Task 38591468

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>
05:49:04 (2528): wrapper (7.9.26016): starting
05:49:04 (2528): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A17_A12_0.pdb
QB_A17_A12_0.xml
QB_A17_A12_equil.pdb
QB_A17_A12.inpcrd
QB_A17_A12_input.yaml
QB_A17_A12_mdlambda.pdb
QB_A17_A12_min.pdb
QB_A17_A12_npt.pdb
QB_A17_A12.pdb
QB_A17_A12.prmtop
QB_A17_A12_sys.xml
QB_A17_A12_therm.pdb
run.bat
run.sh
05:49:06 (2528): Library/usr/bin/tar.exe exited; CPU time 0.000000
05:49:06 (2528): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835200} normal block at 0x00000191E285FA80, 8 bytes long.
 Data: <        > 00 00 C5 E2 91 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833968} normal block at 0x00000191E284E4A0, 1080 bytes long.
 Data: <                > F4 AD 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {316} normal block at 0x00000191E28527B0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
00:01:35 (55792): wrapper (7.9.26016): starting
00:01:35 (55792): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x0000016ED6826D90, 8 bytes long.
 Data: <    n   > 00 00 D2 D6 6E 01 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x0000016ED6828060, 1080 bytes long.
 Data: <                > A0 17 00 00 CD CD CD CD C0 01 00 00 00 00 00 00 
Object dump complete.
23:45:00 (45508): wrapper (7.9.26016): starting
23:45:00 (45508): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x000001F0CB866740, 8 bytes long.
 Data: <        > 00 00 ED CB F0 01 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x000001F0CB868280, 1080 bytes long.
 Data: <        \       > 90 7F 00 00 CD CD CD CD 5C 00 00 00 00 00 00 00 
Object dump complete.
23:45:00 (56860): wrapper (7.9.26016): starting
23:45:00 (56860): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x000001F6557B6F10, 8 bytes long.
 Data: <  vU    > 00 00 76 55 F6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x000001F6557B8280, 1080 bytes long.
 Data: <                > 94 DF 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
23:45:00 (65012): wrapper (7.9.26016): starting
23:45:00 (65012): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x00000286DABF67E0, 8 bytes long.
 Data: <        > 00 00 B6 DA 86 02 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x00000286DABF8280, 1080 bytes long.
 Data: <d               > 64 FD 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
23:45:00 (13808): wrapper (7.9.26016): starting
23:45:00 (13808): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x000001E6BF7E77A0, 8 bytes long.
 Data: <  (     > 00 00 28 C1 E6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x000001E6BF7E8BC0, 1080 bytes long.
 Data: < &              > BC 26 01 00 CD CD CD CD B8 01 00 00 00 00 00 00 
Object dump complete.
00:05:06 (70560): wrapper (7.9.26016): starting
00:05:06 (70560): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x000001934DCF8C40, 8 bytes long.
 Data: <  &N    > 00 00 26 4E 93 01 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x000001934DCF9AC0, 1080 bytes long.
 Data: <                > A4 14 01 00 CD CD CD CD B0 01 00 00 00 00 00 00 
Object dump complete.
00:09:18 (14832): wrapper (7.9.26016): starting
00:09:18 (14832): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1541} normal block at 0x0000020979EE6D00, 8 bytes long.
 Data: <   y    > 00 00 E6 79 09 02 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x0000020979EE8110, 1080 bytes long.
 Data: <$j              > 24 6A 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
00:15:17 (43476): wrapper (7.9.26016): starting
00:15:17 (43476): 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'
00:15:43 (43476): C:/Windows/system32/cmd.exe exited; CPU time 19.000000
00:15:43 (43476): app exit status: 0x16
00:15:43 (43476): 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: 825644 bytes.
Dumping objects ->
{1629} normal block at 0x0000021F777E7F20, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1618} normal block at 0x0000021F777E8070, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1607} normal block at 0x0000021F777E7DD0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1596} normal block at 0x0000021F777E7D60, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1585} normal block at 0x0000021F777E7EB0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1554} normal block at 0x0000021F777D0020, 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) : {1541} normal block at 0x0000021F777E6790, 8 bytes long.
 Data: <   w    > 00 00 EA 77 1F 02 00 00 
{310} normal block at 0x0000021F777E6F60, 8 bytes long.
 Data: <  ~w    > 80 82 7E 77 1F 02 00 00 
{301} normal block at 0x0000021F777D30B0, 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 0x0000021F777E7050, 16 bytes long.
