Task 38596379

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
20:08:31 (9128): wrapper (7.9.26016): starting
20:08:31 (9128): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A08_A09_0.pdb
QB_A08_A09_0.xml
QB_A08_A09.inpcrd
QB_A08_A09_input.yaml
QB_A08_A09.pdb
QB_A08_A09.prmtop
QB_A08_A09_sys.xml
run.bat
run.sh
20:08:38 (9128): Library/usr/bin/tar.exe exited; CPU time 0.000000
20:08:38 (9128): 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:\BOINC\slots\16\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 D:\BOINC\slots\16\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/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl.metadata
    Downloading packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
  Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
     ---------------------------------------- 1.0/1.0 MB 12.0 MB/s eta 0:00:00
  Downloading setuptools_scm-10.0.5-py3-none-any.whl (21 kB)
  Downloading packaging-26.0-py3-none-any.whl (74 kB)
  Downloading vcs_versioning-1.1.1-py3-none-any.whl (79 kB)
  Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
    Creating D:\BOINC\slots\16\pip-build-env-e8l5dlcw\overlay\Scripts
  Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1
  Running command Getting requirements to build wheel
  D:\BOINC\slots\16\pip-build-env-e8l5dlcw\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
  D:\BOINC\slots\16\pip-build-env-e8l5dlcw\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)
  D:\BOINC\slots\16\pip-build-env-e8l5dlcw\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 D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info
  writing D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\dependency_links.txt
  writing entry points to D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\entry_points.txt
  writing requirements to D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\requires.txt
  writing top-level names to D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\top_level.txt
  writing manifest file 'D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\SOURCES.txt'
  D:\BOINC\slots\16\pip-build-env-e8l5dlcw\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 'D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm.egg-info\SOURCES.txt'
  creating 'D:\BOINC\slots\16\pip-modern-metadata-ez5lugea\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  D:\BOINC\slots\16\pip-build-env-e8l5dlcw\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
  D:\BOINC\slots\16\pip-build-env-e8l5dlcw\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 'D:\\BOINC\\slots\\16\\pip-wheel-d06d9g8o\\.tmp-4v93uh15\\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:\BOINC\slots\16\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) : {3835403} normal block at 0x000002F309EEB800, 8 bytes long.
 Data: <  H     > 00 00 48 0A F3 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833972} normal block at 0x000002F30BA9EA00, 1080 bytes long.
 Data: <lJ              > 6C 4A 00 00 CD CD CD CD F8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {318} normal block at 0x000002F309EE6C00, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
11:18:01 (896): wrapper (7.9.26016): starting
11:18:01 (896): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
Ya existe el subdirectorio o el archivo D:\BOINC\slots\16\tmp.
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
15:24:14 (896): C:/Windows/system32/cmd.exe exited; CPU time 10016.859375
15:24:14 (896): called boinc_finish(0)
0 bytes in 0 Free Blocks.
456 bytes in 8 Normal Blocks.
2288 bytes in 2 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 65726437 bytes.
Dumping objects ->
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 Data: <  s X           > 90 CA 73 F5 58 02 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x00000258F573CA90, 40 bytes long.
 Data: < cu X    |u X   > 00 63 75 F5 58 02 00 00 80 7C 75 F5 58 02 00 00 
{268} normal block at 0x00000258F5756A30, 16 bytes long.
 Data: < ru X           > B0 72 75 F5 58 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x00000258F5756940, 16 bytes long.
 Data: < ru X           > 88 72 75 F5 58 02 00 00 00 00 00 00 00 00 00 00 
{266} normal block at 0x00000258F5751010, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{265} normal block at 0x00000258F5756080, 16 bytes long.
 Data: <`ru X           > 60 72 75 F5 58 02 00 00 00 00 00 00 00 00 00 00 
{264} normal block at 0x00000258F5757260, 992 bytes long.
 Data: < `u X     u X   > 80 60 75 F5 58 02 00 00 10 10 75 F5 58 02 00 00 
{100} normal block at 0x00000258F5750230, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{99} normal block at 0x00000258F574B750, 16 bytes long.
 Data: <0 s X           > 30 F8 73 F5 58 02 00 00 00 00 00 00 00 00 00 00 
{98} normal block at 0x00000258F573F830, 40 bytes long.
 Data: <P t X   0 u X   > 50 B7 74 F5 58 02 00 00 30 02 75 F5 58 02 00 00 
{77} normal block at 0x00000258F574BB10, 16 bytes long.
 Data: <   y            > 80 EA ED 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x00000258F574BC00, 16 bytes long.
 Data: <@  y            > 40 E9 ED 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x00000258F574BA20, 16 bytes long.
 Data: < W y            > F8 57 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x00000258F574C060, 16 bytes long.
 Data: < W y            > D8 57 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x00000258F574C100, 16 bytes long.
 Data: <P  y            > 50 04 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x00000258F574B430, 16 bytes long.
 Data: <0  y            > 30 04 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x00000258F574B2F0, 16 bytes long.
 Data: <   y            > E0 02 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{70} normal block at 0x00000258F574B520, 16 bytes long.
 Data: <   y            > 10 04 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x00000258F574B840, 16 bytes long.
 Data: <p  y            > 70 04 EA 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x00000258F574BF70, 16 bytes long.
 Data: <   y            > 18 C0 E8 79 F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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