Task 38583449

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>
06:38:29 (8848): wrapper (7.9.26016): starting
06:38:29 (8848): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A01_A16_0.pdb
QB_A01_A16_0.xml
QB_A01_A16_equil.pdb
QB_A01_A16.inpcrd
QB_A01_A16_input.yaml
QB_A01_A16_mdlambda.pdb
QB_A01_A16_min.pdb
QB_A01_A16_npt.pdb
QB_A01_A16.pdb
QB_A01_A16.prmtop
QB_A01_A16_sys.xml
QB_A01_A16_therm.pdb
run.bat
run.sh
06:38:33 (8848): Library/usr/bin/tar.exe exited; CPU time 0.000000
06:38:33 (8848): 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\14\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.
  Running command pip subprocess to install build dependencies
  Using pip 24.3.1 from C:\ProgramData\BOINC\slots\14\Lib\site-packages\pip (python 3.11)
  Collecting setuptools
    Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl.metadata
    Downloading setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
  Collecting setuptools-scm>=8
    Obtaining dependency information for setuptools-scm>=8 from https://files.pythonhosted.org/packages/3d/ea/ac2bf868899d0d2e82ef72d350d97a846110c709bacf2d968431576ca915/setuptools_scm-9.2.2-py3-none-any.whl.metadata
    Downloading setuptools_scm-9.2.2-py3-none-any.whl.metadata (7.7 kB)
  Collecting packaging>=20 (from setuptools-scm>=8)
    Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl.metadata
    Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
  Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB)
     ---------------------------------------- 1.2/1.2 MB 6.0 MB/s eta 0:00:00
  Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
  Using cached packaging-25.0-py3-none-any.whl (66 kB)
  Installing collected packages: setuptools, packaging, setuptools-scm
    Creating C:\ProgramData\BOINC\slots\14\pip-build-env-diys_6m5\overlay\Scripts
  Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
  Running command Getting requirements to build wheel
  C:\ProgramData\BOINC\slots\14\pip-build-env-diys_6m5\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
    warnings.warn(self.message)
  running egg_info
  writing atom_openmm.egg-info\PKG-INFO
  writing dependency_links to atom_openmm.egg-info\dependency_links.txt
  writing entry points to atom_openmm.egg-info\entry_points.txt
  writing requirements to atom_openmm.egg-info\requires.txt
  writing top-level names to atom_openmm.egg-info\top_level.txt
  listing git files failed - pretending there aren't any
  reading manifest file 'atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'atom_openmm.egg-info\SOURCES.txt'
  Running command Preparing metadata (pyproject.toml)
  C:\ProgramData\BOINC\slots\14\pip-build-env-diys_6m5\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
    warnings.warn(self.message)
  running dist_info
  creating C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\14\pip-modern-metadata-5hy17awv\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\14\pip-build-env-diys_6m5\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
    warnings.warn(self.message)
  running bdist_wheel
  running build
  running build_py
  creating build\lib\atom_openmm
  copying atom_openmm\abfe_explicit.py -> build\lib\atom_openmm
  copying atom_openmm\abfe_production.py -> build\lib\atom_openmm
  copying atom_openmm\abfe_structprep.py -> build\lib\atom_openmm
  copying atom_openmm\async_re.py -> build\lib\atom_openmm
  copying atom_openmm\gibbs_sampling.py -> build\lib\atom_openmm
  copying atom_openmm\local_openmm_transport.py -> build\lib\atom_openmm
  copying atom_openmm\make_atm_system_from_amber.py -> build\lib\atom_openmm
  copying atom_openmm\make_atm_system_from_pdb.py -> build\lib\atom_openmm
  copying atom_openmm\make_atm_system_from_rcpt_lig.py -> build\lib\atom_openmm
  copying atom_openmm\ommreplica.py -> build\lib\atom_openmm
  copying atom_openmm\ommsystem.py -> build\lib\atom_openmm
  copying atom_openmm\ommworker.py -> build\lib\atom_openmm
  copying atom_openmm\openmm_async_re.py -> build\lib\atom_openmm
  copying atom_openmm\rbfe_explicit.py -> build\lib\atom_openmm
  copying atom_openmm\rbfe_production.py -> build\lib\atom_openmm
  copying atom_openmm\rbfe_structprep.py -> build\lib\atom_openmm
  copying atom_openmm\temperatureRE_explicit.py -> build\lib\atom_openmm
  copying atom_openmm\transport.py -> build\lib\atom_openmm
  copying atom_openmm\uwham.py -> build\lib\atom_openmm
  copying atom_openmm\__init__.py -> build\lib\atom_openmm
  creating build\lib\atom_openmm\utils
  copying atom_openmm\utils\AtomUtils.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\config.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\singal_guard.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\timer.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\__init__.py -> build\lib\atom_openmm\utils
