Task 38670404

Stderr output

<core_client_version>8.2.11</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
07:34:20 (7908): wrapper (7.9.26016): starting
07:34:20 (7908): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A34_A12_0.pdb
QB_A34_A12_0.xml
QB_A34_A12_input.yaml
QB_A34_A12.pdb
QB_A34_A12.prmtop
QB_A34_A12_sys.xml
run.bat
run.sh
07:34:24 (7908): Library/usr/bin/tar.exe exited; CPU time 0.000000
07:34:24 (7908): 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 'D:\boinc\data\slots\5\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 'D:\boinc\data\slots\5\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.
08:39:17 (5988): wrapper (7.9.26016): starting
08:39:17 (5988): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\boinc\data\slots\5\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\openmm_async_re.py", line 432, in __init__
    replica = OMMReplicaATM(i, self.basename, self.service_worker, self.logger, self.keywords)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "D:\boinc\data\slots\5\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
  File "D:\boinc\data\slots\5\Lib\site-packages\openmm\openmm.py", line 4738, in setState
    return _openmm.Context_setState(self, state)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Called setPositions() on a Context with the wrong number of positions

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "D:\boinc\data\slots\5\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\openmm_async_re.py", line 86, in update_state_of_replica
    stateid = self.status[repl]['stateid_current']
              ^^^^^^^^^^^
  File "D:\boinc\data\slots\5\Lib\site-packages\atom_openmm\async_re.py", line 131, in __getattribute__
    return object.__getattribute__(self,name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'openmm_job_RBFE' object has no attribute 'status'
08:40:15 (5988): C:/Windows/system32/cmd.exe exited; CPU time 45.750000
08:40:15 (5988): app exit status: 0x16
08:40:15 (5988): called boinc_finish(195)
0 bytes in 0 Free Blocks.
176 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: 430331 bytes.
Dumping objects ->
{1767} normal block at 0x000001EDB923EE10, 48 bytes long.
 Data: <PATH=D:\boinc\da> 50 41 54 48 3D 44 3A 5C 62 6F 69 6E 63 5C 64 61 
{1756} normal block at 0x000001EDB923FB90, 32 bytes long.
 Data: <HOME=D:\boinc\da> 48 4F 4D 45 3D 44 3A 5C 62 6F 69 6E 63 5C 64 61 
{1745} normal block at 0x000001EDB923FF50, 32 bytes long.
 Data: <TMP=D:\boinc\dat> 54 4D 50 3D 44 3A 5C 62 6F 69 6E 63 5C 64 61 74 
{1734} normal block at 0x000001EDB923FBF0, 32 bytes long.
 Data: <TEMP=D:\boinc\da> 54 45 4D 50 3D 44 3A 5C 62 6F 69 6E 63 5C 64 61 
{1723} normal block at 0x000001EDB9240250, 32 bytes long.
 Data: <TMPDIR=D:\boinc\> 54 4D 50 44 49 52 3D 44 3A 5C 62 6F 69 6E 63 5C 
{1692} normal block at 0x000001EDB923F040, 48 bytes long.
 Data: <PATH=D:\boinc\da> 50 41 54 48 3D 44 3A 5C 62 6F 69 6E 63 5C 64 61 
..\api\boinc_api.cpp(309) : {1679} normal block at 0x000001EDB92454F0, 8 bytes long.
 Data: <        > 00 00 BB BA ED 01 00 00 
{298} normal block at 0x000001EDB9244910, 8 bytes long.
 Data: < `$     > A0 60 24 B9 ED 01 00 00 
{289} normal block at 0x000001EDB92447C0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{288} normal block at 0x000001EDB92451D0, 16 bytes long.
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{287} normal block at 0x000001EDB9245130, 16 bytes long.
 Data: < _$             > 80 5F 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001EDB92404F0, 32 bytes long.
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{285} normal block at 0x000001EDB92457C0, 16 bytes long.
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{284} normal block at 0x000001EDB9244F00, 16 bytes long.
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{283} normal block at 0x000001EDB92448C0, 16 bytes long.
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{282} normal block at 0x000001EDB9245450, 16 bytes long.
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{281} normal block at 0x000001EDB923EFD0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{280} normal block at 0x000001EDB9244CD0, 16 bytes long.
 Data: <XG$             > 58 47 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001EDB92405B0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{278} normal block at 0x000001EDB9245770, 16 bytes long.
 Data: <0G$             > 30 47 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001EDB9244C80, 16 bytes long.
