Task 38653731

Stderr output

<core_client_version>8.2.11</core_client_version>
<![CDATA[
<stderr_txt>
14:14:48 (8480): wrapper (7.9.26016): starting
14:14:48 (8480): 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
14:15:13 (8480): Library/usr/bin/tar.exe exited; CPU time 0.125000
14:15:13 (8480): 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\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.
  Running command pip subprocess to install build dependencies
  Using pip 24.3.1 from C:\ProgramData\BOINC\slots\1\Lib\site-packages\pip (python 3.11)
  Collecting setuptools
    Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/ef/55/6dc6d6bb953bdfc52519a0059592c52b6e3b8ad51cf8256dffceb55b0610/setuptools-84.2.1-py3-none-any.whl.metadata
    Downloading setuptools-84.2.1-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/da/f5/54538a1f17ea753c42b0928dc2e62986d463f8c393340b9a1e602f2d4dd9/setuptools_scm-10.3.4-py3-none-any.whl.metadata
    Downloading setuptools_scm-10.3.4-py3-none-any.whl.metadata (6.7 kB)
  Collecting vcs-versioning<3,>=2.5.0.dev0 (from setuptools-scm>=8)
    Obtaining dependency information for vcs-versioning<3,>=2.5.0.dev0 from https://files.pythonhosted.org/packages/73/1d/ad4064bf12f4503bf61e65d74c93c523672776d25ee0a06aaf42ae09ef3f/vcs_versioning-2.6.0-py3-none-any.whl.metadata
    Downloading vcs_versioning-2.6.0-py3-none-any.whl.metadata (1.7 kB)
  Collecting packaging>=20 (from setuptools-scm>=8)
    Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/63/34/ba1c580383c9eada3711951fef0795c80b829a078d72188184bcab9dd527/packaging-26.3-py3-none-any.whl.metadata
    Downloading packaging-26.3-py3-none-any.whl.metadata (3.5 kB)
  Downloading setuptools-84.2.1-py3-none-any.whl (876 kB)
     -------------------------------------- 876.3/876.3 kB 818.8 kB/s eta 0:00:00
  Downloading setuptools_scm-10.3.4-py3-none-any.whl (33 kB)
  Downloading packaging-26.3-py3-none-any.whl (129 kB)
  Downloading vcs_versioning-2.6.0-py3-none-any.whl (123 kB)
  Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
    Creating C:\ProgramData\BOINC\slots\1\pip-build-env-8y5gpij3\overlay\Scripts
  Successfully installed packaging-26.3 setuptools-84.2.1 setuptools-scm-10.3.4 vcs-versioning-2.6.0
  Running command Getting requirements to build wheel
  C:\ProgramData\BOINC\slots\1\pip-build-env-8y5gpij3\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:236: UserWarning: version of None already set
    warnings.warn(f"version of {self.dist_name} already set")
  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
  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\1\pip-build-env-8y5gpij3\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:236: UserWarning: version of None already set
    warnings.warn(f"version of {self.dist_name} already set")
  running dist_info
  creating C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\SOURCES.txt'
  reading manifest file 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-lqd2_65n\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\1\pip-build-env-8y5gpij3\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:236: UserWarning: version of None already set
    warnings.warn(f"version of {self.dist_name} already set")
  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
  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\\1\\pip-wheel-j3o1nfx1\\.tmp-fj39earv\\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\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: r*/*.xtc: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
15:54:23 (8480): C:/Windows/system32/cmd.exe exited; CPU time 5361.250000
15:54:23 (8480): 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: 76438441 bytes.
Dumping objects ->
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 Data: <@               > 40 E9 92 BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001E4B4D41560, 16 bytes long.
 Data: < W              > F8 57 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001E4B4D41420, 16 bytes long.
 Data: < W              > D8 57 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001E4B4D416A0, 16 bytes long.
 Data: <P               > 50 04 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001E4B4D40DE0, 16 bytes long.
 Data: <0               > 30 04 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001E4B4D416F0, 16 bytes long.
 Data: <                > E0 02 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001E4B4D411A0, 16 bytes long.
 Data: <                > 10 04 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001E4B4D417E0, 16 bytes long.
 Data: <p               > 70 04 8F BC F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001E4B4D41740, 16 bytes long.
 Data: <                > 18 C0 8D BC F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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