Task 38692568

Stderr output

<core_client_version>8.2.11</core_client_version>
<![CDATA[
<message>
(null) nelze spustit.
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
00:54:10 (26808): wrapper (7.9.26016): starting
00:54:10 (26808): 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
00:54:12 (26808): Library/usr/bin/tar.exe exited; CPU time 0.015625
00:54:12 (26808): 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 'E:\_BOINC\slots\4\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 'E:\_BOINC\slots\4\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) : {3835278} normal block at 0x0000022F1B039C40, 8 bytes long.
 Data: <    /   > 00 00 01 1B 2F 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x0000022F1DB29050, 1080 bytes long.
 Data: < %              > AC 25 00 00 CD CD CD CD 80 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x0000022F1B0444B0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
10:10:45 (24316): wrapper (7.9.26016): starting
10:10:45 (24316): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file E:\_BOINC\slots\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
10:23:44 (2464): wrapper (7.9.26016): starting
10:23:44 (2464): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file E:\_BOINC\slots\4\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "E:\_BOINC\slots\4\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 "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "E:\_BOINC\slots\4\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "E:\_BOINC\slots\4\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 "E:\_BOINC\slots\4\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "E:\_BOINC\slots\4\Lib\site-packages\atom_openmm\openmm_async_re.py", line 86, in update_state_of_replica
    stateid = self.status[repl]['stateid_current']
              ^^^^^^^^^^^
  File "E:\_BOINC\slots\4\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'
10:24:06 (2464): C:/Windows/system32/cmd.exe exited; CPU time 14.000000
10:24:06 (2464): app exit status: 0x16
10:24:06 (2464): called boinc_finish(195)
0 bytes in 0 Free Blocks.
494 bytes in 8 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: 408437 bytes.
Dumping objects ->
{1715} normal block at 0x000001495F845660, 48 bytes long.
 Data: <PATH=E:\_BOINC\s> 50 41 54 48 3D 45 3A 5C 5F 42 4F 49 4E 43 5C 73 
{1704} normal block at 0x000001495F843530, 32 bytes long.
 Data: <HOME=E:\_BOINC\s> 48 4F 4D 45 3D 45 3A 5C 5F 42 4F 49 4E 43 5C 73 
{1693} normal block at 0x000001495F844130, 32 bytes long.
 Data: <TMP=E:\_BOINC\sl> 54 4D 50 3D 45 3A 5C 5F 42 4F 49 4E 43 5C 73 6C 
{1682} normal block at 0x000001495F843950, 32 bytes long.
 Data: <TEMP=E:\_BOINC\s> 54 45 4D 50 3D 45 3A 5C 5F 42 4F 49 4E 43 5C 73 
{1671} normal block at 0x000001495F8437D0, 32 bytes long.
 Data: <TMPDIR=E:\_BOINC> 54 4D 50 44 49 52 3D 45 3A 5C 5F 42 4F 49 4E 43 
{1640} normal block at 0x000001495F845510, 48 bytes long.
 Data: <PATH=E:\_BOINC\s> 50 41 54 48 3D 45 3A 5C 5F 42 4F 49 4E 43 5C 73 
{1629} normal block at 0x000001495F8488D0, 159 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {1626} normal block at 0x000001495F849C00, 8 bytes long.
 Data: <   _I   > 00 00 A0 5F 49 01 00 00 
{957} normal block at 0x000001495F848AF0, 159 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{303} normal block at 0x000001495F8490C0, 8 bytes long.
 Data: <   _I   > C0 A4 84 5F 49 01 00 00 
{294} normal block at 0x000001495F82EC80, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{293} normal block at 0x000001495F849070, 16 bytes long.
 Data: <   _I           > C8 A3 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x000001495F848E90, 16 bytes long.
 Data: <   _I           > A0 A3 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x000001495F843E90, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{290} normal block at 0x000001495F8496B0, 16 bytes long.
 Data: <x  _I           > 78 A3 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x000001495F848E40, 16 bytes long.
 Data: <P  _I           > 50 A3 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{288} normal block at 0x000001495F849B60, 16 bytes long.
