Task 38632615

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
14:38:01 (11668): wrapper (7.9.26016): starting
14:38:01 (11668): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A26_A01_0.pdb
QB_A26_A01_0.xml
QB_A26_A01.inpcrd
QB_A26_A01_input.yaml
QB_A26_A01.pdb
QB_A26_A01.prmtop
QB_A26_A01_sys.xml
run.bat
run.sh
14:38:02 (11668): Library/usr/bin/tar.exe exited; CPU time 0.000000
14:38:02 (11668): 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 'D:\BOINC\slots\3\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 'D:\BOINC\slots\3\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) : {3835386} normal block at 0x000001B6E4C55470, 8 bytes long.
 Data: <        > 00 00 1C E5 B6 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833950} normal block at 0x000001B6E4C54730, 1080 bytes long.
 Data: <                > 1C 0C 00 00 CD CD CD CD CC 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {307} normal block at 0x000001B6E4C40690, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
16:47:42 (30276): wrapper (7.9.26016): starting
16:47:42 (30276): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1736} normal block at 0x0000012FC50C6230, 8 bytes long.
 Data: <  H /   > 00 00 48 C5 2F 01 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x0000012FC50C6800, 1080 bytes long.
 Data: <tb              > 74 62 00 00 CD CD CD CD B8 01 00 00 00 00 00 00 
Object dump complete.
16:53:24 (344): wrapper (7.9.26016): starting
16:53:24 (344): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1736} normal block at 0x0000028C2C306300, 8 bytes long.
 Data: <  -,    > 00 00 2D 2C 8C 02 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x0000028C2C307320, 1080 bytes long.
 Data: <                > F0 09 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
21:46:10 (25864): wrapper (7.9.26016): starting
21:46:10 (25864): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1736} normal block at 0x00000260E5AA5BF0, 8 bytes long.
 Data: <    `   > 00 00 A1 E5 60 02 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x00000260E5AA6850, 1080 bytes long.
 Data: <8               > 38 80 00 00 CD CD CD CD A8 01 00 00 00 00 00 00 
Object dump complete.
23:01:20 (34720): wrapper (7.9.26016): starting
23:01:20 (34720): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1736} normal block at 0x0000019CFAD75E70, 8 bytes long.
 Data: <  3     > 00 00 33 FB 9C 01 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x0000019CFAD76850, 1080 bytes long.
 Data: <X|              > 58 7C 00 00 CD CD CD CD B4 01 00 00 00 00 00 00 
Object dump complete.
04:43:40 (19112): wrapper (7.9.26016): starting
04:43:40 (19112): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1736} normal block at 0x0000021A7EBE62B0, 8 bytes long.
 Data: <   ~    > 00 00 B8 7E 1A 02 00 00 
..\lib\diagnostics_win.cpp(417) : {300} normal block at 0x0000021A7EBE6830, 1080 bytes long.
 Data: < v              > FC 76 00 00 CD CD CD CD 8C 01 00 00 00 00 00 00 
Object dump complete.
10:10:48 (12344): wrapper (7.9.26016): starting
10:10:48 (12344): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "D:\BOINC\slots\3\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 "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "D:\BOINC\slots\3\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\slots\3\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 "D:\BOINC\slots\3\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "D:\BOINC\slots\3\Lib\site-packages\atom_openmm\openmm_async_re.py", line 86, in update_state_of_replica
    stateid = self.status[repl]['stateid_current']
              ^^^^^^^^^^^
  File "D:\BOINC\slots\3\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'
10:11:07 (12344): C:/Windows/system32/cmd.exe exited; CPU time 10.218750
10:11:07 (12344): app exit status: 0x16
10:11:07 (12344): called boinc_finish(195)
0 bytes in 0 Free Blocks.
176 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: 320420 bytes.
Dumping objects ->
{1824} normal block at 0x0000021B7FA14DA0, 48 bytes long.
 Data: <PATH=D:\BOINC\sl> 50 41 54 48 3D 44 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1813} normal block at 0x0000021B7FA10520, 32 bytes long.
 Data: <HOME=D:\BOINC\sl> 48 4F 4D 45 3D 44 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1802} normal block at 0x0000021B7FA10880, 32 bytes long.
 Data: <TMP=D:\BOINC\slo> 54 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 73 6C 6F 
{1791} normal block at 0x0000021B7FA10B80, 32 bytes long.
 Data: <TEMP=D:\BOINC\sl> 54 45 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 73 6C 
{1780} normal block at 0x0000021B7FA10E80, 32 bytes long.
 Data: <TMPDIR=D:\BOINC\> 54 4D 50 44 49 52 3D 44 3A 5C 42 4F 49 4E 43 5C 
{1749} normal block at 0x0000021B7FA14D30, 48 bytes long.
 Data: <PATH=D:\BOINC\sl> 50 41 54 48 3D 44 3A 5C 42 4F 49 4E 43 5C 73 6C 
..\api\boinc_api.cpp(309) : {1736} normal block at 0x0000021B7FA15A60, 8 bytes long.
 Data: <        > 00 00 9D 7F 1B 02 00 00 
{301} normal block at 0x0000021B7FA160F0, 8 bytes long.
 Data: <Ph      > 50 68 A1 7F 1B 02 00 00 
{292} normal block at 0x0000021B7FA01DF0, 80 bytes long.
 Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C 
{291} normal block at 0x0000021B7FA160A0, 16 bytes long.
 Data: <Xg              > 58 67 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{290} normal block at 0x0000021B7FA16050, 16 bytes long.
 Data: <0g              > 30 67 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{289} normal block at 0x0000021B7FA113C0, 32 bytes long.
 Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D 
{288} normal block at 0x0000021B7FA16320, 16 bytes long.
 Data: < g              > 08 67 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{287} normal block at 0x0000021B7FA16000, 16 bytes long.
 Data: < f              > E0 66 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{286} normal block at 0x0000021B7FA15740, 16 bytes long.
 Data: < f              > B8 66 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{285} normal block at 0x0000021B7FA15EC0, 16 bytes long.
 Data: < f              > 90 66 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{284} normal block at 0x0000021B7FA149B0, 48 bytes long.
 Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F 
{283} normal block at 0x0000021B7FA15F60, 16 bytes long.
 Data: <x               > 78 F0 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{282} normal block at 0x0000021B7FA108E0, 32 bytes long.
 Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69 
{281} normal block at 0x0000021B7FA162D0, 16 bytes long.
 Data: <P               > 50 F0 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{279} normal block at 0x0000021B7FA15E70, 16 bytes long.
 Data: <(               > 28 F0 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x0000021B7FA15BA0, 16 bytes long.
 Data: <                > 00 F0 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x0000021B7FA15CE0, 16 bytes long.
 Data: <                > D8 EF 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{276} normal block at 0x0000021B7FA154C0, 16 bytes long.
 Data: <                > B0 EF 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x0000021B7FA16280, 16 bytes long.
 Data: <                > 88 EF 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x0000021B7FA10E20, 32 bytes long.
 Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55 
{273} normal block at 0x0000021B7FA158D0, 16 bytes long.
 Data: <`               > 60 EF 9F 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x0000021B7F9FEF60, 320 bytes long.
 Data: < X              > D0 58 A1 7F 1B 02 00 00 20 0E A1 7F 1B 02 00 00 
{271} normal block at 0x0000021B7FA15C90, 16 bytes long.
 Data: <pf              > 70 66 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{270} normal block at 0x0000021B7FA159C0, 16 bytes long.
 Data: <Hf              > 48 66 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x0000021B7FA10760, 32 bytes long.
 Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65 
{268} normal block at 0x0000021B7FA15C40, 16 bytes long.
 Data: < f              > 20 66 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000021B7FA10D60, 32 bytes long.
 Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62 
{266} normal block at 0x0000021B7FA15E20, 16 bytes long.
 Data: <he              > 68 65 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{265} normal block at 0x0000021B7FA15970, 16 bytes long.
 Data: <@e              > 40 65 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x0000021B7FA15510, 16 bytes long.
 Data: < e              > 18 65 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000021B7FA15FB0, 16 bytes long.
 Data: < d              > F0 64 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000021B7FA15D30, 16 bytes long.
 Data: < d              > C8 64 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{261} normal block at 0x0000021B7FA15A10, 16 bytes long.
 Data: < d              > A0 64 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000021B7FA161E0, 16 bytes long.
 Data: <`O              > 60 4F A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{258} normal block at 0x0000021B7FA14F60, 40 bytes long.
 Data: < a      0M      > E0 61 A1 7F 1B 02 00 00 30 4D A1 7F 1B 02 00 00 
{257} normal block at 0x0000021B7FA15DD0, 16 bytes long.
 Data: < d              > 80 64 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000021B7FA16230, 16 bytes long.
 Data: <Xd              > 58 64 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{255} normal block at 0x0000021B7FA10A60, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{254} normal block at 0x0000021B7FA15470, 16 bytes long.
 Data: <0d              > 30 64 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x0000021B7FA16430, 992 bytes long.
 Data: <pT      `       > 70 54 A1 7F 1B 02 00 00 60 0A A1 7F 1B 02 00 00 
{89} normal block at 0x0000021B7FA10D00, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{88} normal block at 0x0000021B7FA0D510, 16 bytes long.
 Data: <`H              > 60 48 A1 7F 1B 02 00 00 00 00 00 00 00 00 00 00 
{87} normal block at 0x0000021B7FA14860, 40 bytes long.
 Data: <                > 10 D5 A0 7F 1B 02 00 00 00 0D A1 7F 1B 02 00 00 
{66} normal block at 0x0000021B7FA0DB00, 16 bytes long.
 Data: <   U            > 80 EA 9E 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000021B7FA0DAB0, 16 bytes long.
 Data: <@  U            > 40 E9 9E 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000021B7FA0CED0, 16 bytes long.
 Data: < W U            > F8 57 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000021B7FA0D380, 16 bytes long.
 Data: < W U            > D8 57 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000021B7FA0D9C0, 16 bytes long.
 Data: <P  U            > 50 04 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000021B7FA0D1A0, 16 bytes long.
 Data: <0  U            > 30 04 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000021B7FA0D600, 16 bytes long.
 Data: <   U            > E0 02 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000021B7FA0DA10, 16 bytes long.
 Data: <   U            > 10 04 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000021B7FA0D7E0, 16 bytes long.
 Data: <p  U            > 70 04 9B 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x0000021B7FA0DCE0, 16 bytes long.
 Data: <   U            > 18 C0 99 55 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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