Task 38678505

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>
14:54:29 (30908): wrapper (7.9.26016): starting
14:54:29 (30908): 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
14:54:30 (30908): Library/usr/bin/tar.exe exited; CPU time 0.000000
14:54:30 (30908): 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\29\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\29\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) : {3835109} normal block at 0x00000272D51EDF50, 8 bytes long.
 Data: <    r   > 00 00 0B D5 72 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833958} normal block at 0x00000272D7491330, 1080 bytes long.
 Data: < F      8       > A4 46 00 00 CD CD CD CD 38 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x00000272D51E5060, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
15:10:07 (25848): wrapper (7.9.26016): starting
15:10:07 (25848): 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\29\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x000001D87B7851D0, 8 bytes long.
 Data: <  n{    > 00 00 6E 7B D8 01 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x000001D87B785890, 1080 bytes long.
 Data: <tZ      \       > 74 5A 00 00 CD CD CD CD 5C 01 00 00 00 00 00 00 
Object dump complete.
15:20:38 (38108): wrapper (7.9.26016): starting
15:20:38 (38108): 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\29\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x0000017E1E1F50E0, 8 bytes long.
 Data: <    ~   > 00 00 0B 1E 7E 01 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x0000017E1E1F5890, 1080 bytes long.
 Data: < {      p       > F8 7B 00 00 CD CD CD CD 70 01 00 00 00 00 00 00 
Object dump complete.
15:34:09 (34980): wrapper (7.9.26016): starting
15:34:09 (34980): 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\29\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1455} normal block at 0x0000022BB6CC4FA0, 8 bytes long.
 Data: <    +   > 00 00 A6 B6 2B 02 00 00 
..\lib\diagnostics_win.cpp(417) : {304} normal block at 0x0000022BB6CC5890, 1080 bytes long.
 Data: < w      \       > B0 77 00 00 CD CD CD CD 5C 01 00 00 00 00 00 00 
Object dump complete.
15:47:16 (30364): wrapper (7.9.26016): starting
15:47:16 (30364): 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\29\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\29\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\29\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\29\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\29\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\29\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\29\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\29\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\29\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\29\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\29\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\29\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\29\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'
15:47:31 (30364): C:/Windows/system32/cmd.exe exited; CPU time 9.796875
15:47:31 (30364): app exit status: 0x16
15:47:31 (30364): 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: 390235 bytes.
Dumping objects ->
{1543} normal block at 0x0000024ABFAE3980, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1532} normal block at 0x0000024ABFAE38A0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1521} normal block at 0x0000024ABFAE3910, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1510} normal block at 0x0000024ABFAE3E50, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1499} normal block at 0x0000024ABFAE3C90, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1468} normal block at 0x0000024ABFACEC90, 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) : {1455} normal block at 0x0000024ABFAE5400, 8 bytes long.
 Data: <    J   > 00 00 8B BF 4A 02 00 00 
{305} normal block at 0x0000024ABFAE5090, 8 bytes long.
 Data: < X  J   > 90 58 AE BF 4A 02 00 00 
{296} normal block at 0x0000024ABFAE01F0, 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 0x0000024ABFAE4A50, 16 bytes long.
 Data: < W  J           > 98 57 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x0000024ABFAE51D0, 16 bytes long.
 Data: <pW  J           > 70 57 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{293} normal block at 0x0000024ABFADF390, 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 0x0000024ABFAE4A00, 16 bytes long.
 Data: <HW  J           > 48 57 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x0000024ABFAE4960, 16 bytes long.
 Data: < W  J           > 20 57 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000024ABFAE45F0, 16 bytes long.
 Data: < V  J           > F8 56 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000024ABFAE4730, 16 bytes long.
 Data: < V  J           > D0 56 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x0000024ABFAE3FA0, 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 0x0000024ABFAE4910, 16 bytes long.
 Data: <X   J           > 58 E0 AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000024ABFADF330, 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 0x0000024ABFAE48C0, 16 bytes long.
