Task 38643637

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>
20:15:19 (35800): wrapper (7.9.26016): starting
20:15:19 (35800): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A01_A05_0.pdb
QB_A01_A05_0.xml
QB_A01_A05.inpcrd
QB_A01_A05_input.yaml
QB_A01_A05.pdb
QB_A01_A05.prmtop
QB_A01_A05_sys.xml
run.bat
run.sh
20:15:21 (35800): Library/usr/bin/tar.exe exited; CPU time 0.000000
20:15:21 (35800): 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 'D:\ProgramData\BOINC\slots\0\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 'D:\ProgramData\BOINC\slots\0\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) : {3835391} normal block at 0x000001685A41E300, 8 bytes long.
 Data: <   [h   > 00 00 E2 5B 68 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833966} normal block at 0x000001685A40DC30, 1080 bytes long.
 Data: <                > D8 8A 00 00 CD CD CD CD D0 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {315} normal block at 0x000001685A411B60, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
07:39:33 (35828): wrapper (7.9.26016): starting
07:39:33 (35828): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\0\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 "D:\ProgramData\BOINC\slots\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\ProgramData\BOINC\slots\0\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
07:47:26 (35828): C:/Windows/system32/cmd.exe exited; CPU time 439.000000
07:47:26 (35828): app exit status: 0x16
07:47:26 (35828): called boinc_finish(195)
0 bytes in 0 Free Blocks.
538 bytes in 8 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: 9196658 bytes.
Dumping objects ->
{1822} normal block at 0x0000025328134490, 48 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1811} normal block at 0x0000025328134420, 48 bytes long.
 Data: <HOME=D:\ProgramD> 48 4F 4D 45 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1800} normal block at 0x0000025328134110, 48 bytes long.
 Data: <TMP=D:\ProgramDa> 54 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1789} normal block at 0x0000025328134260, 48 bytes long.
 Data: <TEMP=D:\ProgramD> 54 45 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1778} normal block at 0x0000025328134730, 48 bytes long.
 Data: <TMPDIR=D:\Progra> 54 4D 50 44 49 52 3D 44 3A 5C 50 72 6F 67 72 61 
{1747} normal block at 0x0000025328131630, 64 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1736} normal block at 0x0000025328120B50, 141 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {1733} normal block at 0x0000025328136BA0, 8 bytes long.
 Data: <  F(S   > 00 00 46 28 53 02 00 00 
{1008} normal block at 0x0000025328120C30, 141 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{309} normal block at 0x00000253281367E0, 8 bytes long.
 Data: < p (S   > D0 70 13 28 53 02 00 00 
{300} normal block at 0x0000025328122980, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{299} normal block at 0x0000025328135FC0, 16 bytes long.
 Data: < o (S           > D8 6F 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x00000253281361F0, 16 bytes long.
 Data: < o (S           > B0 6F 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x0000025328130270, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{296} normal block at 0x0000025328136880, 16 bytes long.
 Data: < o (S           > 88 6F 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000025328136150, 16 bytes long.
 Data: <`o (S           > 60 6F 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000253281365B0, 16 bytes long.
 Data: <8o (S           > 38 6F 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000025328136BF0, 16 bytes long.
 Data: < o (S           > 10 6F 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000025328134650, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{291} normal block at 0x0000025328136B50, 16 bytes long.
 Data: <   (S           > 88 F7 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000025328130570, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{289} normal block at 0x0000025328136330, 16 bytes long.
 Data: <`  (S           > 60 F7 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000025328136970, 16 bytes long.
 Data: <8  (S           > 38 F7 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000025328136290, 16 bytes long.
 Data: <   (S           > 10 F7 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000025328135CF0, 16 bytes long.
 Data: <   (S           > E8 F6 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000253281369C0, 16 bytes long.
 Data: <   (S           > C0 F6 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000025328136740, 16 bytes long.
 Data: <   (S           > 98 F6 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000025328130450, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{281} normal block at 0x0000025328136920, 16 bytes long.
 Data: <p  (S           > 70 F6 11 28 53 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002532811F670, 320 bytes long.
 Data: < i (S   P  (S   > 20 69 13 28 53 02 00 00 50 04 13 28 53 02 00 00 
{279} normal block at 0x0000025328135E30, 16 bytes long.
 Data: < n (S           > F0 6E 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000025328135DE0, 16 bytes long.
 Data: < n (S           > C8 6E 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000025328130150, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{276} normal block at 0x0000025328136600, 16 bytes long.
 Data: < n (S           > A0 6E 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000002532812FEB0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{274} normal block at 0x0000025328136240, 16 bytes long.
 Data: < m (S           > E8 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000025328135E80, 16 bytes long.
 Data: < m (S           > C0 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000025328136830, 16 bytes long.
 Data: < m (S           > 98 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000025328136420, 16 bytes long.
 Data: <pm (S           > 70 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000025328136380, 16 bytes long.
 Data: <Hm (S           > 48 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000253281368D0, 16 bytes long.
 Data: < m (S           > 20 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000253281366F0, 16 bytes long.
 Data: < E (S           > 00 45 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000025328134500, 40 bytes long.
 Data: < f (S   0  (S   > F0 66 13 28 53 02 00 00 30 16 13 28 53 02 00 00 
{265} normal block at 0x0000025328136B00, 16 bytes long.
 Data: < m (S           > 00 6D 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000253281362E0, 16 bytes long.
 Data: < l (S           > D8 6C 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000253281302D0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{262} normal block at 0x0000025328136790, 16 bytes long.
 Data: < l (S           > B0 6C 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000025328136CB0, 992 bytes long.
 Data: < g (S      (S   > 90 67 13 28 53 02 00 00 D0 02 13 28 53 02 00 00 
{97} normal block at 0x000002532812FF70, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{96} normal block at 0x000002532812E2B0, 16 bytes long.
 Data: < G (S           > A0 47 13 28 53 02 00 00 00 00 00 00 00 00 00 00 
{95} normal block at 0x00000253281347A0, 40 bytes long.
 Data: <   (S   p  (S   > B0 E2 12 28 53 02 00 00 70 FF 12 28 53 02 00 00 
{74} normal block at 0x000002532812DE00, 16 bytes long.
 Data: <                > 80 EA FD 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000002532812E030, 16 bytes long.
 Data: <@               > 40 E9 FD 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000002532812DDB0, 16 bytes long.
 Data: < W              > F8 57 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000002532812DEA0, 16 bytes long.
 Data: < W              > D8 57 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002532812E170, 16 bytes long.
 Data: <P               > 50 04 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002532812E260, 16 bytes long.
 Data: <0               > 30 04 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002532812E3F0, 16 bytes long.
 Data: <                > E0 02 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002532812E530, 16 bytes long.
 Data: <                > 10 04 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002532812D720, 16 bytes long.
 Data: <p               > 70 04 FA 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002532812D860, 16 bytes long.
 Data: <                > 18 C0 F8 86 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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