Task 38644365

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
03:32:29 (5704): wrapper (7.9.26016): starting
03:32:29 (5704): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A18_A04_0.pdb
QB_A18_A04_0.xml
QB_A18_A04.inpcrd
QB_A18_A04_input.yaml
QB_A18_A04.pdb
QB_A18_A04.prmtop
QB_A18_A04_sys.xml
run.bat
run.sh
03:32:31 (5704): Library/usr/bin/tar.exe exited; CPU time 0.000000
03:32:31 (5704): 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:\BOINCdata\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:\BOINCdata\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.
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:\BOINCdata\slots\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\BOINCdata\slots\1\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\BOINCdata\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
03:33:31 (5704): C:/Windows/system32/cmd.exe exited; CPU time 42.968750
03:33:31 (5704): app exit status: 0x16
03:33:31 (5704): called boinc_finish(195)
0 bytes in 0 Free Blocks.
536 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: 596595 bytes.
Dumping objects ->
{3835229} normal block at 0x0000024B885C73C0, 48 bytes long.
 Data: <PATH=C:\BOINCdat> 50 41 54 48 3D 43 3A 5C 42 4F 49 4E 43 64 61 74 
{3835218} normal block at 0x0000024B8A253BC0, 32 bytes long.
 Data: <HOME=C:\BOINCdat> 48 4F 4D 45 3D 43 3A 5C 42 4F 49 4E 43 64 61 74 
{3835207} normal block at 0x0000024B8A254640, 32 bytes long.
 Data: <TMP=C:\BOINCdata> 54 4D 50 3D 43 3A 5C 42 4F 49 4E 43 64 61 74 61 
{3835196} normal block at 0x0000024B8A253FE0, 32 bytes long.
 Data: <TEMP=C:\BOINCdat> 54 45 4D 50 3D 43 3A 5C 42 4F 49 4E 43 64 61 74 
{3835185} normal block at 0x0000024B8A2538C0, 32 bytes long.
 Data: <TMPDIR=C:\BOINCd> 54 4D 50 44 49 52 3D 43 3A 5C 42 4F 49 4E 43 64 
{3835154} normal block at 0x0000024B885C6780, 48 bytes long.
 Data: <PATH=C:\BOINCdat> 50 41 54 48 3D 43 3A 5C 42 4F 49 4E 43 64 61 74 
{3835143} normal block at 0x0000024B8A1B1ED0, 180 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) : {3835140} normal block at 0x0000024B885980A0, 8 bytes long.
 Data: <  P K   > 00 00 50 88 4B 02 00 00 
{3834543} normal block at 0x0000024B8A1B1A20, 180 bytes long.
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{3833947} normal block at 0x0000024B88597740, 8 bytes long.
 Data: <@&#170;X K   > 40 AA 58 88 4B 02 00 00 
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x0000024B885A21C0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000024B8858DC60, 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 0x0000024B885A32F0, 16 bytes long.
 Data: <&#248;CZ K           > F8 43 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000024B885A3390, 16 bytes long.
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{287} normal block at 0x0000024B8859E2D0, 32 bytes long.
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{286} normal block at 0x0000024B885A3D40, 16 bytes long.
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{285} normal block at 0x0000024B885A3BB0, 16 bytes long.
 Data: < CZ K           > 80 43 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000024B885A32A0, 16 bytes long.
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{283} normal block at 0x0000024B885A3C50, 16 bytes long.
 Data: <0CZ K           > 30 43 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000024B8859C310, 48 bytes long.
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{281} normal block at 0x0000024B885A3570, 16 bytes long.
 Data: <H&#208;Y K           > 48 D0 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000024B8859EAB0, 32 bytes long.
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{279} normal block at 0x0000024B885A3B60, 16 bytes long.
 Data: < &#208;Y K           > 20 D0 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000024B885A3F20, 16 bytes long.
 Data: <&#248;&#207;Y K           > F8 CF 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000024B885A3ED0, 16 bytes long.
 Data: <&#208;&#207;Y K           > D0 CF 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000024B885A3E80, 16 bytes long.
 Data: <&#168;&#207;Y K           > A8 CF 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000024B885A3250, 16 bytes long.
 Data: < &#207;Y K           > 80 CF 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000024B885A3A20, 16 bytes long.
 Data: <X&#207;Y K           > 58 CF 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000024B8859EA50, 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 0x0000024B885A3AC0, 16 bytes long.
 Data: <0&#207;Y K           > 30 CF 59 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000024B8859CF30, 320 bytes long.
 Data: <&#192;:Z K   P&#234;Y K   > C0 3A 5A 88 4B 02 00 00 50 EA 59 88 4B 02 00 00 
{269} normal block at 0x0000024B885A37F0, 16 bytes long.
 Data: < CZ K           > 10 43 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000024B885A3E30, 16 bytes long.
 Data: <&#232;BZ K           > E8 42 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000024B8859EF30, 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 0x0000024B885A3B10, 16 bytes long.
 Data: <&#192;BZ K           > C0 42 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000024B8859E990, 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 0x0000024B885A3D90, 16 bytes long.
 Data: < BZ K           > 08 42 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000024B885A39D0, 16 bytes long.
 Data: <&#224;AZ K           > E0 41 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000024B885A3FC0, 16 bytes long.
 Data: <&#184;AZ K           > B8 41 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000024B885A4060, 16 bytes long.
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{260} normal block at 0x0000024B885A3660, 16 bytes long.
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{259} normal block at 0x0000024B885A3750, 16 bytes long.
 Data: <@AZ K           > 40 41 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000024B885A3110, 16 bytes long.
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{256} normal block at 0x0000024B8859C2A0, 40 bytes long.
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{255} normal block at 0x0000024B885A3980, 16 bytes long.
 Data: < AZ K           > 20 41 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x0000024B885A3200, 16 bytes long.
 Data: <&#248;@Z K           > F8 40 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x0000024B8859E8D0, 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 0x0000024B885A3840, 16 bytes long.
 Data: <&#208;@Z K           > D0 40 5A 88 4B 02 00 00 00 00 00 00 00 00 00 00 
{251} normal block at 0x0000024B885A40D0, 992 bytes long.
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{87} normal block at 0x0000024B8859E330, 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 0x0000024B88597BA0, 16 bytes long.
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{85} normal block at 0x0000024B8859C460, 40 bytes long.
 Data: <&#160;{Y K   0&#227;Y K   > A0 7B 59 88 4B 02 00 00 30 E3 59 88 4B 02 00 00 
{64} normal block at 0x0000024B885976A0, 16 bytes long.
 Data: < &#234;W&#221;&#247;           > 80 EA 57 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000024B88597830, 16 bytes long.
 Data: <@&#233;W&#221;&#247;           > 40 E9 57 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000024B885971F0, 16 bytes long.
 Data: <&#248;WT&#221;&#247;           > F8 57 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000024B885977E0, 16 bytes long.
 Data: <&#216;WT&#221;&#247;           > D8 57 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000024B88598000, 16 bytes long.
 Data: <P T&#221;&#247;           > 50 04 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000024B88597CE0, 16 bytes long.
 Data: <0 T&#221;&#247;           > 30 04 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000024B88597A10, 16 bytes long.
 Data: <&#224; T&#221;&#247;           > E0 02 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x0000024B88597470, 16 bytes long.
 Data: <  T&#221;&#247;           > 10 04 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x0000024B88597FB0, 16 bytes long.
 Data: <p T&#221;&#247;           > 70 04 54 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x0000024B88597DD0, 16 bytes long.
 Data: < &#192;R&#221;&#247;           > 18 C0 52 DD F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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