Task 38583665

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<stderr_txt>
08:04:50 (23332): wrapper (7.9.26016): starting
08:04:50 (23332): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A27_A21_0.pdb
QB_A27_A21_0.xml
QB_A27_A21_equil.pdb
QB_A27_A21.inpcrd
QB_A27_A21_input.yaml
QB_A27_A21_mdlambda.pdb
QB_A27_A21_min.pdb
QB_A27_A21_npt.pdb
QB_A27_A21.pdb
QB_A27_A21.prmtop
QB_A27_A21_sys.xml
QB_A27_A21_therm.pdb
run.bat
run.sh
08:04:53 (23332): Library/usr/bin/tar.exe exited; CPU time 0.000000
08:04:53 (23332): 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\2\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\2\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
    Downloading 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 29.4 MB/s eta 0:00:00
  Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
  Downloading packaging-25.0-py3-none-any.whl (66 kB)
  Installing collected packages: setuptools, packaging, setuptools-scm
    Creating C:\ProgramData\BOINC\slots\2\pip-build-env-jcd4tv4k\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\2\pip-build-env-jcd4tv4k\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\2\pip-build-env-jcd4tv4k\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\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\2\pip-modern-metadata-u3leg2kk\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\2\pip-build-env-jcd4tv4k\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\2\pip-wheel-a8z5r540\.tmp-u7bv3zhn\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\2\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) : {3835269} normal block at 0x000002058521F6B0, 8 bytes long.
 Data: <        > 00 00 1C 85 05 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833970} normal block at 0x0000020586F682D0, 1080 bytes long.
 Data: < A              > D8 41 00 00 CD CD CD CD DC 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {317} normal block at 0x0000020585216E40, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
15:11:00 (26424): wrapper (7.9.26016): starting
15:11:00 (26424): 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\2\tmp already exists.
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
15:40:22 (26424): C:/Windows/system32/cmd.exe exited; CPU time 1730.546875
15:40:22 (26424): 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: 38769694 bytes.
Dumping objects ->
{1697} normal block at 0x000002A4D2FC4210, 48 bytes long.
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{1686} normal block at 0x000002A4D2FC41A0, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1675} normal block at 0x000002A4D2FC46E0, 48 bytes long.
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{1664} normal block at 0x000002A4D2FC3FE0, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1653} normal block at 0x000002A4D2FC43D0, 48 bytes long.
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{1622} normal block at 0x000002A4D2FB01C0, 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) : {1609} normal block at 0x000002A4D2FC4C90, 8 bytes long.
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{311} normal block at 0x000002A4D2FC5410, 8 bytes long.
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{302} normal block at 0x000002A4D2FB1E20, 80 bytes long.
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{301} normal block at 0x000002A4D2FC5B40, 16 bytes long.
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{300} normal block at 0x000002A4D2FC5690, 16 bytes long.
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{297} normal block at 0x000002A4D2FC5AA0, 16 bytes long.
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{296} normal block at 0x000002A4D2FC4F10, 16 bytes long.
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{285} normal block at 0x000002A4D2FC5A50, 16 bytes long.
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{282} normal block at 0x000002A4D2FAF4A0, 320 bytes long.
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{279} normal block at 0x000002A4D2FBFF10, 32 bytes long.
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{278} normal block at 0x000002A4D2FC5960, 16 bytes long.
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{272} normal block at 0x000002A4D2FC53C0, 16 bytes long.
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{271} normal block at 0x000002A4D2FC4CE0, 16 bytes long.
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{269} normal block at 0x000002A4D2FC4C40, 16 bytes long.
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{268} normal block at 0x000002A4D2FC4130, 40 bytes long.
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{267} normal block at 0x000002A4D2FC50A0, 16 bytes long.
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{266} normal block at 0x000002A4D2FC4FB0, 16 bytes long.
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{265} normal block at 0x000002A4D2FC0630, 32 bytes long.
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{264} normal block at 0x000002A4D2FC5910, 16 bytes long.
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{263} normal block at 0x000002A4D2FC5BB0, 992 bytes long.
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 Data: <        p       > D0 D6 FB D2 A4 02 00 00 70 02 FC D2 A4 02 00 00 
{76} normal block at 0x000002A4D2FBE300, 16 bytes long.
 Data: <  c             > 80 EA 63 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x000002A4D2FBD950, 16 bytes long.
 Data: <@ c             > 40 E9 63 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x000002A4D2FBDCC0, 16 bytes long.
 Data: < W`             > F8 57 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000002A4D2FBD5E0, 16 bytes long.
 Data: < W`             > D8 57 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000002A4D2FBE2B0, 16 bytes long.
 Data: <P `             > 50 04 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000002A4D2FBD590, 16 bytes long.
 Data: <0 `             > 30 04 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x000002A4D2FBDF40, 16 bytes long.
 Data: <  `             > E0 02 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x000002A4D2FBD4F0, 16 bytes long.
 Data: <  `             > 10 04 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x000002A4D2FBE170, 16 bytes long.
 Data: <p `             > 70 04 60 DE F6 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x000002A4D2FBD900, 16 bytes long.
 Data: <  ^             > 18 C0 5E DE F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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