17068): Library/usr/bin/tar.exe exited; CPU time 0.000000
10:23:40 (17068): 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\1\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\1\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) : {3835162} normal block at 0x000002A7CC32D720, 8 bytes long.
 Data: <  }     > 00 00 7D CC A7 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x000002A7CC358CB0, 1080 bytes long.
 Data: < (              > 80 28 00 00 CD CD CD CD 90 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x000002A7CC320BD0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
16:38:38 (18320): wrapper (7.9.26016): starting
16:38:38 (18320): 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\1\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1510} normal block at 0x0000025431864E20, 8 bytes long.
 Data: <   1T   > 00 00 C4 31 54 02 00 00 
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x00000254318657B0, 1080 bytes long.
 Data: < G              > 18 47 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
16:43:53 (21992): wrapper (7.9.26016): starting
16:43:53 (21992): 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\1\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\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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\1\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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
18:08:53 (21992): C:/Windows/system32/cmd.exe exited; CPU time 5052.750000
18:08:53 (21992): app exit status: 0x16
18:08:53 (21992): 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: 79679910 bytes.
Dumping objects ->
{1598} normal block at 0x000001E67FA538C0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1587} normal block at 0x000001E67FA537E0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1576} normal block at 0x000001E67FA53AF0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1565} normal block at 0x000001E67FA53D90, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1554} normal block at 0x000001E67FA53C40, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1523} normal block at 0x000001E67FA40590, 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) : {1510} normal block at 0x000001E67FA54900, 8 bytes long.
 Data: <  b     > 00 00 62 01 E6 01 00 00 
{303} normal block at 0x000001E67FA550D0, 8 bytes long.
 Data: <0X      > 30 58 A5 7F E6 01 00 00 
{294} normal block at 0x000001E67FA42370, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{293} normal block at 0x000001E67FA54AE0, 16 bytes long.
 Data: <8W              > 38 57 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001E67FA546D0, 16 bytes long.
 Data: < W              > 10 57 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001E67FA51380, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{290} normal block at 0x000001E67FA544A0, 16 bytes long.
 Data: < V              > E8 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001E67FA55080, 16 bytes long.
 Data: < V              > C0 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001E67FA54A90, 16 bytes long.
 Data: < V              > 98 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001E67FA54680, 16 bytes long.
 Data: <pV              > 70 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001E67FA53850, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x000001E67FA55030, 16 bytes long.
 Data: <                > B8 B2 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001E67FA51020, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{283} normal block at 0x000001E67FA54E00, 16 bytes long.
 Data: <                > 90 B2 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001E67FA54A40, 16 bytes long.
 Data: <h               > 68 B2 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001E67FA54950, 16 bytes long.
 Data: <@               > 40 B2 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001E67FA54810, 16 bytes long.
 Data: <                > 18 B2 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001E67FA547C0, 16 bytes long.
 Data: <                > F0 B1 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001E67FA54770, 16 bytes long.
 Data: <                > C8 B1 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001E67FA512C0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{275} normal block at 0x000001E67FA549F0, 16 bytes long.
 Data: <                > A0 B1 A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001E67FA3B1A0, 320 bytes long.
 Data: < I              > F0 49 A5 7F E6 01 00 00 C0 12 A5 7F E6 01 00 00 
{273} normal block at 0x000001E67FA544F0, 16 bytes long.
 Data: <PV              > 50 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001E67FA548B0, 16 bytes long.
 Data: <(V              > 28 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001E67FA50CC0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{270} normal block at 0x000001E67FA55260, 16 bytes long.
 Data: < V              > 00 56 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001E67FA50C00, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{268} normal block at 0x000001E67FA553A0, 16 bytes long.
 Data: <HU              > 48 55 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001E67FA54E50, 16 bytes long.
 Data: < U              > 20 55 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001E67FA54860, 16 bytes long.
 Data: < T              > F8 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001E67FA55210, 16 bytes long.
 Data: < T              > D0 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001E67FA55300, 16 bytes long.
 Data: < T              > A8 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001E67FA54EA0, 16 bytes long.
 Data: < T              > 80 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001E67FA54720, 16 bytes long.
 Data: < 9              > A0 39 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001E67FA539A0, 40 bytes long.
 Data: < G              > 20 47 A5 7F E6 01 00 00 90 05 A4 7F E6 01 00 00 
{259} normal block at 0x000001E67FA54CC0, 16 bytes long.
 Data: <`T              > 60 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001E67FA54FE0, 16 bytes long.
 Data: <8T              > 38 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000001E67FA51260, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{256} normal block at 0x000001E67FA551C0, 16 bytes long.
 Data: < T              > 10 54 A5 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000001E67FA55410, 992 bytes long.
 Data: < Q      `       > C0 51 A5 7F E6 01 00 00 60 12 A5 7F E6 01 00 00 
{91} normal block at 0x000001E67FA50A80, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{90} normal block at 0x000001E67FA4D850, 16 bytes long.
 Data: <                > C0 BA A3 7F E6 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x000001E67FA3BAC0, 40 bytes long.
 Data: <P               > 50 D8 A4 7F E6 01 00 00 80 0A A5 7F E6 01 00 00 
{68} normal block at 0x000001E67FA4CE50, 16 bytes long.
 Data: <  `             > 80 EA 60 B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001E67FA4D800, 16 bytes long.
 Data: <@ `             > 40 E9 60 B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001E67FA4D760, 16 bytes long.
 Data: < W]             > F8 57 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001E67FA4D620, 16 bytes long.
 Data: < W]             > D8 57 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001E67FA4CF40, 16 bytes long.
 Data: <P ]             > 50 04 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001E67FA4D670, 16 bytes long.
 Data: <0 ]             > 30 04 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001E67FA4CE00, 16 bytes long.
 Data: <  ]             > E0 02 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001E67FA4D8F0, 16 bytes long.
 Data: <  ]             > 10 04 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001E67FA4DA30, 16 bytes long.
 Data: <p ]             > 70 04 5D B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001E67FA4D5D0, 16 bytes long.
 Data: <  [             > 18 C0 5B B4 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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