Task 38582037

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>
22:35:11 (14632): wrapper (7.9.26016): starting
22:35:11 (14632): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A40_A25_0.pdb
QB_A40_A25_0.xml
QB_A40_A25_equil.pdb
QB_A40_A25.inpcrd
QB_A40_A25_input.yaml
QB_A40_A25_mdlambda.pdb
QB_A40_A25_min.pdb
QB_A40_A25_npt.pdb
QB_A40_A25.pdb
QB_A40_A25.prmtop
QB_A40_A25_sys.xml
QB_A40_A25_therm.pdb
run.bat
run.sh
22:35:13 (14632): Library/usr/bin/tar.exe exited; CPU time 0.015625
22:35:13 (14632): 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.
09:16:19 (22256): wrapper (7.9.26016): starting
09:16:19 (22256): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A40_A25_0.pdb
QB_A40_A25_0.xml
QB_A40_A25_equil.pdb
QB_A40_A25.inpcrd
QB_A40_A25_input.yaml
QB_A40_A25_mdlambda.pdb
QB_A40_A25_min.pdb
QB_A40_A25_npt.pdb
QB_A40_A25.pdb
QB_A40_A25.prmtop
QB_A40_A25_sys.xml
QB_A40_A25_therm.pdb
run.bat
run.sh
09:16:20 (22256): Library/usr/bin/tar.exe exited; CPU time 0.000000
09:16:20 (22256): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\0\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\0\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\openmm\openmm.py", line 19618, in deserialize
    raise ValueError("Invalid input string")
ValueError: Invalid input string

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\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 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\0\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\0\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'
09:16:29 (22256): C:/Windows/system32/cmd.exe exited; CPU time 0.000000
09:16:29 (22256): app exit status: 0x16
09:16:29 (22256): called boinc_finish(195)
0 bytes in 0 Free Blocks.
616 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: 291093 bytes.
Dumping objects ->
{1657} normal block at 0x0000022ABC5C5780, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1646} normal block at 0x0000022ABC5C5940, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1635} normal block at 0x0000022ABC5C58D0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1624} normal block at 0x0000022ABC5C59B0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1613} normal block at 0x0000022ABC5C56A0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1582} normal block at 0x0000022ABC5B0DD0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1571} normal block at 0x0000022ABC5AD4A0, 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) : {1568} normal block at 0x0000022ABC5C6560, 8 bytes long.
 Data: <  W *   > 00 00 57 BC 2A 02 00 00 
{937} normal block at 0x0000022ABC5ADC20, 180 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{307} normal block at 0x0000022ABC5C61F0, 8 bytes long.
 Data: < t\ *   > B0 74 5C BC 2A 02 00 00 
{298} normal block at 0x0000022ABC5B2340, 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 0x0000022ABC5C6240, 16 bytes long.
 Data: < s\ *           > B8 73 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000022ABC5C6AB0, 16 bytes long.
 Data: < s\ *           > 90 73 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000022ABC5C1770, 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 0x0000022ABC5C6510, 16 bytes long.
 Data: <hs\ *           > 68 73 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000022ABC5C6DD0, 16 bytes long.
 Data: <@s\ *           > 40 73 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000022ABC5C66F0, 16 bytes long.
 Data: < s\ *           > 18 73 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000022ABC5C63D0, 16 bytes long.
 Data: < r\ *           > F0 72 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000022ABC5C5D30, 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 0x0000022ABC5C62E0, 16 bytes long.
 Data: <  Z *           > D8 B6 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000022ABC5C1470, 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 0x0000022ABC5C6150, 16 bytes long.
 Data: <  Z *           > B0 B6 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000022ABC5C64C0, 16 bytes long.
 Data: <  Z *           > 88 B6 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000022ABC5C6E20, 16 bytes long.
 Data: <` Z *           > 60 B6 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000022ABC5C6880, 16 bytes long.
 Data: <8 Z *           > 38 B6 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000022ABC5C6B50, 16 bytes long.
 Data: <  Z *           > 10 B6 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000022ABC5C6C90, 16 bytes long.
 Data: <  Z *           > E8 B5 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000022ABC5C1650, 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 0x0000022ABC5C61A0, 16 bytes long.
 Data: <  Z *           > C0 B5 5A BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000022ABC5AB5C0, 320 bytes long.
 Data: < a\ *   P \ *   > A0 61 5C BC 2A 02 00 00 50 16 5C BC 2A 02 00 00 
{277} normal block at 0x0000022ABC5C66A0, 16 bytes long.
 Data: < r\ *           > D0 72 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000022ABC5C6B00, 16 bytes long.
 Data: < r\ *           > A8 72 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000022ABC5C2070, 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 0x0000022ABC5C6830, 16 bytes long.
 Data: < r\ *           > 80 72 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000022ABC5C18F0, 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 0x0000022ABC5C6380, 16 bytes long.
 Data: < q\ *           > C8 71 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000022ABC5C6100, 16 bytes long.
 Data: < q\ *           > A0 71 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000022ABC5C6D30, 16 bytes long.
 Data: <xq\ *           > 78 71 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000022ABC5C6600, 16 bytes long.
 Data: <Pq\ *           > 50 71 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000022ABC5C6740, 16 bytes long.
 Data: <(q\ *           > 28 71 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000022ABC5C6790, 16 bytes long.
 Data: < q\ *           > 00 71 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000022ABC5C6BF0, 16 bytes long.
 Data: < W\ *           > 10 57 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000022ABC5C5710, 40 bytes long.
 Data: < k\ *     [ *   > F0 6B 5C BC 2A 02 00 00 D0 0D 5B BC 2A 02 00 00 
{263} normal block at 0x0000022ABC5C6CE0, 16 bytes long.
 Data: < p\ *           > E0 70 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000022ABC5C6BA0, 16 bytes long.
 Data: < p\ *           > B8 70 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000022ABC5C1710, 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 0x0000022ABC5C67E0, 16 bytes long.
 Data: < p\ *           > 90 70 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000022ABC5C7090, 992 bytes long.
 Data: < g\ *     \ *   > E0 67 5C BC 2A 02 00 00 10 17 5C BC 2A 02 00 00 
{95} normal block at 0x0000022ABC5C1CB0, 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 0x0000022ABC5BE170, 16 bytes long.
 Data: <0V\ *           > 30 56 5C BC 2A 02 00 00 00 00 00 00 00 00 00 00 
{93} normal block at 0x0000022ABC5C5630, 40 bytes long.
 Data: <p [ *     \ *   > 70 E1 5B BC 2A 02 00 00 B0 1C 5C BC 2A 02 00 00 
{72} normal block at 0x0000022ABC5BD950, 16 bytes long.
 Data: <                > 80 EA AB 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x0000022ABC5BD9F0, 16 bytes long.
 Data: <@               > 40 E9 AB 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x0000022ABC5BE0D0, 16 bytes long.
 Data: < W              > F8 57 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000022ABC5BE620, 16 bytes long.
 Data: < W              > D8 57 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000022ABC5BDBD0, 16 bytes long.
 Data: <P               > 50 04 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000022ABC5BE800, 16 bytes long.
 Data: <0               > 30 04 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000022ABC5BDDB0, 16 bytes long.
 Data: <                > E0 02 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000022ABC5BE080, 16 bytes long.
 Data: <                > 10 04 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000022ABC5BD900, 16 bytes long.
 Data: <p               > 70 04 A8 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000022ABC5BE850, 16 bytes long.
 Data: <                > 18 C0 A6 03 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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