Task 38584172

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
15:35:27 (25032): wrapper (7.9.26016): starting
15:35:27 (25032): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A03_A31_0.pdb
QB_A03_A31_0.xml
QB_A03_A31_equil.pdb
QB_A03_A31.inpcrd
QB_A03_A31_input.yaml
QB_A03_A31_mdlambda.pdb
QB_A03_A31_min.pdb
QB_A03_A31_npt.pdb
QB_A03_A31.pdb
QB_A03_A31.prmtop
QB_A03_A31_sys.xml
QB_A03_A31_therm.pdb
run.bat
run.sh
15:35:29 (25032): Library/usr/bin/tar.exe exited; CPU time 0.015625
15:35:29 (25032): 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\32\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\32\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) : {3835133} normal block at 0x000001EE1B9AE130, 8 bytes long.
 Data: <        > 00 00 96 1B EE 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833968} normal block at 0x000001EE1BA8EA50, 1080 bytes long.
 Data: <hm              > 68 6D 00 00 CD CD CD CD 98 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {316} normal block at 0x000001EE1B9A19C0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
22:50:25 (27388): wrapper (7.9.26016): starting
22:50:25 (27388): 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\32\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\32\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\32\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\32\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\32\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\32\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\32\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\32\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\32\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\32\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\32\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\32\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\32\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'
22:51:14 (27388): C:/Windows/system32/cmd.exe exited; CPU time 33.921875
22:51:14 (27388): app exit status: 0x16
22:51:14 (27388): 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: 790241 bytes.
Dumping objects ->
{1562} normal block at 0x0000027925126570, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1551} normal block at 0x0000027925125F50, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1540} normal block at 0x00000279251263B0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1529} normal block at 0x0000027925126500, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1518} normal block at 0x00000279251260A0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1487} normal block at 0x000002792510F5F0, 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) : {1474} normal block at 0x0000027925127260, 8 bytes long.
 Data: <   %y   > 00 00 0D 25 79 02 00 00 
{310} normal block at 0x0000027925127440, 8 bytes long.
 Data: < | %y   > 90 7C 12 25 79 02 00 00 
{301} normal block at 0x0000027925110E40, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{300} normal block at 0x0000027925127670, 16 bytes long.
 Data: < { %y           > 98 7B 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x0000027925127300, 16 bytes long.
 Data: <p{ %y           > 70 7B 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x000002792511FAB0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{297} normal block at 0x0000027925126F90, 16 bytes long.
 Data: <H{ %y           > 48 7B 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000027925126DB0, 16 bytes long.
 Data: < { %y           > 20 7B 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000027925126F40, 16 bytes long.
 Data: < z %y           > F8 7A 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000027925127120, 16 bytes long.
 Data: < z %y           > D0 7A 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000027925125FC0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{292} normal block at 0x00000279251271C0, 16 bytes long.
 Data: <   %y           > 08 19 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000002792511F870, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{290} normal block at 0x0000027925127620, 16 bytes long.
 Data: <   %y           > E0 18 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x00000279251268B0, 16 bytes long.
 Data: <   %y           > B8 18 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000027925127580, 16 bytes long.
 Data: <   %y           > 90 18 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x00000279251273A0, 16 bytes long.
 Data: <h  %y           > 68 18 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x00000279251270D0, 16 bytes long.
 Data: <@  %y           > 40 18 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000027925126EF0, 16 bytes long.
 Data: <   %y           > 18 18 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x000002792511F810, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{282} normal block at 0x00000279251274E0, 16 bytes long.
 Data: <   %y           > F0 17 11 25 79 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000279251117F0, 320 bytes long.
 Data: < t %y      %y   > E0 74 12 25 79 02 00 00 10 F8 11 25 79 02 00 00 
{280} normal block at 0x0000027925127080, 16 bytes long.
 Data: < z %y           > B0 7A 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000027925127030, 16 bytes long.
 Data: < z %y           > 88 7A 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000279251201D0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{277} normal block at 0x0000027925127490, 16 bytes long.
 Data: <`z %y           > 60 7A 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000002792511F990, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{275} normal block at 0x0000027925127530, 16 bytes long.
 Data: < y %y           > A8 79 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000027925126EA0, 16 bytes long.
 Data: < y %y           > 80 79 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000027925126BD0, 16 bytes long.
 Data: <Xy %y           > 58 79 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000279251276C0, 16 bytes long.
 Data: <0y %y           > 30 79 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000027925126FE0, 16 bytes long.
 Data: < y %y           > 08 79 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000279251272B0, 16 bytes long.
 Data: < x %y           > E0 78 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000279251273F0, 16 bytes long.
 Data: < ^ %y           > E0 5E 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000027925125EE0, 40 bytes long.
 Data: < s %y      %y   > F0 73 12 25 79 02 00 00 F0 F5 10 25 79 02 00 00 
{266} normal block at 0x0000027925127350, 16 bytes long.
 Data: < x %y           > C0 78 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000027925127170, 16 bytes long.
 Data: < x %y           > 98 78 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000002792511F690, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{263} normal block at 0x0000027925127210, 16 bytes long.
 Data: <px %y           > 70 78 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000027925127870, 992 bytes long.
 Data: < r %y      %y   > 10 72 12 25 79 02 00 00 90 F6 11 25 79 02 00 00 
{98} normal block at 0x000002792511FCF0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{97} normal block at 0x000002792511E140, 16 bytes long.
 Data: <0` %y           > 30 60 12 25 79 02 00 00 00 00 00 00 00 00 00 00 
{96} normal block at 0x0000027925126030, 40 bytes long.
 Data: <@  %y      %y   > 40 E1 11 25 79 02 00 00 F0 FC 11 25 79 02 00 00 
{75} normal block at 0x000002792511DE70, 16 bytes long.
 Data: <                > 80 EA C0 AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x000002792511D6A0, 16 bytes long.
 Data: <@               > 40 E9 C0 AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000002792511DC40, 16 bytes long.
 Data: < W              > F8 57 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000002792511D650, 16 bytes long.
 Data: < W              > D8 57 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000002792511E0F0, 16 bytes long.
 Data: <P               > 50 04 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002792511D9C0, 16 bytes long.
 Data: <0               > 30 04 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002792511E050, 16 bytes long.
 Data: <                > E0 02 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002792511DA10, 16 bytes long.
 Data: <                > 10 04 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002792511D970, 16 bytes long.
 Data: <p               > 70 04 BD AF F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000002792511E000, 16 bytes long.
 Data: <                > 18 C0 BB AF F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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