Task 38582502

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
01:58:07 (48012): wrapper (7.9.26016): starting
01:58:07 (48012): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A25_A28_0.pdb
QB_A25_A28_0.xml
QB_A25_A28_equil.pdb
QB_A25_A28.inpcrd
QB_A25_A28_input.yaml
QB_A25_A28_mdlambda.pdb
QB_A25_A28_min.pdb
QB_A25_A28_npt.pdb
QB_A25_A28.pdb
QB_A25_A28.prmtop
QB_A25_A28_sys.xml
QB_A25_A28_therm.pdb
run.bat
run.sh
01:58:46 (48012): Library/usr/bin/tar.exe exited; CPU time 0.031250
01:58:46 (48012): 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:\ProgramData\BOINC\slots\1\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.
22:29:30 (29756): wrapper (7.9.26016): starting
22:29:30 (29756): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\1\tmp already exists.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1525} normal block at 0x000001C79B3E5BF0, 8 bytes long.
 Data: <  n     > 00 00 6E 9B C7 01 00 00 
..\lib\diagnostics_win.cpp(417) : {309} normal block at 0x000001C79B3E6C60, 1080 bytes long.
 Data: < t              > 94 74 00 00 CD CD CD CD B0 01 00 00 00 00 00 00 
Object dump complete.
14:10:23 (22476): wrapper (7.9.26016): starting
14:10:24 (22476): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\1\tmp already exists.
  Running command pip subprocess to install build dependencies
  Using pip 24.3.1 from D:\ProgramData\BOINC\slots\1\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
    Using cached 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)
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
  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 D:\ProgramData\BOINC\slots\1\pip-build-env-objepih3\overlay\Scripts
  Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
  Running command Getting requirements to build wheel
  D:\ProgramData\BOINC\slots\1\pip-build-env-objepih3\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)
  D:\ProgramData\BOINC\slots\1\pip-build-env-objepih3\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 D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info
  writing D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\dependency_links.txt
  writing entry points to D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\entry_points.txt
  writing requirements to D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\requires.txt
  writing top-level names to D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\top_level.txt
  writing manifest file 'D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm.egg-info\SOURCES.txt'
  creating 'D:\ProgramData\BOINC\slots\1\pip-modern-metadata-eazounjn\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  D:\ProgramData\BOINC\slots\1\pip-build-env-objepih3\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 'D:\ProgramData\BOINC\slots\1\pip-wheel-q9x6j2ay\.tmp-bnrfi3h8\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 'D:\ProgramData\BOINC\slots\1\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.
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
17:02:47 (22476): C:/Windows/system32/cmd.exe exited; CPU time 8641.875000
17:02:47 (22476): called boinc_finish(0)
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: 254399688 bytes.
Dumping objects ->
{1613} normal block at 0x00000284E1364A30, 48 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1602} normal block at 0x00000284E1364D40, 48 bytes long.
 Data: <HOME=D:\ProgramD> 48 4F 4D 45 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1591} normal block at 0x00000284E1364CD0, 48 bytes long.
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{1580} normal block at 0x00000284E1364FE0, 48 bytes long.
 Data: <TEMP=D:\ProgramD> 54 45 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
{1569} normal block at 0x00000284E13650C0, 48 bytes long.
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{1538} normal block at 0x00000284E134F380, 64 bytes long.
 Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 
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{73} normal block at 0x00000284E135D730, 16 bytes long.
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{72} normal block at 0x00000284E135DD20, 16 bytes long.
 Data: < W x            > D8 57 7F 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000284E135DC80, 16 bytes long.
 Data: <P  x            > 50 04 7F 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000284E135D910, 16 bytes long.
 Data: <0  x            > 30 04 7F 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000284E135D9B0, 16 bytes long.
 Data: <   x            > E0 02 7F 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000284E135E090, 16 bytes long.
 Data: <   x            > 10 04 7F 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x00000284E135DCD0, 16 bytes long.
 Data: <p  x            > 70 04 7F 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x00000284E135DBE0, 16 bytes long.
 Data: <  }x            > 18 C0 7D 78 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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