 Data: <(  _I           > 28 A3 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x000001495F849020, 16 bytes long.
 Data: <   _I           > 00 A3 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x000001495F8455F0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{285} normal block at 0x000001495F848F80, 16 bytes long.
 Data: <xS _I           > 78 53 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x000001495F8438F0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{283} normal block at 0x000001495F849BB0, 16 bytes long.
 Data: <PS _I           > 50 53 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x000001495F848DA0, 16 bytes long.
 Data: <(S _I           > 28 53 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x000001495F849930, 16 bytes long.
 Data: < S _I           > 00 53 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x000001495F848D50, 16 bytes long.
 Data: < R _I           > D8 52 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x000001495F8497A0, 16 bytes long.
 Data: < R _I           > B0 52 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x000001495F849570, 16 bytes long.
 Data: < R _I           > 88 52 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x000001495F844190, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{275} normal block at 0x000001495F849430, 16 bytes long.
 Data: <`R _I           > 60 52 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x000001495F845260, 320 bytes long.
 Data: <0  _I    A _I   > 30 94 84 5F 49 01 00 00 90 41 84 5F 49 01 00 00 
{273} normal block at 0x000001495F849390, 16 bytes long.
 Data: <   _I           > E0 A2 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001495F849AC0, 16 bytes long.
 Data: <   _I           > B8 A2 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001495F8434D0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{270} normal block at 0x000001495F849980, 16 bytes long.
 Data: <   _I           > 90 A2 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001495F844310, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{268} normal block at 0x000001495F848D00, 16 bytes long.
 Data: <   _I           > D8 A1 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x000001495F849250, 16 bytes long.
 Data: <   _I           > B0 A1 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x000001495F849520, 16 bytes long.
 Data: <   _I           > 88 A1 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x000001495F8494D0, 16 bytes long.
 Data: <`  _I           > 60 A1 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x000001495F849B10, 16 bytes long.
 Data: <8  _I           > 38 A1 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x000001495F849840, 16 bytes long.
 Data: <   _I           > 10 A1 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x000001495F848FD0, 16 bytes long.
 Data: < U _I           > 80 55 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x000001495F845580, 40 bytes long.
 Data: <   _I    U _I   > D0 8F 84 5F 49 01 00 00 10 55 84 5F 49 01 00 00 
{259} normal block at 0x000001495F849660, 16 bytes long.
 Data: <   _I           > F0 A0 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x000001495F848F30, 16 bytes long.
 Data: <   _I           > C8 A0 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x000001495F843CB0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{256} normal block at 0x000001495F849110, 16 bytes long.
 Data: <   _I           > A0 A0 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x000001495F84A0A0, 992 bytes long.
 Data: <   _I    < _I   > 10 91 84 5F 49 01 00 00 B0 3C 84 5F 49 01 00 00 
{91} normal block at 0x000001495F843DD0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{90} normal block at 0x000001495F83C8C0, 16 bytes long.
 Data: <0T _I           > 30 54 84 5F 49 01 00 00 00 00 00 00 00 00 00 00 
{89} normal block at 0x000001495F845430, 40 bytes long.
 Data: <   _I    = _I   > C0 C8 83 5F 49 01 00 00 D0 3D 84 5F 49 01 00 00 
{68} normal block at 0x000001495F83C7D0, 16 bytes long.
 Data: <                > 80 EA AE AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000001495F83C730, 16 bytes long.
 Data: <@               > 40 E9 AE AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001495F83C640, 16 bytes long.
 Data: < W              > F8 57 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001495F83C1E0, 16 bytes long.
 Data: < W              > D8 57 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001495F83C190, 16 bytes long.
 Data: <P               > 50 04 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001495F83C140, 16 bytes long.
 Data: <0               > 30 04 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001495F83C6E0, 16 bytes long.
 Data: <                > E0 02 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001495F83CB40, 16 bytes long.
 Data: <                > 10 04 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001495F83C780, 16 bytes long.
 Data: <p               > 70 04 AB AD F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001495F83C0F0, 16 bytes long.
 Data: <                > 18 C0 A9 AD F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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