Task 38628663

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>
23:24:46 (21808): wrapper (7.9.26016): starting
23:24:46 (21808): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A16_A08_0.pdb
QB_A16_A08_0.xml
QB_A16_A08.inpcrd
QB_A16_A08_input.yaml
QB_A16_A08.pdb
QB_A16_A08.prmtop
QB_A16_A08_sys.xml
run.bat
run.sh
23:24:50 (21808): Library/usr/bin/tar.exe exited; CPU time 0.000000
23:24:50 (21808): 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) : {3835113} normal block at 0x000002279D26DC10, 8 bytes long.
 Data: <  | '   > 00 00 7C 9D 27 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x000002279D25DA30, 1080 bytes long.
 Data: <,[      H       > 2C 5B 00 00 CD CD CD CD 48 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x000002279D260830, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
02:15:20 (22860): wrapper (7.9.26016): starting
02:15:20 (22860): 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
05:00:18 (22860): C:/Windows/system32/cmd.exe exited; CPU time 9788.515625
05:00:18 (22860): app exit status: 0x16
05:00:18 (22860): 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: 145006089 bytes.
Dumping objects ->
{1549} normal block at 0x0000012ECE717A60, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1538} normal block at 0x0000012ECE717AD0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1527} normal block at 0x0000012ECE717440, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1516} normal block at 0x0000012ECE717910, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1505} normal block at 0x0000012ECE717520, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1474} normal block at 0x0000012ECE6FFD30, 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) : {1461} normal block at 0x0000012ECE716740, 8 bytes long.
 Data: <    .   > 00 00 12 D0 2E 01 00 00 
{303} normal block at 0x0000012ECE716060, 8 bytes long.
 Data: < |q .   > 00 7C 71 CE 2E 01 00 00 
{294} normal block at 0x0000012ECE701FF0, 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 0x0000012ECE716560, 16 bytes long.
 Data: < rq .           > F8 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000012ECE716240, 16 bytes long.
 Data: < rq .           > D0 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000012ECE710F90, 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 0x0000012ECE7168D0, 16 bytes long.
 Data: < rq .           > A8 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000012ECE7166F0, 16 bytes long.
 Data: < rq .           > 80 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000012ECE7169C0, 16 bytes long.
 Data: <Xrq .           > 58 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000012ECE7165B0, 16 bytes long.
 Data: <0rq .           > 30 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000012ECE7174B0, 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 0x0000012ECE716C40, 16 bytes long.
 Data: <  p .           > 98 00 70 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000012ECE7115F0, 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 0x0000012ECE716920, 16 bytes long.
 Data: <p p .           > 70 00 70 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000012ECE7161F0, 16 bytes long.
 Data: <H p .           > 48 00 70 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000012ECE7161A0, 16 bytes long.
 Data: <  p .           > 20 00 70 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000012ECE716880, 16 bytes long.
 Data: <  o .           > F8 FF 6F CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000012ECE7166A0, 16 bytes long.
 Data: <  o .           > D0 FF 6F CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000012ECE716BF0, 16 bytes long.
 Data: <  o .           > A8 FF 6F CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000012ECE711590, 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 0x0000012ECE716BA0, 16 bytes long.
 Data: <  o .           > 80 FF 6F CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000012ECE6FFF80, 320 bytes long.
 Data: < kq .     q .   > A0 6B 71 CE 2E 01 00 00 90 15 71 CE 2E 01 00 00 
{273} normal block at 0x0000012ECE716470, 16 bytes long.
 Data: < rq .           > 10 72 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000012ECE716600, 16 bytes long.
 Data: < qq .           > E8 71 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000012ECE711890, 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 0x0000012ECE716D30, 16 bytes long.
 Data: < qq .           > C0 71 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000012ECE710C90, 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 0x0000012ECE716420, 16 bytes long.
 Data: < qq .           > 08 71 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000012ECE716650, 16 bytes long.
 Data: < pq .           > E0 70 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000012ECE716B00, 16 bytes long.
 Data: < pq .           > B8 70 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000012ECE716330, 16 bytes long.
 Data: < pq .           > 90 70 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000012ECE716010, 16 bytes long.
 Data: <hpq .           > 68 70 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000012ECE716AB0, 16 bytes long.
 Data: <@pq .           > 40 70 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000012ECE716B50, 16 bytes long.
 Data: <  o .           > D0 C3 6F CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000012ECE6FC3D0, 40 bytes long.
 Data: <Pkq .   0 o .   > 50 6B 71 CE 2E 01 00 00 30 FD 6F CE 2E 01 00 00 
{259} normal block at 0x0000012ECE716830, 16 bytes long.
 Data: < pq .           > 20 70 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000012ECE716100, 16 bytes long.
 Data: < oq .           > F8 6F 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000012ECE7117D0, 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 0x0000012ECE7167E0, 16 bytes long.
 Data: < oq .           > D0 6F 71 CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000012ECE716FD0, 992 bytes long.
 Data: < gq .     q .   > E0 67 71 CE 2E 01 00 00 D0 17 71 CE 2E 01 00 00 
{91} normal block at 0x0000012ECE711650, 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 0x0000012ECE70D560, 16 bytes long.
 Data: <  o .           > A0 E2 6F CE 2E 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x0000012ECE6FE2A0, 40 bytes long.
 Data: <` p .   P q .   > 60 D5 70 CE 2E 01 00 00 50 16 71 CE 2E 01 00 00 
{68} normal block at 0x0000012ECE70D1F0, 16 bytes long.
 Data: <   -            > 80 EA 18 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000012ECE70D510, 16 bytes long.
 Data: <@  -            > 40 E9 18 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000012ECE70D880, 16 bytes long.
 Data: < W -            > F8 57 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000012ECE70D290, 16 bytes long.
 Data: < W -            > D8 57 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000012ECE70D830, 16 bytes long.
 Data: <P  -            > 50 04 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000012ECE70D4C0, 16 bytes long.
 Data: <0  -            > 30 04 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000012ECE70D420, 16 bytes long.
 Data: <   -            > E0 02 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000012ECE70E000, 16 bytes long.
 Data: <   -            > 10 04 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000012ECE70D3D0, 16 bytes long.
 Data: <p  -            > 70 04 15 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000012ECE70DC40, 16 bytes long.
 Data: <   -            > 18 C0 13 2D F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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