Task 38644204

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>
09:35:28 (11232): wrapper (7.9.26016): starting
09:35:28 (11232): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A04_A02_0.pdb
QB_A04_A02_0.xml
QB_A04_A02.inpcrd
QB_A04_A02_input.yaml
QB_A04_A02.pdb
QB_A04_A02.prmtop
QB_A04_A02_sys.xml
run.bat
run.sh
09:35:31 (11232): Library/usr/bin/tar.exe exited; CPU time 0.000000
09:35:31 (11232): 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\1\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\1\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) : {3835105} normal block at 0x000002526CA771C0, 8 bytes long.
 Data: <  RnR   > 00 00 52 6E 52 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833962} normal block at 0x000002526E702150, 1080 bytes long.
 Data: < &              > C0 26 00 00 CD CD CD CD D8 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x000002526CA81760, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
11:48:01 (7000): wrapper (7.9.26016): starting
11:48:01 (7000): 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\1\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\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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\1\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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
18:00:33 (7000): C:/Windows/system32/cmd.exe exited; CPU time 21572.406250
18:00:33 (7000): app exit status: 0x16
18:00:33 (7000): 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: 242577436 bytes.
Dumping objects ->
{1537} normal block at 0x000001B949E4F6E0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1526} normal block at 0x000001B949E4F600, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1515} normal block at 0x000001B949E4F590, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1504} normal block at 0x000001B949E4F050, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1493} normal block at 0x000001B949E4F280, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1462} normal block at 0x000001B949E36C60, 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) : {1449} normal block at 0x000001B949E554A0, 8 bytes long.
 Data: <   I    > 00 00 DE 49 B9 01 00 00 
{307} normal block at 0x000001B949E55040, 8 bytes long.
 Data: < \ I    > F0 5C E5 49 B9 01 00 00 
{298} normal block at 0x000001B949E3F060, 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 0x000001B949E54960, 16 bytes long.
 Data: < [ I            > F8 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x000001B949E55450, 16 bytes long.
 Data: < [ I            > D0 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x000001B949E4DBA0, 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 0x000001B949E554F0, 16 bytes long.
 Data: < [ I            > A8 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001B949E557C0, 16 bytes long.
 Data: < [ I            > 80 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001B949E55770, 16 bytes long.
 Data: <X[ I            > 58 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001B949E54B40, 16 bytes long.
 Data: <0[ I            > 30 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001B949E4F210, 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 0x000001B949E550E0, 16 bytes long.
 Data: < G I            > A8 47 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001B949E4D7E0, 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 0x000001B949E54D70, 16 bytes long.
 Data: < G I            > 80 47 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001B949E54CD0, 16 bytes long.
 Data: <XG I            > 58 47 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001B949E54C30, 16 bytes long.
 Data: <0G I            > 30 47 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000001B949E54FF0, 16 bytes long.
 Data: < G I            > 08 47 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001B949E55860, 16 bytes long.
 Data: < F I            > E0 46 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001B949E54E60, 16 bytes long.
 Data: < F I            > B8 46 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001B949E4D4E0, 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 0x000001B949E55400, 16 bytes long.
 Data: < F I            > 90 46 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001B949E54690, 320 bytes long.
 Data: < T I       I    > 00 54 E5 49 B9 01 00 00 E0 D4 E4 49 B9 01 00 00 
{277} normal block at 0x000001B949E55630, 16 bytes long.
 Data: < [ I            > 10 5B E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001B949E54F00, 16 bytes long.
 Data: < Z I            > E8 5A E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001B949E4E3E0, 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 0x000001B949E553B0, 16 bytes long.
 Data: < Z I            > C0 5A E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001B949E4E0E0, 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 0x000001B949E54A50, 16 bytes long.
 Data: < Z I            > 08 5A E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001B949E54AF0, 16 bytes long.
 Data: < Y I            > E0 59 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001B949E55360, 16 bytes long.
 Data: < Y I            > B8 59 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001B949E555E0, 16 bytes long.
 Data: < Y I            > 90 59 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001B949E549B0, 16 bytes long.
 Data: <hY I            > 68 59 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001B949E552C0, 16 bytes long.
 Data: <@Y I            > 40 59 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001B949E55220, 16 bytes long.
 Data: <   I            > 20 F5 E4 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001B949E4F520, 40 bytes long.
 Data: < R I    `l I    > 20 52 E5 49 B9 01 00 00 60 6C E3 49 B9 01 00 00 
{263} normal block at 0x000001B949E55590, 16 bytes long.
 Data: < Y I            > 20 59 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001B949E55720, 16 bytes long.
 Data: < X I            > F8 58 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001B949E4E020, 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 0x000001B949E556D0, 16 bytes long.
 Data: < X I            > D0 58 E5 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001B949E558D0, 992 bytes long.
 Data: < V I       I    > D0 56 E5 49 B9 01 00 00 20 E0 E4 49 B9 01 00 00 
{95} normal block at 0x000001B949E4DA20, 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 0x000001B949E48B60, 16 bytes long.
 Data: <@  I            > 40 F4 E4 49 B9 01 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x000001B949E4F440, 40 bytes long.
 Data: <`  I       I    > 60 8B E4 49 B9 01 00 00 20 DA E4 49 B9 01 00 00 
{72} normal block at 0x000001B949E488E0, 16 bytes long.
 Data: <  8N            > 80 EA 38 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000001B949E49290, 16 bytes long.
 Data: <@ 8N            > 40 E9 38 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000001B949E49060, 16 bytes long.
 Data: < W5N            > F8 57 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000001B949E493D0, 16 bytes long.
 Data: < W5N            > D8 57 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001B949E48840, 16 bytes long.
 Data: <P 5N            > 50 04 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001B949E487F0, 16 bytes long.
 Data: <0 5N            > 30 04 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001B949E48DE0, 16 bytes long.
 Data: <  5N            > E0 02 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001B949E49560, 16 bytes long.
 Data: <  5N            > 10 04 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001B949E48E30, 16 bytes long.
 Data: <p 5N            > 70 04 35 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001B949E48A70, 16 bytes long.
 Data: <  3N            > 18 C0 33 4E F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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