Task 38595993

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>
23:05:49 (31408): wrapper (7.9.26016): starting
23:05:49 (31408): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A06_A13_0.pdb
QB_A06_A13_0.xml
QB_A06_A13_equil.pdb
QB_A06_A13.inpcrd
QB_A06_A13_input.yaml
QB_A06_A13_mdlambda.pdb
QB_A06_A13_min.pdb
QB_A06_A13_npt.pdb
QB_A06_A13.pdb
QB_A06_A13.prmtop
QB_A06_A13_sys.xml
QB_A06_A13_therm.pdb
run.bat
run.sh
23:05:50 (31408): Library/usr/bin/tar.exe exited; CPU time 0.000000
23:05:50 (31408): 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\12\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\12\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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835102} normal block at 0x00000245572BD3A0, 8 bytes long.
 Data: <  aWE   > 00 00 61 57 45 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833956} normal block at 0x0000024558EF5110, 1080 bytes long.
 Data: < 8              > 0C 38 00 00 CD CD CD CD A4 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {310} normal block at 0x00000245572B0DC0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
23:57:53 (22188): wrapper (7.9.26016): starting
23:57:53 (22188): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1449} normal block at 0x00000257FC6F5800, 8 bytes long.
 Data: <    W   > 00 00 B9 FC 57 02 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x00000257FC6F6820, 1080 bytes long.
 Data: < y              > DC 79 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
00:53:42 (25508): wrapper (7.9.26016): starting
00:53:42 (25508): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1449} normal block at 0x00000247E8345A30, 8 bytes long.
 Data: <    G   > 00 00 81 E8 47 02 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x00000247E8346820, 1080 bytes long.
 Data: < <              > 9C 3C 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
08:53:05 (17020): wrapper (7.9.26016): starting
08:53:05 (17020): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1449} normal block at 0x000001816B405760, 8 bytes long.
 Data: <   k    > 00 00 90 6B 81 01 00 00 
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x000001816B4067D0, 1080 bytes long.
 Data: <L$              > 4C 24 00 00 CD CD CD CD BC 01 00 00 00 00 00 00 
Object dump complete.
14:09:25 (9008): wrapper (7.9.26016): starting
14:09:25 (9008): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\12\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\12\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\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\12\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\12\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\12\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'
14:10:40 (9008): C:/Windows/system32/cmd.exe exited; CPU time 59.312500
14:10:40 (9008): app exit status: 0x16
14:10:40 (9008): 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: 1233187 bytes.
Dumping objects ->
{1537} normal block at 0x000001EF7E004910, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1526} normal block at 0x000001EF7E004A60, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1515} normal block at 0x000001EF7E004830, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1504} normal block at 0x000001EF7E0048A0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1493} normal block at 0x000001EF7E004B40, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1462} normal block at 0x000001EF7DFEF1B0, 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) : {1449} normal block at 0x000001EF7E005710, 8 bytes long.
 Data: <   }    > 00 00 F8 7D EF 01 00 00 
{304} normal block at 0x000001EF7E006200, 8 bytes long.
 Data: < h ~    > 20 68 00 7E EF 01 00 00 
{295} normal block at 0x000001EF7DFF22D0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{294} normal block at 0x000001EF7E006110, 16 bytes long.
 Data: <(g ~            > 28 67 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001EF7E0059E0, 16 bytes long.
 Data: < g ~            > 00 67 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001EF7E000DF0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{291} normal block at 0x000001EF7E005760, 16 bytes long.
 Data: < f ~            > D8 66 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x000001EF7E0060C0, 16 bytes long.
 Data: < f ~            > B0 66 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001EF7E006070, 16 bytes long.
 Data: < f ~            > 88 66 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001EF7E005620, 16 bytes long.
 Data: <`f ~            > 60 66 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001EF7E004EC0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{286} normal block at 0x000001EF7E006020, 16 bytes long.
 Data: <H  }            > 48 06 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x000001EF7E0016F0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{284} normal block at 0x000001EF7E005F80, 16 bytes long.
