Task 38678699

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>
14:55:12 (38924): wrapper (7.9.26016): starting
14:55:12 (38924): 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
14:55:13 (38924): Library/usr/bin/tar.exe exited; CPU time 0.015625
14:55:13 (38924): 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\1\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\1\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) : {3835165} normal block at 0x000001E02743CF80, 8 bytes long.
 Data: <  ='    > 00 00 3D 27 E0 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833994} normal block at 0x000001E0291DA640, 1080 bytes long.
 Data: <        x       > B0 EA 00 00 CD CD CD CD 78 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {329} normal block at 0x000001E027437D00, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
15:10:42 (8408): wrapper (7.9.26016): starting
15:10:42 (8408): 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\1\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1493} normal block at 0x000002A477E16ED0, 8 bytes long.
 Data: <   y    > 00 00 94 79 A4 02 00 00 
..\lib\diagnostics_win.cpp(417) : {322} normal block at 0x000002A477E15A60, 1080 bytes long.
 Data: <x       T       > 78 D1 00 00 CD CD CD CD 54 01 00 00 00 00 00 00 
Object dump complete.
15:14:20 (17592): wrapper (7.9.26016): starting
15:14:20 (17592): 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\1\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1493} normal block at 0x00000256515A77C0, 8 bytes long.
 Data: <   QV   > 00 00 AA 51 56 02 00 00 
..\lib\diagnostics_win.cpp(417) : {322} normal block at 0x00000256515A6990, 1080 bytes long.
 Data: <                > 00 A1 00 00 CD CD CD CD C0 00 00 00 00 00 00 00 
Object dump complete.
15:24:25 (59684): wrapper (7.9.26016): starting
15:24:25 (59684): 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\1\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\1\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\1\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\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\1\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\1\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\1\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\1\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'
15:24:48 (59684): C:/Windows/system32/cmd.exe exited; CPU time 19.453125
15:24:48 (59684): app exit status: 0x16
15:24:48 (59684): 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: 772230 bytes.
Dumping objects ->
{1581} normal block at 0x0000025B4E7CFD20, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1570} normal block at 0x0000025B4E7CFFC0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1559} normal block at 0x0000025B4E7CFF50, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1548} normal block at 0x0000025B4E7CFA10, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1537} normal block at 0x0000025B4E7CFB60, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1506} normal block at 0x0000025B4E7C1210, 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) : {1493} normal block at 0x0000025B4E7D5740, 8 bytes long.
 Data: <  xN[   > 00 00 78 4E 5B 02 00 00 
{323} normal block at 0x0000025B4E7D5420, 8 bytes long.
 Data: < M}N[   > 20 4D 7D 4E 5B 02 00 00 
{314} normal block at 0x0000025B4E7C8D20, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{313} normal block at 0x0000025B4E7D5CE0, 16 bytes long.
 Data: <hf}N[           > 68 66 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{312} normal block at 0x0000025B4E7D56F0, 16 bytes long.
 Data: <@f}N[           > 40 66 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{311} normal block at 0x0000025B4E7CF7B0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{310} normal block at 0x0000025B4E7D56A0, 16 bytes long.
 Data: < f}N[           > 18 66 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{309} normal block at 0x0000025B4E7D54C0, 16 bytes long.
 Data: < e}N[           > F0 65 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{308} normal block at 0x0000025B4E7D60A0, 16 bytes long.
 Data: < e}N[           > C8 65 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{307} normal block at 0x0000025B4E7D62D0, 16 bytes long.
 Data: < e}N[           > A0 65 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{306} normal block at 0x0000025B4E7CF9A0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{305} normal block at 0x0000025B4E7D5E70, 16 bytes long.
 Data: <  {N[           > 98 D9 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{304} normal block at 0x0000025B4E7CEDF0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{303} normal block at 0x0000025B4E7D5C40, 16 bytes long.
 Data: <p {N[           > 70 D9 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{301} normal block at 0x0000025B4E7D5AB0, 16 bytes long.
 Data: <H {N[           > 48 D9 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{300} normal block at 0x0000025B4E7D5650, 16 bytes long.