 Data: <0   J           > 30 E0 AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x0000024ABFAE4870, 16 bytes long.
 Data: <    J           > 08 E0 AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000024ABFAE4D70, 16 bytes long.
 Data: <    J           > E0 DF AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x0000024ABFAE5180, 16 bytes long.
 Data: <    J           > B8 DF AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x0000024ABFAE4FF0, 16 bytes long.
 Data: <    J           > 90 DF AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000024ABFAE46E0, 16 bytes long.
 Data: <h   J           > 68 DF AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000024ABFADF810, 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 0x0000024ABFAE4FA0, 16 bytes long.
 Data: <@   J           > 40 DF AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000024ABFACDF40, 320 bytes long.
 Data: < O  J       J   > A0 4F AE BF 4A 02 00 00 10 F8 AD BF 4A 02 00 00 
{275} normal block at 0x0000024ABFAE4780, 16 bytes long.
 Data: < V  J           > B0 56 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000024ABFAE5040, 16 bytes long.
 Data: < V  J           > 88 56 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{273} normal block at 0x0000024ABFADED30, 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 0x0000024ABFAE5130, 16 bytes long.
 Data: <`V  J           > 60 56 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x0000024ABFADF5D0, 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 0x0000024ABFAE45A0, 16 bytes long.
 Data: < U  J           > A8 55 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000024ABFAE4690, 16 bytes long.
 Data: < U  J           > 80 55 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x0000024ABFAE5270, 16 bytes long.
 Data: <XU  J           > 58 55 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000024ABFAE4F50, 16 bytes long.
 Data: <0U  J           > 30 55 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x0000024ABFAE4B40, 16 bytes long.
 Data: < U  J           > 08 55 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000024ABFAE4550, 16 bytes long.
 Data: < T  J           > E0 54 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000024ABFAE4500, 16 bytes long.
 Data: <0?  J           > 30 3F AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000024ABFAE3F30, 40 bytes long.
 Data: < E  J       J   > 00 45 AE BF 4A 02 00 00 90 EC AC BF 4A 02 00 00 
{261} normal block at 0x0000024ABFAE44B0, 16 bytes long.
 Data: < T  J           > C0 54 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000024ABFAE4820, 16 bytes long.
 Data: < T  J           > 98 54 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000024ABFADEDF0, 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 0x0000024ABFAE4D20, 16 bytes long.
 Data: <pT  J           > 70 54 AE BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000024ABFAE5470, 992 bytes long.
 Data: < M  J       J   > 20 4D AE BF 4A 02 00 00 F0 ED AD BF 4A 02 00 00 
{93} normal block at 0x0000024ABFADF690, 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 0x0000024ABFADDC30, 16 bytes long.
 Data: <    J           > 00 C2 AC BF 4A 02 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x0000024ABFACC200, 40 bytes long.
 Data: <0   J       J   > 30 DC AD BF 4A 02 00 00 90 F6 AD BF 4A 02 00 00 
{70} normal block at 0x0000024ABFADDA00, 16 bytes long.
 Data: <  !             > 80 EA 21 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000024ABFADE7C0, 16 bytes long.
 Data: <@ !             > 40 E9 21 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000024ABFADDF00, 16 bytes long.
 Data: < W              > F8 57 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000024ABFADDFF0, 16 bytes long.
 Data: < W              > D8 57 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000024ABFADE130, 16 bytes long.
 Data: <P               > 50 04 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000024ABFADDBE0, 16 bytes long.
 Data: <0               > 30 04 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000024ABFADE360, 16 bytes long.
 Data: <                > E0 02 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000024ABFADDEB0, 16 bytes long.
 Data: <                > 10 04 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000024ABFADDA50, 16 bytes long.
 Data: <p               > 70 04 1E 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000024ABFADDB90, 16 bytes long.
 Data: <                > 18 C0 1C 0B F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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