Task 38627384

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>
07:08:04 (371476): wrapper (7.9.26016): starting
07:08:04 (371476): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A24_A29_0.pdb
QB_A24_A29_0.xml
QB_A24_A29.inpcrd
QB_A24_A29_input.yaml
QB_A24_A29.pdb
QB_A24_A29.prmtop
QB_A24_A29_sys.xml
run.bat
run.sh
07:08:06 (371476): Library/usr/bin/tar.exe exited; CPU time 0.046875
07:08:06 (371476): 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) : {3835161} normal block at 0x000001AD374FB290, 8 bytes long.
 Data: <   7    > 00 00 A1 37 AD 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833958} normal block at 0x000001AD374F9530, 1080 bytes long.
 Data: <H       (       > 48 AA 05 00 CD CD CD CD 28 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x000001AD374E05F0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
09:43:28 (385924): wrapper (7.9.26016): starting
09:43:28 (385924): 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) : {1507} normal block at 0x0000019006F1BB10, 8 bytes long.
 Data: <  H     > 00 00 48 07 90 01 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x0000019006F1E1D0, 1080 bytes long.
 Data: <                > F0 E6 05 00 CD CD CD CD 88 02 00 00 00 00 00 00 
Object dump complete.
14:55:08 (392216): wrapper (7.9.26016): starting
14:55:08 (392216): 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) : {1507} normal block at 0x000001A9C148B390, 8 bytes long.
 Data: <        > 00 00 8B C1 A9 01 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x000001A9C148EF70, 1080 bytes long.
 Data: <t               > 74 C3 05 00 CD CD CD CD 80 02 00 00 00 00 00 00 
Object dump complete.
15:29:18 (400380): wrapper (7.9.26016): starting
15:29:18 (400380): 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) : {1507} normal block at 0x00000224C4BBAB70, 8 bytes long.
 Data: <    $   > 00 00 B4 C4 24 02 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x00000224C4BBF090, 1080 bytes long.
 Data: <x#      h       > 78 23 06 00 CD CD CD CD 68 02 00 00 00 00 00 00 
Object dump complete.
20:06:09 (407948): wrapper (7.9.26016): starting
20:06:09 (407948): 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) : {1507} normal block at 0x000001FC08F6B230, 8 bytes long.
 Data: <        > 00 00 F3 08 FC 01 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x000001FC08F6DC10, 1080 bytes long.
 Data: <                > A4 02 06 00 CD CD CD CD 84 02 00 00 00 00 00 00 
Object dump complete.
00:49:59 (391620): wrapper (7.9.26016): starting
00:49:59 (391620): 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'
00:50:14 (391620): C:/Windows/system32/cmd.exe exited; CPU time 9.953125
00:50:14 (391620): app exit status: 0x16
00:50:14 (391620): 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: 384678 bytes.
Dumping objects ->
{1595} normal block at 0x0000017334130D20, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1584} normal block at 0x0000017334131110, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1573} normal block at 0x0000017334131500, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1562} normal block at 0x00000173341310A0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1551} normal block at 0x0000017334144AD0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1520} normal block at 0x000001733412F880, 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) : {1507} normal block at 0x00000173341276C0, 8 bytes long.
 Data: <   4s   > 00 00 0F 34 73 01 00 00 
{305} normal block at 0x00000173341269A0, 8 bytes long.
 Data: <   4s   > 80 F1 12 34 73 01 00 00 
{296} normal block at 0x00000173341173A0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{295} normal block at 0x0000017334126D60, 16 bytes long.
 Data: < ~ 4s           > C8 7E 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000017334126D10, 16 bytes long.
 Data: < ~ 4s           > A0 7E 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x000001733412D9B0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{292} normal block at 0x0000017334127850, 16 bytes long.
 Data: <x~ 4s           > 78 7E 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000017334126950, 16 bytes long.
 Data: <P~ 4s           > 50 7E 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000017334126CC0, 16 bytes long.