 Data: <xy~w            > 78 79 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{299} normal block at 0x0000021F777E6B50, 16 bytes long.
 Data: <Py~w            > 50 79 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{298} normal block at 0x0000021F777E1290, 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 0x0000021F777E6510, 16 bytes long.
 Data: <(y~w            > 28 79 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{296} normal block at 0x0000021F777E7000, 16 bytes long.
 Data: < y~w            > 00 79 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x0000021F777E6A10, 16 bytes long.
 Data: < x~w            > D8 78 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000021F777E6600, 16 bytes long.
 Data: < x~w            > B0 78 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000021F777E7E40, 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 0x0000021F777E71E0, 16 bytes long.
 Data: <  }w            > B8 14 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000021F777E11D0, 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 0x0000021F777E6A60, 16 bytes long.
 Data: <  }w            > 90 14 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000021F777E6BF0, 16 bytes long.
 Data: <h }w            > 68 14 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000021F777E6420, 16 bytes long.
 Data: <@ }w            > 40 14 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000021F777E63D0, 16 bytes long.
 Data: <  }w            > 18 14 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000021F777E64C0, 16 bytes long.
 Data: <  }w            > F0 13 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000021F777E6970, 16 bytes long.
 Data: <  }w            > C8 13 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000021F777E1170, 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 0x0000021F777E6F10, 16 bytes long.
 Data: <  }w            > A0 13 7D 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000021F777D13A0, 320 bytes long.
 Data: < o~w    p ~w    > 10 6F 7E 77 1F 02 00 00 70 11 7E 77 1F 02 00 00 
{280} normal block at 0x0000021F777E70F0, 16 bytes long.
 Data: < x~w            > 90 78 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000021F777E6CE0, 16 bytes long.
 Data: <hx~w            > 68 78 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000021F777E0750, 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 0x0000021F777E6D30, 16 bytes long.
 Data: <@x~w            > 40 78 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000021F777E1110, 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 0x0000021F777E6380, 16 bytes long.
 Data: < w~w            > 88 77 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000021F777E62E0, 16 bytes long.
 Data: <`w~w            > 60 77 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000021F777E70A0, 16 bytes long.
 Data: <8w~w            > 38 77 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000021F777E69C0, 16 bytes long.
 Data: < w~w            > 10 77 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000021F777E6EC0, 16 bytes long.
 Data: < v~w            > E8 76 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000021F777E7190, 16 bytes long.
 Data: < v~w            > C0 76 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000021F777E6880, 16 bytes long.
 Data: <P |w            > 50 E0 7C 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000021F777CE050, 40 bytes long.
 Data: < h~w      }w    > 80 68 7E 77 1F 02 00 00 20 00 7D 77 1F 02 00 00 
{266} normal block at 0x0000021F777E65B0, 16 bytes long.
 Data: < v~w            > A0 76 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000021F777E6920, 16 bytes long.
 Data: <xv~w            > 78 76 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000021F777E10B0, 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 0x0000021F777E6330, 16 bytes long.
 Data: <Pv~w            > 50 76 7E 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000021F777E7650, 992 bytes long.
 Data: <0c~w      ~w    > 30 63 7E 77 1F 02 00 00 B0 10 7E 77 1F 02 00 00 
{98} normal block at 0x0000021F777E0CF0, 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 0x0000021F777DE630, 16 bytes long.
 Data: <  |w            > 00 F2 7C 77 1F 02 00 00 00 00 00 00 00 00 00 00 
{96} normal block at 0x0000021F777CF200, 40 bytes long.
 Data: <0 }w      ~w    > 30 E6 7D 77 1F 02 00 00 F0 0C 7E 77 1F 02 00 00 
{75} normal block at 0x0000021F777DF120, 16 bytes long.
 Data: <  *t            > 80 EA 2A 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x0000021F777DE860, 16 bytes long.
 Data: <@ *t            > 40 E9 2A 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x0000021F777DF1C0, 16 bytes long.
 Data: < W't            > F8 57 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x0000021F777DEB30, 16 bytes long.
 Data: < W't            > D8 57 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x0000021F777DE680, 16 bytes long.
 Data: <P 't            > 50 04 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x0000021F777DE450, 16 bytes long.
 Data: <0 't            > 30 04 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000021F777DE770, 16 bytes long.
 Data: <  't            > E0 02 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000021F777DEF40, 16 bytes long.
 Data: <  't            > 10 04 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000021F777DE900, 16 bytes long.
 Data: <p 't            > 70 04 27 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000021F777DEA90, 16 bytes long.
 Data: <  %t            > 18 C0 25 74 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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