Task 38642678

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
System operacyjny nie mo�e uruchomi� (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
20:16:26 (19708): wrapper (7.9.26016): starting
20:16:26 (19708): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A17_A08_0.pdb
QB_A17_A08_0.xml
QB_A17_A08.inpcrd
QB_A17_A08_input.yaml
QB_A17_A08.pdb
QB_A17_A08.prmtop
QB_A17_A08_sys.xml
run.bat
run.sh
20:16:28 (19708): Library/usr/bin/tar.exe exited; CPU time 0.000000
20:16:28 (19708): 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.
10:16:08 (27760): wrapper (7.9.26016): starting
10:16:08 (27760): 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.
10:21:01 (10072): wrapper (7.9.26016): starting
10:21:01 (10072): 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) : {1525} normal block at 0x0000026B59A35CC0, 8 bytes long.
 Data: <   Yk   > 00 00 E9 59 6B 02 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x0000026B59A36D80, 1080 bytes long.
 Data: < '      p       > E8 27 00 00 CD CD CD CD 70 00 00 00 00 00 00 00 
Object dump complete.
18:32:35 (23380): wrapper (7.9.26016): starting
18:32:35 (23380): 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.
18:28:48 (6604): wrapper (7.9.26016): starting
18:28:48 (6604): 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
21:01:25 (6604): C:/Windows/system32/cmd.exe exited; CPU time 7268.406250
21:01:25 (6604): app exit status: 0x16
21:01:25 (6604): 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: 146694708 bytes.
Dumping objects ->
{1615} normal block at 0x000002A996935120, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1604} normal block at 0x000002A9969353C0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1593} normal block at 0x000002A9969354A0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1582} normal block at 0x000002A996935270, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1571} normal block at 0x000002A996935430, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1540} normal block at 0x000002A99691E9C0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1529} normal block at 0x000002A99691BA30, 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) : {1525} normal block at 0x000002A996936620, 8 bytes long.
 Data: <        > 00 00 DD 96 A9 02 00 00 
{906} normal block at 0x000002A99691D360, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{304} normal block at 0x000002A996936440, 8 bytes long.
 Data: < p      > A0 70 93 96 A9 02 00 00 
{295} normal block at 0x000002A996927A70, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{294} normal block at 0x000002A996936210, 16 bytes long.
 Data: < o              > A8 6F 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000002A996936BC0, 16 bytes long.
 Data: < o              > 80 6F 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000002A99692F440, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{291} normal block at 0x000002A996936B70, 16 bytes long.
 Data: <Xo              > 58 6F 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000002A996935CC0, 16 bytes long.
 Data: <0o              > 30 6F 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000002A9969360D0, 16 bytes long.
 Data: < o              > 08 6F 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000002A9969363F0, 16 bytes long.
 Data: < n              > E0 6E 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000002A996935350, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{286} normal block at 0x000002A996936710, 16 bytes long.
 Data: <X               > 58 FE 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000002A99692FE00, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{284} normal block at 0x000002A996936B20, 16 bytes long.
 Data: <0               > 30 FE 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000002A996936530, 16 bytes long.
 Data: <                > 08 FE 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000002A996936940, 16 bytes long.
 Data: <                > E0 FD 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000002A9969364E0, 16 bytes long.
 Data: <                > B8 FD 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000002A996936080, 16 bytes long.
 Data: <                > 90 FD 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000002A9969366C0, 16 bytes long.
 Data: <h               > 68 FD 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000002A99692F920, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{276} normal block at 0x000002A996936670, 16 bytes long.
 Data: <@               > 40 FD 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000002A99691FD40, 320 bytes long.
 Data: <pf              > 70 66 93 96 A9 02 00 00 20 F9 92 96 A9 02 00 00 
{274} normal block at 0x000002A9969367B0, 16 bytes long.
 Data: < n              > C0 6E 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000002A9969365D0, 16 bytes long.
 Data: < n              > 98 6E 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000002A99692FDA0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{271} normal block at 0x000002A996936030, 16 bytes long.
 Data: <pn              > 70 6E 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000002A99692F7A0, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{269} normal block at 0x000002A996936760, 16 bytes long.
 Data: < m              > B8 6D 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000002A996936A80, 16 bytes long.
 Data: < m              > 90 6D 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000002A996935D10, 16 bytes long.
 Data: <hm              > 68 6D 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000002A996936A30, 16 bytes long.
 Data: <@m              > 40 6D 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000002A996936580, 16 bytes long.
 Data: < m              > 18 6D 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002A996936850, 16 bytes long.
 Data: < l              > F0 6C 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000002A9969361C0, 16 bytes long.
 Data: < U              > 80 55 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000002A996935580, 40 bytes long.
 Data: < a              > C0 61 93 96 A9 02 00 00 C0 E9 91 96 A9 02 00 00 
{260} normal block at 0x000002A9969368F0, 16 bytes long.
 Data: < l              > D0 6C 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000002A9969369E0, 16 bytes long.
 Data: < l              > A8 6C 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000002A996930220, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{257} normal block at 0x000002A996936120, 16 bytes long.
 Data: < l              > 80 6C 93 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000002A996936C80, 992 bytes long.
 Data: < a              > 20 61 93 96 A9 02 00 00 20 02 93 96 A9 02 00 00 
{92} normal block at 0x000002A99692F5C0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{91} normal block at 0x000002A99692D5F0, 16 bytes long.
 Data: <                > 00 D9 91 96 A9 02 00 00 00 00 00 00 00 00 00 00 
{90} normal block at 0x000002A99691D900, 40 bytes long.
 Data: <                > F0 D5 92 96 A9 02 00 00 C0 F5 92 96 A9 02 00 00 
{69} normal block at 0x000002A99692DBE0, 16 bytes long.
 Data: <   L            > 80 EA 18 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002A99692DEB0, 16 bytes long.
 Data: <@  L            > 40 E9 18 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002A99692D960, 16 bytes long.
 Data: < W L            > F8 57 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002A99692D3C0, 16 bytes long.
 Data: < W L            > D8 57 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000002A99692D550, 16 bytes long.
 Data: <P  L            > 50 04 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002A99692D500, 16 bytes long.
 Data: <0  L            > 30 04 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002A99692DB40, 16 bytes long.
 Data: <   L            > E0 02 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002A99692DE10, 16 bytes long.
 Data: <   L            > 10 04 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002A99692DF00, 16 bytes long.
 Data: <p  L            > 70 04 15 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002A99692DDC0, 16 bytes long.
 Data: <   L            > 18 C0 13 4C F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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