 Data: <(~ 4s           > 28 7E 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000173341272B0, 16 bytes long.
 Data: < ~ 4s           > 00 7E 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000017334144C90, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{287} normal block at 0x0000017334126C20, 16 bytes long.
 Data: < . 4s           > D8 2E 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001733412E2B0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{285} normal block at 0x0000017334126BD0, 16 bytes long.
 Data: < . 4s           > B0 2E 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000017334127670, 16 bytes long.
 Data: < . 4s           > 88 2E 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000017334127300, 16 bytes long.
 Data: <`. 4s           > 60 2E 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000017334127260, 16 bytes long.
 Data: <8. 4s           > 38 2E 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000173341277B0, 16 bytes long.
 Data: < . 4s           > 10 2E 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000017334126EF0, 16 bytes long.
 Data: < - 4s           > E8 2D 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001733412E370, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{277} normal block at 0x0000017334127620, 16 bytes long.
 Data: < - 4s           > C0 2D 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000017334142DC0, 320 bytes long.
 Data: < v 4s   p  4s   > 20 76 12 34 73 01 00 00 70 E3 12 34 73 01 00 00 
{275} normal block at 0x00000173341275D0, 16 bytes long.
 Data: < } 4s           > E0 7D 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000173341271C0, 16 bytes long.
 Data: < } 4s           > B8 7D 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x000001733412E070, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{272} normal block at 0x0000017334126B30, 16 bytes long.
 Data: < } 4s           > 90 7D 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001733412D950, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{270} normal block at 0x0000017334127030, 16 bytes long.
 Data: < | 4s           > D8 7C 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000173341274E0, 16 bytes long.
 Data: < | 4s           > B0 7C 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000173341270D0, 16 bytes long.
 Data: < | 4s           > 88 7C 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000173341273A0, 16 bytes long.
 Data: <`| 4s           > 60 7C 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000017334126E00, 16 bytes long.
 Data: <8| 4s           > 38 7C 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000017334127800, 16 bytes long.
 Data: < | 4s           > 10 7C 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000017334126AE0, 16 bytes long.
 Data: <pM 4s           > 70 4D 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000017334144D70, 40 bytes long.
 Data: < j 4s      4s   > E0 6A 12 34 73 01 00 00 80 F8 12 34 73 01 00 00 
{261} normal block at 0x0000017334126FE0, 16 bytes long.
 Data: < { 4s           > F0 7B 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000017334126C70, 16 bytes long.
 Data: < { 4s           > C8 7B 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000017334122110, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{258} normal block at 0x0000017334126F90, 16 bytes long.
 Data: < { 4s           > A0 7B 12 34 73 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000017334127BA0, 992 bytes long.
 Data: < o 4s    ! 4s   > 90 6F 12 34 73 01 00 00 10 21 12 34 73 01 00 00 
{93} normal block at 0x00000173341216F0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{92} normal block at 0x0000017334126F40, 16 bytes long.
 Data: < L 4s           > 20 4C 14 34 73 01 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x0000017334144C20, 40 bytes long.
 Data: <@o 4s      4s   > 40 6F 12 34 73 01 00 00 F0 16 12 34 73 01 00 00 
{70} normal block at 0x0000017334127710, 16 bytes long.
 Data: <                > 80 EA AC AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000017334137B50, 16 bytes long.
 Data: <@               > 40 E9 AC AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000017334137AB0, 16 bytes long.
 Data: < W              > F8 57 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000017334137A60, 16 bytes long.
 Data: < W              > D8 57 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000017334137A10, 16 bytes long.
 Data: <P               > 50 04 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000173341379C0, 16 bytes long.
 Data: <0               > 30 04 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000017334138820, 16 bytes long.
 Data: <                > E0 02 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000017334137B00, 16 bytes long.
 Data: <                > 10 04 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000173341387D0, 16 bytes long.
 Data: <p               > 70 04 A9 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000017334138730, 16 bytes long.
 Data: <                > 18 C0 A7 AF F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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