Task 38637257

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
09:51:09 (3180): wrapper (7.9.26016): starting
09:51:09 (3180): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A23_A16_0.pdb
QB_A23_A16_0.xml
QB_A23_A16.inpcrd
QB_A23_A16_input.yaml
QB_A23_A16.pdb
QB_A23_A16.prmtop
QB_A23_A16_sys.xml
run.bat
run.sh
09:51:44 (3180): Library/usr/bin/tar.exe exited; CPU time 0.031250
09:51:44 (3180): 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\0\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\0\Lib\site-packages\pip (python 3.11)
  Collecting setuptools
    Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/9d/76/f789f7a86709c6b087c5a2f52f911838cad707cc613162401badc665acfe/setuptools-82.0.1-py3-none-any.whl.metadata
    Downloading setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
  Collecting setuptools-scm>=8
    Obtaining dependency information for setuptools-scm>=8 from https://files.pythonhosted.org/packages/5c/e1/342c4434df56aa537f6ce7647eefee521d96fbb828b08acd709865767652/setuptools_scm-10.0.5-py3-none-any.whl.metadata
    Downloading setuptools_scm-10.0.5-py3-none-any.whl.metadata (6.5 kB)
  Collecting vcs-versioning>=1.0.0.dev0 (from setuptools-scm>=8)
    Obtaining dependency information for vcs-versioning>=1.0.0.dev0 from https://files.pythonhosted.org/packages/e6/60/73603fbcdbe5e803855bcce4414f94eaeed449083bd8183e67161af78188/vcs_versioning-1.1.1-py3-none-any.whl.metadata
    Downloading vcs_versioning-1.1.1-py3-none-any.whl.metadata (1.6 kB)
  Collecting packaging>=20 (from setuptools-scm>=8)
    Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/df/b2/87e62e8c3e2f4b32e5fe99e0b86d576da1312593b39f47d8ceef365e95ed/packaging-26.2-py3-none-any.whl.metadata
    Downloading packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
  Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
     ---------------------------------------- 1.0/1.0 MB 7.9 MB/s eta 0:00:00
  Downloading setuptools_scm-10.0.5-py3-none-any.whl (21 kB)
  Downloading packaging-26.2-py3-none-any.whl (100 kB)
  Downloading vcs_versioning-1.1.1-py3-none-any.whl (79 kB)
  Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
    Creating C:\ProgramData\BOINC\slots\0\pip-build-env-u59f9sso\overlay\Scripts
  Successfully installed packaging-26.2 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1
  Running command Getting requirements to build wheel
  C:\ProgramData\BOINC\slots\0\pip-build-env-u59f9sso\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: 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
  C:\ProgramData\BOINC\slots\0\pip-build-env-u59f9sso\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
    return get_active_overrides().subprocess_timeout
  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\0\pip-build-env-u59f9sso\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
    warnings.warn(f"version of {self.dist_name} already set")
  running dist_info
  creating C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\SOURCES.txt'
  C:\ProgramData\BOINC\slots\0\pip-build-env-u59f9sso\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
    return get_active_overrides().subprocess_timeout
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-r7d06hkj\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\0\pip-build-env-u59f9sso\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: 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
  C:\ProgramData\BOINC\slots\0\pip-build-env-u59f9sso\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
    return get_active_overrides().subprocess_timeout
  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\\0\\pip-wheel-fly3aa6u\\.tmp-8id0f7og\\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\0\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.
09:54:09 (14620): wrapper (7.9.26016): starting
09:54:09 (14620): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
tar: run.log: file changed as we read it
16:39:50 (14620): C:/Windows/system32/cmd.exe exited; CPU time 24338.031250
16:39:50 (14620): called boinc_finish(0)
0 bytes in 0 Free Blocks.
426 bytes in 8 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: 312332111 bytes.
Dumping objects ->
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 Data: < g       D      > B0 67 CC 13 CB 01 00 00 C0 44 CC 13 CB 01 00 00 
{90} normal block at 0x000001CB13CC42E0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{89} normal block at 0x000001CB13CC6990, 16 bytes long.
 Data: < .              > D0 2E CC 13 CB 01 00 00 00 00 00 00 00 00 00 00 
{88} normal block at 0x000001CB13CC2ED0, 40 bytes long.
 Data: < i       B      > 90 69 CC 13 CB 01 00 00 E0 42 CC 13 CB 01 00 00 
{67} normal block at 0x000001CB13CC6670, 16 bytes long.
 Data: <                > 80 EA 99 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x000001CB13CC6C10, 16 bytes long.
 Data: <@               > 40 E9 99 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x000001CB13CC63A0, 16 bytes long.
 Data: < W              > F8 57 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000001CB13CC6BC0, 16 bytes long.
 Data: < W              > D8 57 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001CB13CBD240, 16 bytes long.
 Data: <P               > 50 04 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001CB13CBD1A0, 16 bytes long.
 Data: <0               > 30 04 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001CB13CBD150, 16 bytes long.
 Data: <                > E0 02 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001CB13CBDD80, 16 bytes long.
 Data: <                > 10 04 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001CB13CBDD30, 16 bytes long.
 Data: <p               > 70 04 96 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000001CB13CBD7E0, 16 bytes long.
 Data: <                > 18 C0 94 D9 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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