Task 38644362

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>
08:10:16 (37124): wrapper (7.9.26016): starting
08:10:16 (37124): 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
08:10:18 (37124): Library/usr/bin/tar.exe exited; CPU time 0.000000
08:10:18 (37124): 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\16\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\16\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) : {3835393} normal block at 0x000001F4B7A8FA50, 8 bytes long.
 Data: <        > 00 00 E9 B7 F4 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833958} normal block at 0x000001F4B97F3DE0, 1080 bytes long.
 Data: <H       (       > 48 82 00 00 CD CD CD CD 28 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x000001F4B7A85FB0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
08:47:01 (44076): wrapper (7.9.26016): starting
08:47:01 (44076): 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\16\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
13:47:45 (20640): wrapper (7.9.26016): starting
13:47:45 (20640): 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\16\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\16\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\16\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\16\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\16\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\16\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\16\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\16\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\16\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\16\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
18:48:22 (20640): C:/Windows/system32/cmd.exe exited; CPU time 17775.406250
18:48:22 (20640): app exit status: 0x16
18:48:22 (20640): 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: 386060143 bytes.
Dumping objects ->
{1827} normal block at 0x00000227FB583BB0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1816} normal block at 0x00000227FB584080, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1805} normal block at 0x00000227FB583FA0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1794} normal block at 0x00000227FB583B40, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1783} normal block at 0x00000227FB583D70, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1752} normal block at 0x00000227FB56F9C0, 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) : {1739} normal block at 0x00000227FB586080, 8 bytes long.
 Data: <  U '   > 00 00 55 FB 27 02 00 00 
{305} normal block at 0x00000227FB5857C0, 8 bytes long.
 Data: < kX '   > 00 6B 58 FB 27 02 00 00 
{296} normal block at 0x00000227FB577DC0, 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 0x00000227FB586580, 16 bytes long.
 Data: < jX '           > 08 6A 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000227FB585A90, 16 bytes long.
 Data: < iX '           > E0 69 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x00000227FB5810D0, 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 0x00000227FB5859F0, 16 bytes long.
 Data: < iX '           > B8 69 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000227FB586530, 16 bytes long.
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{290} normal block at 0x00000227FB5859A0, 16 bytes long.
 Data: <hiX '           > 68 69 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000227FB585F90, 16 bytes long.
 Data: <@iX '           > 40 69 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000227FB583AD0, 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 0x00000227FB585950, 16 bytes long.
 Data: <  W '           > B8 A3 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x00000227FB580E30, 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 0x00000227FB585E00, 16 bytes long.
 Data: <  W '           > 90 A3 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000227FB585F40, 16 bytes long.
 Data: <h W '           > 68 A3 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000227FB585900, 16 bytes long.
 Data: <@ W '           > 40 A3 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000227FB5860D0, 16 bytes long.
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{280} normal block at 0x00000227FB585B30, 16 bytes long.
 Data: <  W '           > F0 A2 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000227FB585EF0, 16 bytes long.
 Data: <  W '           > C8 A2 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000227FB581670, 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 0x00000227FB5862B0, 16 bytes long.
 Data: <  W '           > A0 A2 57 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x00000227FB57A2A0, 320 bytes long.
 Data: < bX '   p X '   > B0 62 58 FB 27 02 00 00 70 16 58 FB 27 02 00 00 
{275} normal block at 0x00000227FB586350, 16 bytes long.
 Data: < iX '           > 20 69 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000227FB586030, 16 bytes long.
 Data: < hX '           > F8 68 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000227FB581790, 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 0x00000227FB585D10, 16 bytes long.
 Data: < hX '           > D0 68 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000227FB581730, 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 0x00000227FB585FE0, 16 bytes long.
 Data: < hX '           > 18 68 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000227FB586260, 16 bytes long.
 Data: < gX '           > F0 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000227FB5864E0, 16 bytes long.
 Data: < gX '           > C8 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000227FB585810, 16 bytes long.
 Data: < gX '           > A0 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000227FB585DB0, 16 bytes long.
 Data: <xgX '           > 78 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000227FB585720, 16 bytes long.
 Data: <PgX '           > 50 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000227FB5861C0, 16 bytes long.
 Data: < @X '           > 10 40 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x00000227FB584010, 40 bytes long.
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{261} normal block at 0x00000227FB5858B0, 16 bytes long.
 Data: <0gX '           > 30 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000227FB5863F0, 16 bytes long.
 Data: < gX '           > 08 67 58 FB 27 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000227FB581370, 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 0x00000227FB5865D0, 16 bytes long.
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{257} normal block at 0x00000227FB5866E0, 992 bytes long.
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{93} normal block at 0x00000227FB580D70, 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 0x00000227FB57FBE0, 16 bytes long.
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{91} normal block at 0x00000227FB5841D0, 40 bytes long.
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{70} normal block at 0x00000227FB57FC30, 16 bytes long.
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{69} normal block at 0x00000227FB57FDC0, 16 bytes long.
 Data: <@  b            > 40 E9 93 62 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000227FB580A40, 16 bytes long.
 Data: < W b            > F8 57 90 62 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000227FB580180, 16 bytes long.
 Data: < W b            > D8 57 90 62 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000227FB580AE0, 16 bytes long.
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{65} normal block at 0x00000227FB5803B0, 16 bytes long.
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{64} normal block at 0x00000227FB57FD70, 16 bytes long.
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{63} normal block at 0x00000227FB580540, 16 bytes long.
 Data: <   b            > 10 04 90 62 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000227FB57FFA0, 16 bytes long.
 Data: <p  b            > 70 04 90 62 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000227FB580360, 16 bytes long.
 Data: <   b            > 18 C0 8E 62 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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