Task 38643151

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>
07:07:56 (27232): wrapper (7.9.26016): starting
07:07:56 (27232): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A26_A17_0.pdb
QB_A26_A17_0.xml
QB_A26_A17.inpcrd
QB_A26_A17_input.yaml
QB_A26_A17.pdb
QB_A26_A17.prmtop
QB_A26_A17_sys.xml
run.bat
run.sh
07:07:59 (27232): Library/usr/bin/tar.exe exited; CPU time 0.000000
07:08:00 (27232): 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\15\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\15\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) : {3835175} normal block at 0x000001FC10F7DBD0, 8 bytes long.
 Data: <  9     > 00 00 39 11 FC 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x000001FC10F6DA50, 1080 bytes long.
 Data: <X}              > 58 7D 00 00 CD CD CD CD 9C 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x000001FC10F71840, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
20:00:00 (13804): wrapper (7.9.26016): starting
20:00:00 (13804): 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\15\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\15\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\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\15\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\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
22:03:46 (13804): C:/Windows/system32/cmd.exe exited; CPU time 5397.093750
22:03:46 (13804): app exit status: 0x16
22:03:46 (13804): 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: 145335261 bytes.
Dumping objects ->
{1608} normal block at 0x0000017036795640, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1597} normal block at 0x0000017036795100, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1586} normal block at 0x00000170367956B0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1575} normal block at 0x00000170367951E0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1564} normal block at 0x0000017036795410, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1533} normal block at 0x0000017036780AD0, 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) : {1520} normal block at 0x0000017036796650, 8 bytes long.
 Data: <   8p   > 00 00 04 38 70 01 00 00 
{306} normal block at 0x0000017036796AB0, 8 bytes long.
 Data: < py6p   > 80 70 79 36 70 01 00 00 
{297} normal block at 0x0000017036781F30, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{296} normal block at 0x0000017036796290, 16 bytes long.
 Data: < oy6p           > 88 6F 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000017036796060, 16 bytes long.
 Data: <`oy6p           > 60 6F 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000017036790680, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{293} normal block at 0x0000017036796A10, 16 bytes long.
 Data: <8oy6p           > 38 6F 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000017036796240, 16 bytes long.
 Data: < oy6p           > 10 6F 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000170367961F0, 16 bytes long.
 Data: < ny6p           > E8 6E 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000017036796A60, 16 bytes long.
 Data: < ny6p           > C0 6E 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000170367952C0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{288} normal block at 0x0000017036796B50, 16 bytes long.
 Data: <  w6p           > A8 F5 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001703678FE40, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{286} normal block at 0x00000170367969C0, 16 bytes long.
 Data: <  w6p           > 80 F5 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000170367961A0, 16 bytes long.
 Data: <X w6p           > 58 F5 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000170367963D0, 16 bytes long.
 Data: <0 w6p           > 30 F5 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000017036795F70, 16 bytes long.
 Data: <  w6p           > 08 F5 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000170367965B0, 16 bytes long.
 Data: <  w6p           > E0 F4 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000017036795FC0, 16 bytes long.
 Data: <  w6p           > B8 F4 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000017036790140, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{278} normal block at 0x0000017036796BA0, 16 bytes long.
 Data: <  w6p           > 90 F4 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001703677F490, 320 bytes long.
 Data: < ky6p   @ y6p   > A0 6B 79 36 70 01 00 00 40 01 79 36 70 01 00 00 
{276} normal block at 0x0000017036796010, 16 bytes long.
 Data: < ny6p           > A0 6E 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000017036796380, 16 bytes long.
 Data: <xny6p           > 78 6E 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001703678FCC0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{273} normal block at 0x00000170367967E0, 16 bytes long.
 Data: <Pny6p           > 50 6E 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000017036790500, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{271} normal block at 0x0000017036795E30, 16 bytes long.
 Data: < my6p           > 98 6D 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000017036796100, 16 bytes long.
 Data: <pmy6p           > 70 6D 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000017036795D40, 16 bytes long.
 Data: <Hmy6p           > 48 6D 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000017036796B00, 16 bytes long.
 Data: < my6p           > 20 6D 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000170367962E0, 16 bytes long.
 Data: < ly6p           > F8 6C 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000017036796920, 16 bytes long.
 Data: < ly6p           > D0 6C 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000017036796150, 16 bytes long.
 Data: <0Sy6p           > 30 53 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000017036795330, 40 bytes long.
 Data: <Pay6p     x6p   > 50 61 79 36 70 01 00 00 D0 0A 78 36 70 01 00 00 
{262} normal block at 0x0000017036795F20, 16 bytes long.
 Data: < ly6p           > B0 6C 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000170367964C0, 16 bytes long.
 Data: < ly6p           > 88 6C 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001703678FBA0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{259} normal block at 0x0000017036796560, 16 bytes long.
 Data: <`ly6p           > 60 6C 79 36 70 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000017036796C60, 992 bytes long.
 Data: <`ey6p     x6p   > 60 65 79 36 70 01 00 00 A0 FB 78 36 70 01 00 00 
{94} normal block at 0x000001703678FA20, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{93} normal block at 0x000001703678D4F0, 16 bytes long.
 Data: <p w6p           > 70 E6 77 36 70 01 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x000001703677E670, 40 bytes long.
 Data: <  x6p     x6p   > F0 D4 78 36 70 01 00 00 20 FA 78 36 70 01 00 00 
{71} normal block at 0x000001703678DC70, 16 bytes long.
 Data: <   g            > 80 EA FD 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000001703678DDB0, 16 bytes long.
 Data: <@  g            > 40 E9 FD 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001703678E1C0, 16 bytes long.
 Data: < W g            > F8 57 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001703678D9A0, 16 bytes long.
 Data: < W g            > D8 57 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001703678DD60, 16 bytes long.
 Data: <P  g            > 50 04 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001703678D950, 16 bytes long.
 Data: <0  g            > 30 04 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001703678D9F0, 16 bytes long.
 Data: <   g            > E0 02 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001703678E2B0, 16 bytes long.
 Data: <   g            > 10 04 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001703678DC20, 16 bytes long.
 Data: <p  g            > 70 04 FA 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001703678D810, 16 bytes long.
 Data: <   g            > 18 C0 F8 67 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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