Task 38660926

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>
20:31:48 (38780): wrapper (7.9.26016): starting
20:31:48 (38780): 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
20:31:49 (38780): Library/usr/bin/tar.exe exited; CPU time 0.015625
20:31:49 (38780): 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) : {3835488} normal block at 0x00000273EA46E140, 8 bytes long.
 Data: <  B s   > 00 00 42 EA 73 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833960} normal block at 0x00000273EC0D43C0, 1080 bytes long.
 Data: < $      d       > BC 24 00 00 CD CD CD CD 64 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {312} normal block at 0x00000273EA471CC0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
20:38:24 (5192): wrapper (7.9.26016): starting
20:38:24 (5192): 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\12\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\12\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) : {1833} normal block at 0x000001BBCA8962D0, 8 bytes long.
 Data: <        > 00 00 DB CA BB 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001BBCA897160, 1080 bytes long.
 Data: < h      D       > A0 68 00 00 CD CD CD CD 44 01 00 00 00 00 00 00 
Object dump complete.
21:11:24 (20580): wrapper (7.9.26016): starting
21:11:24 (20580): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x000002121BD05FF0, 8 bytes long.
 Data: <  %     > 00 00 25 1C 12 02 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000002121BD071F0, 1080 bytes long.
 Data: <l       H       > 6C 16 00 00 CD CD CD CD 48 01 00 00 00 00 00 00 
Object dump complete.
21:39:13 (6880): wrapper (7.9.26016): starting
21:39:13 (6880): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1833} normal block at 0x00000137A6765FF0, 8 bytes long.
 Data: <  l 7   > 00 00 6C A6 37 01 00 00 
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x00000137A67671F0, 1080 bytes long.
 Data: < f      L       > 88 66 00 00 CD CD CD CD 4C 01 00 00 00 00 00 00 
Object dump complete.
21:42:48 (10764): wrapper (7.9.26016): starting
21:42:48 (10764): 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\12\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\12\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\12\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\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\12\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\12\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\12\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'
21:43:13 (10764): C:/Windows/system32/cmd.exe exited; CPU time 18.828125
21:43:13 (10764): app exit status: 0x16
21:43:13 (10764): 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: 555907 bytes.
Dumping objects ->
{1921} normal block at 0x00000207B3245900, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1910} normal block at 0x00000207B3245890, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1899} normal block at 0x00000207B3245510, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1888} normal block at 0x00000207B32453C0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1877} normal block at 0x00000207B32455F0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1846} normal block at 0x00000207B3239680, 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) : {1833} normal block at 0x00000207B3246770, 8 bytes long.
 Data: <  i     > 00 00 69 B3 07 02 00 00 
{306} normal block at 0x00000207B3246AE0, 8 bytes long.
 Data: < q$     > F0 71 24 B3 07 02 00 00 
{297} normal block at 0x00000207B3237140, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{296} normal block at 0x00000207B32469F0, 16 bytes long.
 Data: < p$             > F8 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{295} normal block at 0x00000207B32462C0, 16 bytes long.
 Data: < p$             > D0 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{294} normal block at 0x00000207B323FD10, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{293} normal block at 0x00000207B3246180, 16 bytes long.
 Data: < p$             > A8 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{292} normal block at 0x00000207B32465E0, 16 bytes long.
 Data: < p$             > 80 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{291} normal block at 0x00000207B3245F00, 16 bytes long.
 Data: <Xp$             > 58 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x00000207B3246360, 16 bytes long.
 Data: <0p$             > 30 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x00000207B3245430, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{288} normal block at 0x00000207B3246900, 16 bytes long.
 Data: <  "             > B8 F7 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x00000207B323FCB0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{286} normal block at 0x00000207B3246D10, 16 bytes long.
 Data: <  "             > 90 F7 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x00000207B3245E60, 16 bytes long.
 Data: <h "             > 68 F7 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{283} normal block at 0x00000207B3246680, 16 bytes long.
 Data: <@ "             > 40 F7 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x00000207B32463B0, 16 bytes long.
 Data: <  "             > 18 F7 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{281} normal block at 0x00000207B3246950, 16 bytes long.
 Data: <  "             > F0 F6 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{280} normal block at 0x00000207B3246590, 16 bytes long.
 Data: <  "             > C8 F6 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x00000207B3240310, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{278} normal block at 0x00000207B3246A90, 16 bytes long.
 Data: <  "             > A0 F6 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000207B322F6A0, 320 bytes long.
 Data: < j$       $     > 90 6A 24 B3 07 02 00 00 10 03 24 B3 07 02 00 00 
{276} normal block at 0x00000207B32468B0, 16 bytes long.
 Data: < p$             > 10 70 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000207B3246270, 16 bytes long.
 Data: < o$             > E8 6F 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000207B32402B0, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{273} normal block at 0x00000207B3246540, 16 bytes long.
 Data: < o$             > C0 6F 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000207B323FF50, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{271} normal block at 0x00000207B3246C20, 16 bytes long.
 Data: < o$             > 08 6F 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x00000207B3246220, 16 bytes long.
 Data: < n$             > E0 6E 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000207B3246130, 16 bytes long.
 Data: < n$             > B8 6E 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{268} normal block at 0x00000207B32460E0, 16 bytes long.
 Data: < n$             > 90 6E 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000207B3246720, 16 bytes long.
 Data: <hn$             > 68 6E 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000207B32461D0, 16 bytes long.
 Data: <@n$             > 40 6E 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000207B32466D0, 16 bytes long.
 Data: < R$             > E0 52 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x00000207B32452E0, 40 bytes long.
 Data: < f$       #     > D0 66 24 B3 07 02 00 00 80 96 23 B3 07 02 00 00 
{262} normal block at 0x00000207B3246860, 16 bytes long.
 Data: < n$             > 20 6E 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x00000207B3246400, 16 bytes long.
 Data: < m$             > F8 6D 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x00000207B323FEF0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{259} normal block at 0x00000207B32464F0, 16 bytes long.
 Data: < m$             > D0 6D 24 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x00000207B3246DD0, 992 bytes long.
 Data: < d$       #     > F0 64 24 B3 07 02 00 00 F0 FE 23 B3 07 02 00 00 
{94} normal block at 0x00000207B323F890, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{93} normal block at 0x00000207B323E140, 16 bytes long.
 Data: <  "             > A0 F3 22 B3 07 02 00 00 00 00 00 00 00 00 00 00 
{92} normal block at 0x00000207B322F3A0, 40 bytes long.
 Data: <@ #       #     > 40 E1 23 B3 07 02 00 00 90 F8 23 B3 07 02 00 00 
{71} normal block at 0x00000207B323E550, 16 bytes long.
 Data: <  W:            > 80 EA 57 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000207B323E1E0, 16 bytes long.
 Data: <@ W:            > 40 E9 57 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000207B323E050, 16 bytes long.
 Data: < WT:            > F8 57 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000207B323E410, 16 bytes long.
 Data: < WT:            > D8 57 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000207B323D790, 16 bytes long.
 Data: <P T:            > 50 04 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000207B323DD80, 16 bytes long.
 Data: <0 T:            > 30 04 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x00000207B323D9C0, 16 bytes long.
 Data: <  T:            > E0 02 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x00000207B323E190, 16 bytes long.
 Data: <  T:            > 10 04 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x00000207B323E000, 16 bytes long.
 Data: <p T:            > 70 04 54 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x00000207B323DE20, 16 bytes long.
 Data: <  R:            > 18 C0 52 3A F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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