 Data: <   }            > 20 06 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x000001EF7E005530, 16 bytes long.
 Data: <   }            > F8 05 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001EF7E005F30, 16 bytes long.
 Data: <   }            > D0 05 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001EF7E005B70, 16 bytes long.
 Data: <   }            > A8 05 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001EF7E006160, 16 bytes long.
 Data: <   }            > 80 05 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001EF7E005A80, 16 bytes long.
 Data: <X  }            > 58 05 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001EF7E000A90, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{276} normal block at 0x000001EF7E005490, 16 bytes long.
 Data: <0  }            > 30 05 FF 7D EF 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x000001EF7DFF0530, 320 bytes long.
 Data: < T ~       ~    > 90 54 00 7E EF 01 00 00 90 0A 00 7E EF 01 00 00 
{274} normal block at 0x000001EF7E005EE0, 16 bytes long.
 Data: <@f ~            > 40 66 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001EF7E005C10, 16 bytes long.
 Data: < f ~            > 18 66 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001EF7E000910, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{271} normal block at 0x000001EF7E0055D0, 16 bytes long.
 Data: < e ~            > F0 65 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x000001EF7E000A30, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{269} normal block at 0x000001EF7E005850, 16 bytes long.
 Data: <8e ~            > 38 65 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x000001EF7E005A30, 16 bytes long.
 Data: < e ~            > 10 65 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001EF7E005800, 16 bytes long.
 Data: < d ~            > E8 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001EF7E005580, 16 bytes long.
 Data: < d ~            > C0 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001EF7E005D00, 16 bytes long.
 Data: < d ~            > 98 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001EF7E0056C0, 16 bytes long.
 Data: <pd ~            > 70 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x000001EF7E005FD0, 16 bytes long.
 Data: < L ~            > 20 4C 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001EF7E004C20, 40 bytes long.
 Data: < _ ~       }    > D0 5F 00 7E EF 01 00 00 B0 F1 FE 7D EF 01 00 00 
{260} normal block at 0x000001EF7E0061B0, 16 bytes long.
 Data: <Pd ~            > 50 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x000001EF7E0054E0, 16 bytes long.
 Data: <(d ~            > 28 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001EF7E001750, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{257} normal block at 0x000001EF7E005440, 16 bytes long.
 Data: < d ~            > 00 64 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000001EF7E006400, 992 bytes long.
 Data: <@T ~    P  ~    > 40 54 00 7E EF 01 00 00 50 17 00 7E EF 01 00 00 
{92} normal block at 0x000001EF7E000D30, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{91} normal block at 0x000001EF7DFFD300, 16 bytes long.
 Data: < M ~            > E0 4D 00 7E EF 01 00 00 00 00 00 00 00 00 00 00 
{90} normal block at 0x000001EF7E004DE0, 40 bytes long.
 Data: <   }    0  ~    > 00 D3 FF 7D EF 01 00 00 30 0D 00 7E EF 01 00 00 
{69} normal block at 0x000001EF7DFFD3F0, 16 bytes long.
 Data: <   >            > 80 EA CA 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000001EF7DFFDB70, 16 bytes long.
 Data: <@  >            > 40 E9 CA 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001EF7DFFDDF0, 16 bytes long.
 Data: < W >            > F8 57 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001EF7DFFDE90, 16 bytes long.
 Data: < W >            > D8 57 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001EF7DFFD9E0, 16 bytes long.
 Data: <P  >            > 50 04 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001EF7DFFDAD0, 16 bytes long.
 Data: <0  >            > 30 04 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001EF7DFFD2B0, 16 bytes long.
 Data: <   >            > E0 02 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001EF7DFFD670, 16 bytes long.
 Data: <   >            > 10 04 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001EF7DFFD7B0, 16 bytes long.
 Data: <p  >            > 70 04 C7 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001EF7DFFD440, 16 bytes long.
 Data: <   >            > 18 C0 C5 3E F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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