Task 38666970

Stderr output

<core_client_version>8.2.11</core_client_version>
<![CDATA[
<stderr_txt>
00:59:57 (22592): wrapper (7.9.26016): starting
00:59:57 (22592): 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
00:59:59 (22592): Library/usr/bin/tar.exe exited; CPU time 0.000000
00:59:59 (22592): 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\33\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\33\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 19.2 MB/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\33\pip-build-env-v0outzct\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\33\pip-build-env-v0outzct\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\33\pip-build-env-v0outzct\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\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\SOURCES.txt'
  reading manifest file 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-_0ogjv7_\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\33\pip-build-env-v0outzct\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\\33\\pip-wheel-g6b38ubz\\.tmp-h4s8beuo\\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\33\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) : {3835454} normal block at 0x000001AC75E31800, 8 bytes long.
 Data: <   u    > 00 00 DE 75 AC 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833940} normal block at 0x000001AC75E1FF00, 1080 bytes long.
 Data: < M              > B8 4D 00 00 CD CD CD CD 0C 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {302} normal block at 0x000001AC75E29C10, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
01:45:26 (18212): wrapper (7.9.26016): starting
01:45:26 (18212): 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\33\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: r*/*.xtc: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
01:55:45 (18212): C:/Windows/system32/cmd.exe exited; CPU time 622.593750
01:55:45 (18212): called boinc_finish(0)
0 bytes in 0 Free Blocks.
460 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: 9968151 bytes.
Dumping objects ->
{1898} normal block at 0x00000285E6E63860, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1887} normal block at 0x00000285E6E63470, 48 bytes long.
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{1876} normal block at 0x00000285E6E637F0, 48 bytes long.
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{1865} normal block at 0x00000285E6E639B0, 48 bytes long.
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{1854} normal block at 0x00000285E6E63A20, 48 bytes long.
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{1823} normal block at 0x00000285E6E4B300, 64 bytes long.
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{1812} normal block at 0x00000285E6E4E430, 102 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {1809} normal block at 0x00000285E6E64670, 8 bytes long.
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 Data: <                > E0 F9 E5 E6 85 02 00 00 90 1A E6 E6 85 02 00 00 
{84} normal block at 0x00000285E6E61EB0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{83} normal block at 0x00000285E6E5F800, 16 bytes long.
 Data: <                > 10 EA E5 E6 85 02 00 00 00 00 00 00 00 00 00 00 
{82} normal block at 0x00000285E6E5EA10, 40 bytes long.
 Data: <                > 00 F8 E5 E6 85 02 00 00 B0 1E E6 E6 85 02 00 00 
{61} normal block at 0x00000285E6E5F440, 16 bytes long.
 Data: <  0             > 80 EA 30 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x00000285E6E5EC70, 16 bytes long.
 Data: <@ 0             > 40 E9 30 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x00000285E6E5F0D0, 16 bytes long.
 Data: < W-             > F8 57 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x00000285E6E5EB30, 16 bytes long.
 Data: < W-             > D8 57 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x00000285E6E5EC20, 16 bytes long.
 Data: <P -             > 50 04 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x00000285E6E5EAE0, 16 bytes long.
 Data: <0 -             > 30 04 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x00000285E6E5F080, 16 bytes long.
 Data: <  -             > E0 02 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{54} normal block at 0x00000285E6E5ED60, 16 bytes long.
 Data: <  -             > 10 04 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{53} normal block at 0x00000285E6E5F990, 16 bytes long.
 Data: <p -             > 70 04 2D 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
{52} normal block at 0x00000285E6E5EE00, 16 bytes long.
 Data: <  +             > 18 C0 2B 16 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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