Task 38644255

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>
11:02:27 (11212): wrapper (7.9.26016): starting
11:02:27 (11212): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A09_A08_0.pdb
QB_A09_A08_0.xml
QB_A09_A08.inpcrd
QB_A09_A08_input.yaml
QB_A09_A08.pdb
QB_A09_A08.prmtop
QB_A09_A08_sys.xml
run.bat
run.sh
11:02:36 (11212): Library/usr/bin/tar.exe exited; CPU time 0.000000
11:02:36 (11212): 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.
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
11:23:45 (11212): C:/Windows/system32/cmd.exe exited; CPU time 1200.515625
11:23:45 (11212): app exit status: 0x16
11:23:45 (11212): 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: 16135927 bytes.
Dumping objects ->
{3835180} normal block at 0x00000205A3030C00, 48 bytes long.
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{3835169} normal block at 0x00000205A30314C0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835158} normal block at 0x00000205A3031840, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{3835147} normal block at 0x00000205A3031760, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{3835136} normal block at 0x00000205A3030CE0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{3835105} normal block at 0x00000205A3145D90, 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) : {3835092} normal block at 0x00000205A16263E0, 8 bytes long.
 Data: <  &#240;     > 00 00 F0 A2 05 02 00 00 
{3833947} normal block at 0x00000205A16264D0, 8 bytes long.
 Data: < &#146;a     > 00 92 61 A1 05 02 00 00 
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x00000205A16332B0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000205A161D050, 80 bytes long.
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{289} normal block at 0x00000205A16342F0, 16 bytes long.
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{288} normal block at 0x00000205A16349D0, 16 bytes long.
 Data: <&#192;Tc             > C0 54 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000205A162C370, 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 0x00000205A16348E0, 16 bytes long.
 Data: < Tc             > 98 54 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000205A1634FC0, 16 bytes long.
 Data: <pTc             > 70 54 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000205A16342A0, 16 bytes long.
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{283} normal block at 0x00000205A1634E80, 16 bytes long.
 Data: < Tc             > 20 54 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000205A162B1D0, 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 0x00000205A1634250, 16 bytes long.
 Data: <&#216;[a             > D8 5B 61 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000205A162C070, 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 0x00000205A1634DE0, 16 bytes long.
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{277} normal block at 0x00000205A1634980, 16 bytes long.
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{276} normal block at 0x00000205A1634CF0, 16 bytes long.
 Data: <`[a             > 60 5B 61 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000205A1634CA0, 16 bytes long.
 Data: <8[a             > 38 5B 61 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000205A1634610, 16 bytes long.
 Data: < [a             > 10 5B 61 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x00000205A1634480, 16 bytes long.
 Data: <&#232;Za             > E8 5A 61 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000205A162C3D0, 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 0x00000205A1634200, 16 bytes long.
 Data: <&#192;Za             > C0 5A 61 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000205A1615AC0, 320 bytes long.
 Data: < Bc     &#208;&#195;b     > 00 42 63 A1 05 02 00 00 D0 C3 62 A1 05 02 00 00 
{269} normal block at 0x00000205A16345C0, 16 bytes long.
 Data: < Tc             > 00 54 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000205A1634340, 16 bytes long.
 Data: <&#216;Sc             > D8 53 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000205A162CA30, 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 0x00000205A1634D40, 16 bytes long.
 Data: <&#176;Sc             > B0 53 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x00000205A162CDF0, 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 0x00000205A1634AC0, 16 bytes long.
 Data: <&#248;Rc             > F8 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000205A16344D0, 16 bytes long.
 Data: <&#208;Rc             > D0 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x00000205A1634D90, 16 bytes long.
 Data: <&#168;Rc             > A8 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000205A1634430, 16 bytes long.
 Data: < Rc             > 80 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000205A1635010, 16 bytes long.
 Data: <XRc             > 58 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x00000205A1634C50, 16 bytes long.
 Data: <0Rc             > 30 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x00000205A1634C00, 16 bytes long.
 Data: <&#240;&#176;b             > F0 B0 62 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x00000205A162B0F0, 40 bytes long.
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{255} normal block at 0x00000205A1635150, 16 bytes long.
 Data: < Rc             > 10 52 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x00000205A16343E0, 16 bytes long.
 Data: <&#232;Qc             > E8 51 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x00000205A162C850, 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 0x00000205A1634B10, 16 bytes long.
 Data: <&#192;Qc             > C0 51 63 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{251} normal block at 0x00000205A16351C0, 992 bytes long.
 Data: < Kc     P&#200;b     > 10 4B 63 A1 05 02 00 00 50 C8 62 A1 05 02 00 00 
{87} normal block at 0x00000205A162CAF0, 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 0x00000205A16260C0, 16 bytes long.
 Data: < &#176;b             > 80 B0 62 A1 05 02 00 00 00 00 00 00 00 00 00 00 
{85} normal block at 0x00000205A162B080, 40 bytes long.
 Data: <&#192;`b     &#240;&#202;b     > C0 60 62 A1 05 02 00 00 F0 CA 62 A1 05 02 00 00 
{64} normal block at 0x00000205A1626B60, 16 bytes long.
 Data: < &#234;&#146;&#211;&#247;           > 80 EA 92 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000205A16261B0, 16 bytes long.
 Data: <@&#233;&#146;&#211;&#247;           > 40 E9 92 D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000205A1625E40, 16 bytes long.
 Data: <&#248;W&#143;&#211;&#247;           > F8 57 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x00000205A1626390, 16 bytes long.
 Data: <&#216;W&#143;&#211;&#247;           > D8 57 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000205A1626160, 16 bytes long.
 Data: <P &#143;&#211;&#247;           > 50 04 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x00000205A1626AC0, 16 bytes long.
 Data: <0 &#143;&#211;&#247;           > 30 04 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x00000205A1626A70, 16 bytes long.
 Data: <&#224; &#143;&#211;&#247;           > E0 02 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x00000205A16262F0, 16 bytes long.
 Data: <  &#143;&#211;&#247;           > 10 04 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x00000205A1626250, 16 bytes long.
 Data: <p &#143;&#211;&#247;           > 70 04 8F D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x00000205A1626D40, 16 bytes long.
 Data: < &#192;&#141;&#211;&#247;           > 18 C0 8D D3 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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