  running egg_info
  writing atom_openmm.egg-info\PKG-INFO
  writing dependency_links to atom_openmm.egg-info\dependency_links.txt
  writing entry points to atom_openmm.egg-info\entry_points.txt
  writing requirements to atom_openmm.egg-info\requires.txt
  writing top-level names to atom_openmm.egg-info\top_level.txt
  listing git files failed - pretending there aren't any
  reading manifest file 'atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'atom_openmm.egg-info\SOURCES.txt'
  copying atom_openmm\utils\logging.conf -> build\lib\atom_openmm\utils
  installing to build\bdist.win-amd64\wheel
  running install
  running install_lib
  creating build\bdist.win-amd64\wheel
  creating build\bdist.win-amd64\wheel\atom_openmm
  copying build\lib\atom_openmm\abfe_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\abfe_production.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\abfe_structprep.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\async_re.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\gibbs_sampling.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\local_openmm_transport.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\make_atm_system_from_amber.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\make_atm_system_from_pdb.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\make_atm_system_from_rcpt_lig.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\ommreplica.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\ommsystem.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\ommworker.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\openmm_async_re.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\rbfe_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\rbfe_production.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\rbfe_structprep.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\temperatureRE_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\transport.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  creating build\bdist.win-amd64\wheel\atom_openmm\utils
  copying build\lib\atom_openmm\utils\AtomUtils.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\config.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\logging.conf -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\singal_guard.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\timer.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\__init__.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\uwham.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\__init__.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  running install_egg_info
  Copying atom_openmm.egg-info to build\bdist.win-amd64\wheel\.\atom_openmm-8.4.0-py3.11.egg-info
  running install_scripts
  creating build\bdist.win-amd64\wheel\atom_openmm-8.4.0.dist-info\WHEEL
  creating 'C:\ProgramData\BOINC\slots\14\pip-wheel-9nzks5pu\.tmp-s22kbtl4\atom_openmm-8.4.0-py3-none-any.whl' and adding 'build\bdist.win-amd64\wheel' to it
  adding 'atom_openmm/__init__.py'
  adding 'atom_openmm/abfe_explicit.py'
  adding 'atom_openmm/abfe_production.py'
  adding 'atom_openmm/abfe_structprep.py'
  adding 'atom_openmm/async_re.py'
  adding 'atom_openmm/gibbs_sampling.py'
  adding 'atom_openmm/local_openmm_transport.py'
  adding 'atom_openmm/make_atm_system_from_amber.py'
  adding 'atom_openmm/make_atm_system_from_pdb.py'
  adding 'atom_openmm/make_atm_system_from_rcpt_lig.py'
  adding 'atom_openmm/ommreplica.py'
  adding 'atom_openmm/ommsystem.py'
  adding 'atom_openmm/ommworker.py'
  adding 'atom_openmm/openmm_async_re.py'
  adding 'atom_openmm/rbfe_explicit.py'
  adding 'atom_openmm/rbfe_production.py'
  adding 'atom_openmm/rbfe_structprep.py'
  adding 'atom_openmm/temperatureRE_explicit.py'
  adding 'atom_openmm/transport.py'
  adding 'atom_openmm/uwham.py'
  adding 'atom_openmm/utils/AtomUtils.py'
  adding 'atom_openmm/utils/__init__.py'
  adding 'atom_openmm/utils/config.py'
  adding 'atom_openmm/utils/logging.conf'
  adding 'atom_openmm/utils/singal_guard.py'
  adding 'atom_openmm/utils/timer.py'
  adding 'atom_openmm-8.4.0.dist-info/licenses/LICENSE'
  adding 'atom_openmm-8.4.0.dist-info/METADATA'
  adding 'atom_openmm-8.4.0.dist-info/WHEEL'
  adding 'atom_openmm-8.4.0.dist-info/entry_points.txt'
  adding 'atom_openmm-8.4.0.dist-info/top_level.txt'
  adding 'atom_openmm-8.4.0.dist-info/RECORD'
  removing build\bdist.win-amd64\wheel
  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\14\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.
