Task 38583057

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>
16:11:17 (11684): wrapper (7.9.26016): starting
16:11:17 (11684): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A11_A37_0.pdb
QB_A11_A37_0.xml
QB_A11_A37_equil.pdb
QB_A11_A37.inpcrd
QB_A11_A37_input.yaml
QB_A11_A37_mdlambda.pdb
QB_A11_A37_min.pdb
QB_A11_A37_npt.pdb
QB_A11_A37.pdb
QB_A11_A37.prmtop
QB_A11_A37_sys.xml
QB_A11_A37_therm.pdb
run.bat
run.sh
16:11:20 (11684): Library/usr/bin/tar.exe exited; CPU time 0.000000
16:11:20 (11684): 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\15\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\15\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.
16:49:31 (7500): wrapper (7.9.26016): starting
16:49:31 (7500): 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\15\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\15\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 "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\ommreplica.py", line 42, in __init__
    self.open_xtc()
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\ommreplica.py", line 99, in open_xtc
    self.xtc = XTCFile(self.xtcfile, self.worker.topology, self.ommsystem.MDstepsize, interval=interval, append=append)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\openmm\app\xtcfile.py", line 57, in __init__
    self._modelCount = get_xtc_nframes(self._filename.encode("utf-8"))
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "openmm\\app\\internal\\xtc_utils\\xtc.pyx", line 43, in openmm.app.internal.xtc_utils.get_xtc_nframes
RuntimeError: xtc_read(): could not get natoms


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 "C:\ProgramData\BOINC\slots\15\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\15\Lib\site-packages\atom_openmm\openmm_async_re.py", line 86, in update_state_of_replica
    stateid = self.status[repl]['stateid_current']
              ^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\15\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'
16:50:00 (7500): C:/Windows/system32/cmd.exe exited; CPU time 16.000000
16:50:00 (7500): app exit status: 0x16
16:50:00 (7500): called boinc_finish(195)
0 bytes in 0 Free Blocks.
726 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: 345069 bytes.
Dumping objects ->
{1916} normal block at 0x000001E464B82C80, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1905} normal block at 0x000001E464B82B30, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1894} normal block at 0x000001E464B82F90, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1883} normal block at 0x000001E464B82D60, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1872} normal block at 0x000001E464B82DD0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1841} normal block at 0x000001E464B6EF60, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1830} normal block at 0x000001E464B6BD40, 235 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) : {1827} normal block at 0x000001E464B84780, 8 bytes long.
 Data: <   e    > 00 00 02 65 E4 01 00 00 
{1051} normal block at 0x000001E464B80080, 235 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{303} normal block at 0x000001E464B83A60, 8 bytes long.
 Data: <PX d    > 50 58 B8 64 E4 01 00 00 
{294} normal block at 0x000001E464B71EE0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{293} normal block at 0x000001E464B83E20, 16 bytes long.
 Data: < O d            > B8 4F B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001E464B845A0, 16 bytes long.
 Data: < O d            > 90 4F B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001E464B81080, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{290} normal block at 0x000001E464B841E0, 16 bytes long.
 Data: <hO d            > 68 4F B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001E464B84820, 16 bytes long.
 Data: <@O d            > 40 4F B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001E464B83CE0, 16 bytes long.
 Data: < O d            > 18 4F B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001E464B84460, 16 bytes long.
 Data: < N d            > F0 4E B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001E464B70470, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x000001E464B84730, 16 bytes long.
 Data: <   d            > 08 04 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001E464B80B40, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{283} normal block at 0x000001E464B83DD0, 16 bytes long.
 Data: <   d            > E0 03 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001E464B83F60, 16 bytes long.
 Data: <   d            > B8 03 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001E464B84050, 16 bytes long.
 Data: <   d            > 90 03 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001E464B83A10, 16 bytes long.
 Data: <h  d            > 68 03 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001E464B83C90, 16 bytes long.
 Data: <@  d            > 40 03 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001E464B846E0, 16 bytes long.
 Data: <   d            > 18 03 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001E464B80AE0, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{275} normal block at 0x000001E464B83BA0, 16 bytes long.
 Data: <   d            > F0 02 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001E464B702F0, 320 bytes long.
 Data: < ; d       d    > A0 3B B8 64 E4 01 00 00 E0 0A B8 64 E4 01 00 00 
{273} normal block at 0x000001E464B83970, 16 bytes long.
 Data: < N d            > D0 4E B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001E464B84000, 16 bytes long.
 Data: < N d            > A8 4E B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001E464B80660, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{270} normal block at 0x000001E464B84690, 16 bytes long.
 Data: < N d            > 80 4E B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001E464B80A80, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{268} normal block at 0x000001E464B839C0, 16 bytes long.
 Data: < M d            > C8 4D B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001E464B83B50, 16 bytes long.
 Data: < M d            > A0 4D B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001E464B83BF0, 16 bytes long.
 Data: <xM d            > 78 4D B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001E464B83D30, 16 bytes long.
 Data: <PM d            > 50 4D B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001E464B83F10, 16 bytes long.
 Data: <(M d            > 28 4D B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001E464B84410, 16 bytes long.
 Data: < M d            > 00 4D B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001E464B83AB0, 16 bytes long.
 Data: < S d            > 00 53 B7 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001E464B75300, 40 bytes long.
 Data: < : d    `  d    > B0 3A B8 64 E4 01 00 00 60 EF B6 64 E4 01 00 00 
{259} normal block at 0x000001E464B847D0, 16 bytes long.
 Data: < L d            > E0 4C B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001E464B83C40, 16 bytes long.
 Data: < L d            > B8 4C B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000001E464B812C0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{256} normal block at 0x000001E464B84640, 16 bytes long.
 Data: < L d            > 90 4C B8 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000001E464B84C90, 992 bytes long.
 Data: <@F d       d    > 40 46 B8 64 E4 01 00 00 C0 12 B8 64 E4 01 00 00 
{91} normal block at 0x000001E464B80780, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{90} normal block at 0x000001E464B7D6B0, 16 bytes long.
 Data: <0  d            > 30 FB B6 64 E4 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x000001E464B6FB30, 40 bytes long.
 Data: <   d       d    > B0 D6 B7 64 E4 01 00 00 80 07 B8 64 E4 01 00 00 
{68} normal block at 0x000001E464B7D390, 16 bytes long.
 Data: <   :            > 80 EA 9C 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001E464B7D7F0, 16 bytes long.
 Data: <@  :            > 40 E9 9C 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001E464B7D980, 16 bytes long.
 Data: < W :            > F8 57 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001E464B7D930, 16 bytes long.
 Data: < W :            > D8 57 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001E464B7DBB0, 16 bytes long.
 Data: <P  :            > 50 04 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001E464B7D5C0, 16 bytes long.
 Data: <0  :            > 30 04 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001E464B7D480, 16 bytes long.
 Data: <   :            > E0 02 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001E464B7D4D0, 16 bytes long.
 Data: <   :            > 10 04 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001E464B7D570, 16 bytes long.
 Data: <p  :            > 70 04 99 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001E464B7D430, 16 bytes long.
 Data: <   :            > 18 C0 97 3A F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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