 Data: < G$             > 08 47 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001EDB92452C0, 16 bytes long.
 Data: < F$             > E0 46 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001EDB9244EB0, 16 bytes long.
 Data: < F$             > B8 46 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001EDB9245810, 16 bytes long.
 Data: < F$             > 90 46 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001EDB9244E10, 16 bytes long.
 Data: <hF$             > 68 46 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001EDB92407F0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{270} normal block at 0x000001EDB9245720, 16 bytes long.
 Data: <@F$             > 40 46 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001EDB9244640, 320 bytes long.
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{268} normal block at 0x000001EDB9245270, 16 bytes long.
 Data: < ^$             > C0 5E 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001EDB92456D0, 16 bytes long.
 Data: < ^$             > 98 5E 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001EDB923FDD0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{265} normal block at 0x000001EDB9244FA0, 16 bytes long.
 Data: <p^$             > 70 5E 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001EDB923FD10, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{263} normal block at 0x000001EDB9245680, 16 bytes long.
 Data: < ]$             > B8 5D 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001EDB9244DC0, 16 bytes long.
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{261} normal block at 0x000001EDB9245630, 16 bytes long.
 Data: <h]$             > 68 5D 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001EDB9244FF0, 16 bytes long.
 Data: <@]$             > 40 5D 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001EDB9244A50, 16 bytes long.
 Data: < ]$             > 18 5D 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001EDB9245090, 16 bytes long.
 Data: < \$             > F0 5C 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000001EDB9245040, 16 bytes long.
 Data: <  #             > A0 ED 23 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000001EDB923EDA0, 40 bytes long.
 Data: <@P$     @ #     > 40 50 24 B9 ED 01 00 00 40 F0 23 B9 ED 01 00 00 
{254} normal block at 0x000001EDB9244C30, 16 bytes long.
 Data: < \$             > D0 5C 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x000001EDB92455E0, 16 bytes long.
 Data: < \$             > A8 5C 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{252} normal block at 0x000001EDB9240850, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{251} normal block at 0x000001EDB9244D20, 16 bytes long.
 Data: < \$             > 80 5C 24 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{250} normal block at 0x000001EDB9245C80, 992 bytes long.
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{86} normal block at 0x000001EDB9240730, 32 bytes long.
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{85} normal block at 0x000001EDB923ADF0, 16 bytes long.
 Data: <  #             > 80 EE 23 B9 ED 01 00 00 00 00 00 00 00 00 00 00 
{84} normal block at 0x000001EDB923EE80, 40 bytes long.
 Data: <  #     0 $     > F0 AD 23 B9 ED 01 00 00 30 07 24 B9 ED 01 00 00 
{63} normal block at 0x000001EDB923A9E0, 16 bytes long.
 Data: <  6,            > 80 EA 36 2C F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001EDB923A8A0, 16 bytes long.
 Data: <@ 6,            > 40 E9 36 2C F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001EDB923B480, 16 bytes long.
 Data: < W3,            > F8 57 33 2C F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001EDB923AB70, 16 bytes long.
 Data: < W3,            > D8 57 33 2C F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001EDB923AD50, 16 bytes long.
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{58} normal block at 0x000001EDB923B5C0, 16 bytes long.
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{57} normal block at 0x000001EDB923AB20, 16 bytes long.
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{56} normal block at 0x000001EDB923B430, 16 bytes long.
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{55} normal block at 0x000001EDB923ACB0, 16 bytes long.
 Data: <p 3,            > 70 04 33 2C F6 7F 00 00 00 00 00 00 00 00 00 00 
{54} normal block at 0x000001EDB923A800, 16 bytes long.
 Data: <  1,            > 18 C0 31 2C F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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