16:06:14 (28272): wrapper (7.9.26016): starting
16:06:14 (28272): 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\14\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
16:18:57 (25296): wrapper (7.9.26016): starting
16:18:57 (25296): 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\14\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "C:\ProgramData\BOINC\slots\14\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\14\Lib\site-packages\atom_openmm\ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\openmm\app\simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\14\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\14\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\async_re.py", line 69, in _exit
    self.checkpointJob()
  File "C:\ProgramData\BOINC\slots\14\Lib\site-packages\atom_openmm\openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "C:\ProgramData\BOINC\slots\14\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\14\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'
16:20:00 (25296): C:/Windows/system32/cmd.exe exited; CPU time 48.140625
16:20:00 (25296): app exit status: 0x16
16:20:00 (25296): called boinc_finish(195)
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0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 1242225 bytes.
Dumping objects ->
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{279} normal block at 0x00000159BE68BBF0, 16 bytes long.
 Data: <  h Y           > F0 BF 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{278} normal block at 0x00000159BE68AE80, 16 bytes long.
 Data: <  h Y           > C8 BF 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{277} normal block at 0x00000159BE68B5B0, 16 bytes long.
 Data: <  h Y           > A0 BF 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{275} normal block at 0x00000159BE68B3D0, 16 bytes long.
 Data: < dh Y           > E0 64 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{274} normal block at 0x00000159BE6864E0, 40 bytes long.
 Data: <  h Y     g Y   > D0 B3 68 BE 59 01 00 00 D0 02 67 BE 59 01 00 00 
{273} normal block at 0x00000159BE68B6F0, 16 bytes long.
 Data: <  h Y           > 80 BF 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x00000159BE68B100, 16 bytes long.
 Data: <X h Y           > 58 BF 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x00000159BE685060, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{270} normal block at 0x00000159BE68AFC0, 16 bytes long.
 Data: <0 h Y           > 30 BF 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000159BE68BF30, 992 bytes long.
 Data: <  h Y   `Ph Y   > C0 AF 68 BE 59 01 00 00 60 50 68 BE 59 01 00 00 
{105} normal block at 0x00000159BE684BE0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{104} normal block at 0x00000159BE67C4C0, 16 bytes long.
 Data: <Peh Y           > 50 65 68 BE 59 01 00 00 00 00 00 00 00 00 00 00 
{103} normal block at 0x00000159BE686550, 40 bytes long.
 Data: <  g Y    Kh Y   > C0 C4 67 BE 59 01 00 00 E0 4B 68 BE 59 01 00 00 
{82} normal block at 0x00000159BE67C6F0, 16 bytes long.
 Data: <   [            > 80 EA BC 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{81} normal block at 0x00000159BE67BCF0, 16 bytes long.
 Data: <@  [            > 40 E9 BC 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{80} normal block at 0x00000159BE67C330, 16 bytes long.
 Data: < W [            > F8 57 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{79} normal block at 0x00000159BE67C510, 16 bytes long.
 Data: < W [            > D8 57 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{78} normal block at 0x00000159BE67C5B0, 16 bytes long.
 Data: <P  [            > 50 04 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{77} normal block at 0x00000159BE67C470, 16 bytes long.
 Data: <0  [            > 30 04 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x00000159BE67C650, 16 bytes long.
 Data: <   [            > E0 02 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x00000159BE67C1F0, 16 bytes long.
 Data: <   [            > 10 04 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x00000159BE67C150, 16 bytes long.
 Data: <p  [            > 70 04 B9 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x00000159BE67BCA0, 16 bytes long.
 Data: <   [            > 18 C0 B7 5B F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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