 Data: <  {N[           > 20 D9 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x0000025B4E7D5BF0, 16 bytes long.
 Data: <  {N[           > F8 D8 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x0000025B4E7D5600, 16 bytes long.
 Data: <  {N[           > D0 D8 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{297} normal block at 0x0000025B4E7D5F10, 16 bytes long.
 Data: <  {N[           > A8 D8 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000025B4E7CE970, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{295} normal block at 0x0000025B4E7D5A60, 16 bytes long.
 Data: <  {N[           > 80 D8 7B 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000025B4E7BD880, 320 bytes long.
 Data: <`Z}N[   p |N[   > 60 5A 7D 4E 5B 02 00 00 70 E9 7C 4E 5B 02 00 00 
{293} normal block at 0x0000025B4E7D5970, 16 bytes long.
 Data: < e}N[           > 80 65 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x0000025B4E7D5DD0, 16 bytes long.
 Data: <Xe}N[           > 58 65 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000025B4E7CF0F0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{290} normal block at 0x0000025B4E7D5F60, 16 bytes long.
 Data: <0e}N[           > 30 65 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000025B4E7CF090, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{288} normal block at 0x0000025B4E7D5C90, 16 bytes long.
 Data: <xd}N[           > 78 64 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000025B4E7D58D0, 16 bytes long.
 Data: <Pd}N[           > 50 64 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000025B4E7D6000, 16 bytes long.
 Data: <(d}N[           > 28 64 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000025B4E7D59C0, 16 bytes long.
 Data: < d}N[           > 00 64 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000025B4E7D5A10, 16 bytes long.
 Data: < c}N[           > D8 63 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000025B4E7D61E0, 16 bytes long.
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{281} normal block at 0x0000025B4E7D5E20, 16 bytes long.
 Data: <  |N[           > B0 FC 7C 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000025B4E7CFCB0, 40 bytes long.
 Data: < ^}N[     |N[   > 20 5E 7D 4E 5B 02 00 00 10 12 7C 4E 5B 02 00 00 
{279} normal block at 0x0000025B4E7D5880, 16 bytes long.
 Data: < c}N[           > 90 63 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000025B4E7D5560, 16 bytes long.
 Data: <hc}N[           > 68 63 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000025B4E7CF450, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{276} normal block at 0x0000025B4E7D5BA0, 16 bytes long.
 Data: <@c}N[           > 40 63 7D 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000025B4E7D6340, 992 bytes long.
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{111} normal block at 0x0000025B4E7CEA30, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{110} normal block at 0x0000025B4E7CCEE0, 16 bytes long.
 Data: <0 |N[           > 30 F9 7C 4E 5B 02 00 00 00 00 00 00 00 00 00 00 
{109} normal block at 0x0000025B4E7CF930, 40 bytes long.
 Data: <  |N[   0 |N[   > E0 CE 7C 4E 5B 02 00 00 30 EA 7C 4E 5B 02 00 00 
{88} normal block at 0x0000025B4E7CD390, 16 bytes long.
 Data: <  r"            > 80 EA 72 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{87} normal block at 0x0000025B4E7CCE90, 16 bytes long.
 Data: <@ r"            > 40 E9 72 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{86} normal block at 0x0000025B4E7CCD50, 16 bytes long.
 Data: < Wo"            > F8 57 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{85} normal block at 0x0000025B4E7CCB70, 16 bytes long.
 Data: < Wo"            > D8 57 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{84} normal block at 0x0000025B4E7CCD00, 16 bytes long.
 Data: <P o"            > 50 04 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{83} normal block at 0x0000025B4E7CD520, 16 bytes long.
 Data: <0 o"            > 30 04 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{82} normal block at 0x0000025B4E7CCCB0, 16 bytes long.
 Data: <  o"            > E0 02 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{81} normal block at 0x0000025B4E7CC9E0, 16 bytes long.
 Data: <  o"            > 10 04 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{80} normal block at 0x0000025B4E7CCC60, 16 bytes long.
 Data: <p o"            > 70 04 6F 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
{79} normal block at 0x0000025B4E7CCF30, 16 bytes long.
 Data: <  m"            > 18 C0 6D 22 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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