Task 38642366

Stderr output

<core_client_version>8.2.11</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
11:58:11 (12500): wrapper (7.9.26016): starting
11:58:11 (12500): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A26_A08_0.pdb
QB_A26_A08_0.xml
QB_A26_A08.inpcrd
QB_A26_A08_input.yaml
QB_A26_A08.pdb
QB_A26_A08.prmtop
QB_A26_A08_sys.xml
run.bat
run.sh
11:58:14 (12500): Library/usr/bin/tar.exe exited; CPU time 0.000000
11:58:14 (12500): 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\6\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\6\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) : {3835221} normal block at 0x000001BDA5BE7B50, 8 bytes long.
 Data: <        > 00 00 BC A5 BD 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833962} normal block at 0x000001BDA5BD9F70, 1080 bytes long.
 Data: < &      |       > EC 26 00 00 CD CD CD CD 7C 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x000001BDA5BF1B10, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
22:03:31 (14872): wrapper (7.9.26016): starting
22:03:31 (14872): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
07:03:18 (1924): wrapper (7.9.26016): starting
07:03:18 (1924): 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\6\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1565} normal block at 0x000002A4FF424470, 8 bytes long.
 Data: <  ?     > 00 00 3F FF A4 02 00 00 
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002A4FF425FE0, 1080 bytes long.
 Data: <        D       > E8 09 00 00 CD CD CD CD 44 01 00 00 00 00 00 00 
Object dump complete.
12:16:05 (20928): wrapper (7.9.26016): starting
12:16:05 (20928): 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\6\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\6\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\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\6\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\6\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
16:06:13 (20928): C:/Windows/system32/cmd.exe exited; CPU time 12302.734375
16:06:13 (20928): app exit status: 0x16
16:06:13 (20928): called boinc_finish(195)
0 bytes in 0 Free Blocks.
460 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: 223364664 bytes.
Dumping objects ->
{1654} normal block at 0x0000020A8936CE70, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1643} normal block at 0x0000020A8936CE00, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1632} normal block at 0x0000020A8936CD90, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1621} normal block at 0x0000020A8936D180, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1610} normal block at 0x0000020A8936D110, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1579} normal block at 0x0000020A89357060, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1568} normal block at 0x0000020A8936EE80, 102 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) : {1565} normal block at 0x0000020A89372E70, 8 bytes long.
 Data: <  2     > 00 00 32 89 0A 02 00 00 
{927} normal block at 0x0000020A8935C7F0, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{307} normal block at 0x0000020A89372BA0, 8 bytes long.
 Data: <PR7     > 50 52 37 89 0A 02 00 00 
{298} normal block at 0x0000020A89356950, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{297} normal block at 0x0000020A89372E20, 16 bytes long.
 Data: <XQ7             > 58 51 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000020A89373460, 16 bytes long.
 Data: <0Q7             > 30 51 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000020A8936F260, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{294} normal block at 0x0000020A893731E0, 16 bytes long.
 Data: < Q7             > 08 51 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000020A89373410, 16 bytes long.
 Data: < P7             > E0 50 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000020A893735F0, 16 bytes long.
 Data: < P7             > B8 50 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000020A89372D80, 16 bytes long.
 Data: < P7             > 90 50 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000020A8936D420, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{289} normal block at 0x0000020A89372D30, 16 bytes long.
 Data: < h5             > E8 68 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000020A8936F2C0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{287} normal block at 0x0000020A89373050, 16 bytes long.
 Data: < h5             > C0 68 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000020A89372CE0, 16 bytes long.
 Data: < h5             > 98 68 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000020A893739B0, 16 bytes long.
 Data: <ph5             > 70 68 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000020A89373140, 16 bytes long.
 Data: <Hh5             > 48 68 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000020A89373370, 16 bytes long.
 Data: < h5             > 20 68 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000020A89373960, 16 bytes long.
 Data: < g5             > F8 67 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000020A8936F620, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{279} normal block at 0x0000020A89373320, 16 bytes long.
 Data: < g5             > D0 67 35 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000020A893567D0, 320 bytes long.
 Data: < 37       6     > 20 33 37 89 0A 02 00 00 20 F6 36 89 0A 02 00 00 
{277} normal block at 0x0000020A89373910, 16 bytes long.
 Data: <pP7             > 70 50 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000020A89373000, 16 bytes long.
 Data: <HP7             > 48 50 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000020A8936FE60, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{274} normal block at 0x0000020A89373780, 16 bytes long.
 Data: < P7             > 20 50 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000020A8936F1A0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{272} normal block at 0x0000020A89372C90, 16 bytes long.
 Data: <hO7             > 68 4F 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000020A89372B50, 16 bytes long.
 Data: <@O7             > 40 4F 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000020A893735A0, 16 bytes long.
 Data: < O7             > 18 4F 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000020A893730F0, 16 bytes long.
 Data: < N7             > F0 4E 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000020A89373550, 16 bytes long.
 Data: < N7             > C8 4E 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000020A89373730, 16 bytes long.
 Data: < N7             > A0 4E 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000020A89372F60, 16 bytes long.
 Data: <  6             > B0 D3 36 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000020A8936D3B0, 40 bytes long.
 Data: <`/7     `p5     > 60 2F 37 89 0A 02 00 00 60 70 35 89 0A 02 00 00 
{263} normal block at 0x0000020A89372A60, 16 bytes long.
 Data: < N7             > 80 4E 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000020A89372DD0, 16 bytes long.
 Data: <XN7             > 58 4E 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000020A8936FCE0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{260} normal block at 0x0000020A89372C40, 16 bytes long.
 Data: <0N7             > 30 4E 37 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000020A89374E30, 992 bytes long.
 Data: <@,7       6     > 40 2C 37 89 0A 02 00 00 E0 FC 36 89 0A 02 00 00 
{95} normal block at 0x0000020A8936F4A0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{94} normal block at 0x0000020A89367960, 16 bytes long.
 Data: <@ 6             > 40 D3 36 89 0A 02 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x0000020A8936D340, 40 bytes long.
 Data: <`y6       6     > 60 79 36 89 0A 02 00 00 A0 F4 36 89 0A 02 00 00 
{72} normal block at 0x0000020A893683B0, 16 bytes long.
 Data: <   .            > 80 EA 19 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x0000020A89368360, 16 bytes long.
 Data: <@  .            > 40 E9 19 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x0000020A89367BE0, 16 bytes long.
 Data: < W .            > F8 57 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000020A89368450, 16 bytes long.
 Data: < W .            > D8 57 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000020A89367870, 16 bytes long.
 Data: <P  .            > 50 04 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000020A89368590, 16 bytes long.
 Data: <0  .            > 30 04 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000020A89367730, 16 bytes long.
 Data: <   .            > E0 02 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000020A89367820, 16 bytes long.
 Data: <   .            > 10 04 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000020A89368310, 16 bytes long.
 Data: <p  .            > 70 04 16 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000020A893676E0, 16 bytes long.
 Data: <   .            > 18 C0 14 2E F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra