Task 38581964
| Name | PFKFB3_A17_A37_r0_1-QUICO_ATM_GAFF2_LOMAP_PFKFB3-1-5-RND9421_0 |
| Workunit | 31546349 |
| Created | 12 Dec 2025, 18:05:13 UTC |
| Sent | 12 Dec 2025, 18:05:18 UTC |
| Report deadline | 17 Dec 2025, 18:05:18 UTC |
| Received | 13 Dec 2025, 2:41:17 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 641544 |
| Run time | 6 hours 18 min 21 sec |
| CPU time | 6 hours 3 min 49 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 23,050.17 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 840.85 MB |
| Peak swap size | 10.16 GB |
| Peak disk usage | 3.69 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
13:07:09 (43836): wrapper (7.9.26016): starting
13:07:09 (43836): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A17_A37_0.pdb
QB_A17_A37_0.xml
QB_A17_A37_equil.pdb
QB_A17_A37.inpcrd
QB_A17_A37_input.yaml
QB_A17_A37_mdlambda.pdb
QB_A17_A37_min.pdb
QB_A17_A37_npt.pdb
QB_A17_A37.pdb
QB_A17_A37.prmtop
QB_A17_A37_sys.xml
QB_A17_A37_therm.pdb
run.bat
run.sh
13:07:11 (43836): Library/usr/bin/tar.exe exited; CPU time 0.015625
13:07:11 (43836): 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/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl.metadata
Using cached 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)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
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\33\pip-build-env-1j4lk8ci\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\33\pip-build-env-1j4lk8ci\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\33\pip-build-env-1j4lk8ci\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\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\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-gyr9frqa\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\33\pip-modern-metadata-gyr9frqa\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\33\pip-build-env-1j4lk8ci\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\33\pip-wheel-gi_l1iww\.tmp-skkwvxrh\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) : {3835403} normal block at 0x00000284FA73E6E0, 8 bytes long.
Data: < l > 00 00 6C FA 84 02 00 00
..\lib\diagnostics_win.cpp(417) : {3833964} normal block at 0x00000284FC6EC650, 1080 bytes long.
Data: <L > 4C 98 00 00 CD CD CD CD 18 03 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {314} normal block at 0x00000284FA7365D0, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
16:51:28 (40976): wrapper (7.9.26016): starting
16:51:28 (40976): 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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1746} normal block at 0x000002B320079EB0, 8 bytes long.
Data: < > 00 00 F8 1F B3 02 00 00
..\lib\diagnostics_win.cpp(417) : {307} normal block at 0x000002B32007A980, 1080 bytes long.
Data: <T# > 54 23 00 00 CD CD CD CD E4 01 00 00 00 00 00 00
Object dump complete.
20:34:06 (10292): wrapper (7.9.26016): starting
20:34:06 (10292): 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: Exiting with failure status due to previous errors
21:38:18 (10292): C:/Windows/system32/cmd.exe exited; CPU time 3473.906250
21:38:18 (10292): called boinc_finish(0)
0 bytes in 0 Free Blocks.
256 bytes in 6 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: 93999927 bytes.
Dumping objects ->
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Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1823} normal block at 0x000001747714A020, 48 bytes long.
Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1812} normal block at 0x000001747714A3A0, 48 bytes long.
Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61
{1801} normal block at 0x000001747714A560, 48 bytes long.
Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1790} normal block at 0x000001747714A330, 48 bytes long.
Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61
{1759} normal block at 0x0000017477141AB0, 64 bytes long.
Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
..\api\boinc_api.cpp(309) : {1746} normal block at 0x000001747714AA40, 8 bytes long.
Data: < vt > 00 00 F6 76 74 01 00 00
{308} normal block at 0x000001747714AB80, 8 bytes long.
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{260} normal block at 0x000001747714B930, 992 bytes long.
Data: <` wt = wt > 60 B2 14 77 74 01 00 00 C0 3D 14 77 74 01 00 00
{96} normal block at 0x0000017477144660, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{95} normal block at 0x000001747713DDE0, 16 bytes long.
Data: < wt > C0 A2 14 77 74 01 00 00 00 00 00 00 00 00 00 00
{94} normal block at 0x000001747714A2C0, 40 bytes long.
Data: < wt `F wt > E0 DD 13 77 74 01 00 00 60 46 14 77 74 01 00 00
{73} normal block at 0x000001747713D4D0, 16 bytes long.
Data: < > 80 EA 90 B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{72} normal block at 0x000001747713DCF0, 16 bytes long.
Data: <@ > 40 E9 90 B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{71} normal block at 0x000001747713D250, 16 bytes long.
Data: < W > F8 57 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{70} normal block at 0x000001747713D6B0, 16 bytes long.
Data: < W > D8 57 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{69} normal block at 0x000001747713D430, 16 bytes long.
Data: <P > 50 04 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x000001747713D610, 16 bytes long.
Data: <0 > 30 04 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x000001747713D200, 16 bytes long.
Data: < > E0 02 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x000001747713D5C0, 16 bytes long.
Data: < > 10 04 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x000001747713DA20, 16 bytes long.
Data: <p > 70 04 8D B8 F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x000001747713D930, 16 bytes long.
Data: < > 18 C0 8B B8 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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