Task 38644759

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
System operacyjny nie moze uruchomic (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
14:43:51 (4916): wrapper (7.9.26016): starting
14:43:51 (4916): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A10_0.pdb
QB_A20_A10_0.xml
QB_A20_A10.inpcrd
QB_A20_A10_input.yaml
QB_A20_A10.pdb
QB_A20_A10.prmtop
QB_A20_A10_sys.xml
run.bat
run.sh
14:43:54 (4916): Library/usr/bin/tar.exe exited; CPU time 0.000000
14:43:54 (4916): 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\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 'C:\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) : {3835092} normal block at 0x0000021C4D5C53B0, 8 bytes long.
 Data: <   N    > 00 00 EA 4E 1C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833946} normal block at 0x0000021C4F0F69C0, 1080 bytes long.
 Data: <                > 98 01 00 00 CD CD CD CD D8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x0000021C4D5D07E0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
06:08:39 (15836): wrapper (7.9.26016): starting
06:08:39 (15836): 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\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 "C:\ProgramData\BOINC\slots\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\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 "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\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
07:13:58 (15836): C:/Windows/system32/cmd.exe exited; CPU time 3767.953125
07:13:58 (15836): app exit status: 0x16
07:13:58 (15836): 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: 50363074 bytes.
Dumping objects ->
{1532} normal block at 0x0000021937BBA7E0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1521} normal block at 0x0000021937BBA150, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1510} normal block at 0x0000021937BBA770, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1499} normal block at 0x0000021937BBA1C0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1488} normal block at 0x0000021937BBA690, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1457} normal block at 0x0000021937BA62F0, 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) : {1444} normal block at 0x0000021937BC2020, 8 bytes long.
 Data: <   7    > 00 00 B6 37 19 02 00 00 
{299} normal block at 0x0000021937BC1AD0, 8 bytes long.
 Data: < . 7    > 80 2E BC 37 19 02 00 00 
{290} normal block at 0x0000021937BA5C40, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{289} normal block at 0x0000021937BC27A0, 16 bytes long.
 Data: < - 7            > 88 2D BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000021937BC2750, 16 bytes long.
 Data: <`- 7            > 60 2D BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000021937BBBE60, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{286} normal block at 0x0000021937BC1F30, 16 bytes long.
 Data: <8- 7            > 38 2D BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000021937BC2200, 16 bytes long.
 Data: < - 7            > 10 2D BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000021937BC1E40, 16 bytes long.
 Data: < , 7            > E8 2C BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000021937BC24D0, 16 bytes long.
 Data: < , 7            > C0 2C BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000021937BBA380, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{281} normal block at 0x0000021937BC1DF0, 16 bytes long.
 Data: < [ 7            > D8 5B BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000021937BBC220, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{279} normal block at 0x0000021937BC1DA0, 16 bytes long.
 Data: < [ 7            > B0 5B BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000021937BC1CB0, 16 bytes long.
 Data: < [ 7            > 88 5B BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000021937BC2430, 16 bytes long.
 Data: <`[ 7            > 60 5B BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000021937BC2700, 16 bytes long.
 Data: <8[ 7            > 38 5B BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000021937BC23E0, 16 bytes long.
 Data: < [ 7            > 10 5B BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000021937BC2340, 16 bytes long.
 Data: < Z 7            > E8 5A BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000021937BBB920, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{271} normal block at 0x0000021937BC2160, 16 bytes long.
 Data: < Z 7            > C0 5A BA 37 19 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000021937BA5AC0, 320 bytes long.
 Data: <`! 7       7    > 60 21 BC 37 19 02 00 00 20 B9 BB 37 19 02 00 00 
{269} normal block at 0x0000021937BC1FD0, 16 bytes long.
 Data: < , 7            > A0 2C BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000021937BC2070, 16 bytes long.
 Data: <x, 7            > 78 2C BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000021937BBB500, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{266} normal block at 0x0000021937BC1990, 16 bytes long.
 Data: <P, 7            > 50 2C BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000021937BBBF80, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{264} normal block at 0x0000021937BC1B70, 16 bytes long.
 Data: < + 7            > 98 2B BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000021937BC26B0, 16 bytes long.
 Data: <p+ 7            > 70 2B BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000021937BC1C60, 16 bytes long.
 Data: <H+ 7            > 48 2B BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000021937BC1C10, 16 bytes long.
 Data: < + 7            > 20 2B BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000021937BC1F80, 16 bytes long.
 Data: < * 7            > F8 2A BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000021937BC2390, 16 bytes long.
 Data: < * 7            > D0 2A BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000021937BC2610, 16 bytes long.
 Data: <   7            > D0 A4 BB 37 19 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000021937BBA4D0, 40 bytes long.
 Data: < & 7     b 7    > 10 26 BC 37 19 02 00 00 F0 62 BA 37 19 02 00 00 
{255} normal block at 0x0000021937BC25C0, 16 bytes long.
 Data: < * 7            > B0 2A BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x0000021937BC1EE0, 16 bytes long.
 Data: < * 7            > 88 2A BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x0000021937BBBF20, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{252} normal block at 0x0000021937BC2520, 16 bytes long.
 Data: <`* 7            > 60 2A BC 37 19 02 00 00 00 00 00 00 00 00 00 00 
{251} normal block at 0x0000021937BC2A60, 992 bytes long.
 Data: < % 7       7    > 20 25 BC 37 19 02 00 00 20 BF BB 37 19 02 00 00 
{87} normal block at 0x0000021937BBBE00, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{86} normal block at 0x0000021937BB5730, 16 bytes long.
 Data: <   7            > 20 A6 BB 37 19 02 00 00 00 00 00 00 00 00 00 00 
{85} normal block at 0x0000021937BBA620, 40 bytes long.
 Data: <0W 7       7    > 30 57 BB 37 19 02 00 00 00 BE BB 37 19 02 00 00 
{64} normal block at 0x0000021937BB5E60, 16 bytes long.
 Data: <   u            > 80 EA 09 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000021937BB5CD0, 16 bytes long.
 Data: <@  u            > 40 E9 09 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000021937BB58C0, 16 bytes long.
 Data: < W u            > F8 57 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000021937BB5640, 16 bytes long.
 Data: < W u            > D8 57 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000021937BB5410, 16 bytes long.
 Data: <P  u            > 50 04 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000021937BB5870, 16 bytes long.
 Data: <0  u            > 30 04 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000021937BB5C30, 16 bytes long.
 Data: <   u            > E0 02 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x0000021937BB53C0, 16 bytes long.
 Data: <   u            > 10 04 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x0000021937BB5A50, 16 bytes long.
 Data: <p  u            > 70 04 06 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x0000021937BB6180, 16 bytes long.
 Data: <   u            > 18 C0 04 75 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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