Task 38583401

Name PFKFB3_A33_A37_r0_2-QUICO_ATM_GAFF2_LOMAP_PFKFB3-3-5-RND9175_0
Workunit 31547537
Created 14 Dec 2025, 3:53:06 UTC
Sent 14 Dec 2025, 3:53:14 UTC
Report deadline 19 Dec 2025, 3:53:14 UTC
Received 14 Dec 2025, 9:59:23 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 646331
Run time 4 hours 35 min 3 sec
CPU time 4 hours 13 min 16 sec
Validate state Valid
Credit 750,000.00
Device peak FLOPS 44,868.70 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
windows_x86_64
Peak working set size 777.18 MB
Peak swap size 10.10 GB
Peak disk usage 3.69 GB

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
05:15:59 (12436): wrapper (7.9.26016): starting
05:15:59 (12436): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A33_A37_0.pdb
QB_A33_A37_0.xml
QB_A33_A37_equil.pdb
QB_A33_A37.inpcrd
QB_A33_A37_input.yaml
QB_A33_A37_mdlambda.pdb
QB_A33_A37_min.pdb
QB_A33_A37_npt.pdb
QB_A33_A37.pdb
QB_A33_A37.prmtop
QB_A33_A37_sys.xml
QB_A33_A37_therm.pdb
run.bat
run.sh
05:16:01 (12436): Library/usr/bin/tar.exe exited; CPU time 0.015625
05:16:01 (12436): 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/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
    Using cached 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 20.0 MB/s eta 0:00:00
  Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
  Using cached packaging-25.0-py3-none-any.whl (66 kB)
  Installing collected packages: setuptools, packaging, setuptools-scm
    Creating C:\ProgramData\BOINC\slots\0\pip-build-env-69mnx6wd\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\0\pip-build-env-69mnx6wd\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\0\pip-build-env-69mnx6wd\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\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\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-2mz35a63\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-2mz35a63\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\0\pip-build-env-69mnx6wd\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\0\pip-wheel-j1baa3eh\.tmp-yj50kh6x\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.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835190} normal block at 0x0000016B3392E680, 8 bytes long.
 Data: <  +5k   > 00 00 2B 35 6B 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833978} normal block at 0x0000016B33A0E8F0, 1080 bytes long.
 Data: <        \       > 08 E7 00 00 CD CD CD CD 5C 00 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {321} normal block at 0x0000016B33926770, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
07:58:42 (18032): wrapper (7.9.26016): starting
07:58:42 (18032): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
Un sous-r&#130;pertoire ou un fichier C:\ProgramData\BOINC\slots\0\tmp existe d&#130;j&#133;.
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
10:49:05 (18032): C:/Windows/system32/cmd.exe exited; CPU time 9008.656250
10:49:05 (18032): 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: 139323814 bytes.
Dumping objects ->
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{1604} normal block at 0x0000028C56BB18E0, 48 bytes long.
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{1593} normal block at 0x0000028C56BB19C0, 48 bytes long.
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{1582} normal block at 0x0000028C56BB14F0, 48 bytes long.
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{1571} normal block at 0x0000028C56BB1A30, 48 bytes long.
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{1540} normal block at 0x0000028C56BA01B0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
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 Data: < l V            > 80 6C BB 56 8C 02 00 00 00 00 00 00 00 00 00 00 
{267} normal block at 0x0000028C56BB6C80, 992 bytes long.
 Data: < ^ V       V    > A0 5E BB 56 8C 02 00 00 F0 FB BA 56 8C 02 00 00 
{103} normal block at 0x0000028C56BAFAD0, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{102} normal block at 0x0000028C56BADE70, 16 bytes long.
 Data: <   V            > 80 14 BB 56 8C 02 00 00 00 00 00 00 00 00 00 00 
{101} normal block at 0x0000028C56BB1480, 40 bytes long.
 Data: <p  V       V    > 70 DE BA 56 8C 02 00 00 D0 FA BA 56 8C 02 00 00 
{80} normal block at 0x0000028C56BAE0A0, 16 bytes long.
 Data: <                > 80 EA 84 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{79} normal block at 0x0000028C56BAE050, 16 bytes long.
 Data: <@               > 40 E9 84 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{78} normal block at 0x0000028C56BADA10, 16 bytes long.
 Data: < W              > F8 57 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{77} normal block at 0x0000028C56BAE1E0, 16 bytes long.
 Data: < W              > D8 57 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x0000028C56BAD510, 16 bytes long.
 Data: <P               > 50 04 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x0000028C56BAD470, 16 bytes long.
 Data: <0               > 30 04 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x0000028C56BAE140, 16 bytes long.
 Data: <                > E0 02 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x0000028C56BADFB0, 16 bytes long.
 Data: <                > 10 04 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x0000028C56BAD600, 16 bytes long.
 Data: <p               > 70 04 81 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x0000028C56BADD30, 16 bytes long.
 Data: <                > 18 C0 7F 8E F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>


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