Task 38583633
| Name | PFKFB3_A27_A25_r0_1-QUICO_ATM_GAFF2_LOMAP_PFKFB3-3-5-RND0613_0 |
| Workunit | 31547720 |
| Created | 14 Dec 2025, 11:16:43 UTC |
| Sent | 14 Dec 2025, 11:16:49 UTC |
| Report deadline | 19 Dec 2025, 11:16:49 UTC |
| Received | 18 Dec 2025, 4:20:57 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 637393 |
| Run time | 1 days 0 hours 1 min 26 sec |
| CPU time | 19 hours 31 min 54 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 11,615.01 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 814.14 MB |
| Peak swap size | 10.03 GB |
| Peak disk usage | 3.76 GB |
Stderr output
<core_client_version>8.2.4</core_client_version>
<![CDATA[
<stderr_txt>
20:22:22 (31436): wrapper (7.9.26016): starting
20:22:30 (31436): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A27_A25_0.pdb
QB_A27_A25_0.xml
QB_A27_A25_equil.pdb
QB_A27_A25.inpcrd
QB_A27_A25_input.yaml
QB_A27_A25_mdlambda.pdb
QB_A27_A25_min.pdb
QB_A27_A25_npt.pdb
QB_A27_A25.pdb
QB_A27_A25.prmtop
QB_A27_A25_sys.xml
QB_A27_A25_therm.pdb
run.bat
run.sh
20:22:37 (31436): Library/usr/bin/tar.exe exited; CPU time 0.015625
20:22:37 (31436): 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\data\slots\5\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\data\slots\5\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 D:\BOINC\data\slots\5\pip-build-env-owyq1pag\overlay\Scripts
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
D:\BOINC\data\slots\5\pip-build-env-owyq1pag\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)
D:\BOINC\data\slots\5\pip-build-env-owyq1pag\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 D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info
writing D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\PKG-INFO
writing dependency_links to D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\dependency_links.txt
writing entry points to D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\entry_points.txt
writing requirements to D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\requires.txt
writing top-level names to D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\top_level.txt
writing manifest file 'D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm.egg-info\SOURCES.txt'
creating 'D:\BOINC\data\slots\5\pip-modern-metadata-mh4apr3n\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
D:\BOINC\data\slots\5\pip-build-env-owyq1pag\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 'D:\BOINC\data\slots\5\pip-wheel-uqvtzy37\.tmp-ehvw8a4y\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\data\slots\5\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) : {3835579} normal block at 0x000001800A85D3D0, 8 bytes long.
Data: < u > 00 00 75 0A 80 01 00 00
..\lib\diagnostics_win.cpp(417) : {3834068} normal block at 0x000001800C94B330, 1080 bytes long.
Data: < , $ > 0C 2C 00 00 CD CD CD CD 24 02 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {315} normal block at 0x000001800A845B40, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
14:30:23 (23264): wrapper (7.9.26016): starting
14:30:23 (23264): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
ƒTƒuƒfƒBƒŒƒNƒgƒŠ‚Ü‚½‚̓tƒ@ƒCƒ‹ D:\BOINC\data\slots\5\tmp ‚ÍŠù‚É‘¶Ý‚µ‚Ü‚·B
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1819} normal block at 0x000001DAA201B030, 8 bytes long.
Data: < > 00 00 E5 A1 DA 01 00 00
..\lib\diagnostics_win.cpp(417) : {308} normal block at 0x000001DAA201BB20, 1080 bytes long.
Data: < > 84 1A 00 00 CD CD CD CD CC 01 00 00 00 00 00 00
Object dump complete.
20:53:51 (35240): wrapper (7.9.26016): starting
20:53:51 (35240): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
ƒTƒuƒfƒBƒŒƒNƒgƒŠ‚Ü‚½‚̓tƒ@ƒCƒ‹ D:\BOINC\data\slots\5\tmp ‚ÍŠù‚É‘¶Ý‚µ‚Ü‚·B
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
21:08:20 (35240): C:/Windows/system32/cmd.exe exited; CPU time 678.640625
21:08:20 (35240): called boinc_finish(0)
0 bytes in 0 Free Blocks.
446 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: 17568189 bytes.
Dumping objects ->
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{1897} normal block at 0x00000185A6D04F50, 32 bytes long.
Data: <HOME=D:\BOINC\da> 48 4F 4D 45 3D 44 3A 5C 42 4F 49 4E 43 5C 64 61
{1886} normal block at 0x00000185A6D053D0, 32 bytes long.
Data: <TMP=D:\BOINC\dat> 54 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 64 61 74
{1875} normal block at 0x00000185A6D052B0, 32 bytes long.
Data: <TEMP=D:\BOINC\da> 54 45 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 64 61
{1864} normal block at 0x00000185A6D05130, 32 bytes long.
Data: <TMPDIR=D:\BOINC\> 54 4D 50 44 49 52 3D 44 3A 5C 42 4F 49 4E 43 5C
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Data: <PATH=D:\BOINC\da> 50 41 54 48 3D 44 3A 5C 42 4F 49 4E 43 5C 64 61
{1822} normal block at 0x00000185A6D040E0, 135 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) : {1819} normal block at 0x00000185A6D09AE0, 8 bytes long.
Data: < > 00 00 C7 A6 85 01 00 00
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Data: <01 > 30 31 D0 A6 85 01 00 00 00 00 00 00 00 00 00 00
{266} normal block at 0x00000185A6D03130, 40 bytes long.
Data: <p + > 70 A1 D0 A6 85 01 00 00 F0 2B D0 A6 85 01 00 00
{265} normal block at 0x00000185A6D09630, 16 bytes long.
Data: <p > 70 A5 D0 A6 85 01 00 00 00 00 00 00 00 00 00 00
{264} normal block at 0x00000185A6D09F40, 16 bytes long.
Data: <H > 48 A5 D0 A6 85 01 00 00 00 00 00 00 00 00 00 00
{263} normal block at 0x00000185A6D04DD0, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{262} normal block at 0x00000185A6D095E0, 16 bytes long.
Data: < > 20 A5 D0 A6 85 01 00 00 00 00 00 00 00 00 00 00
{261} normal block at 0x00000185A6D0A520, 992 bytes long.
Data: < M > E0 95 D0 A6 85 01 00 00 D0 4D D0 A6 85 01 00 00
{97} normal block at 0x00000185A6D04950, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{96} normal block at 0x00000185A6CFDAF0, 16 bytes long.
Data: < + > 80 2B D0 A6 85 01 00 00 00 00 00 00 00 00 00 00
{95} normal block at 0x00000185A6D02B80, 40 bytes long.
Data: < PI > F0 DA CF A6 85 01 00 00 50 49 D0 A6 85 01 00 00
{72} normal block at 0x00000185A6CFD5F0, 16 bytes long.
Data: < > 80 EA 9D 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{71} normal block at 0x00000185A6CFD5A0, 16 bytes long.
Data: <@ > 40 E9 9D 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{70} normal block at 0x00000185A6CFD7D0, 16 bytes long.
Data: < W > F8 57 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{69} normal block at 0x00000185A6CFD1E0, 16 bytes long.
Data: < W > D8 57 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x00000185A6CFDD70, 16 bytes long.
Data: <P > 50 04 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x00000185A6CFDB90, 16 bytes long.
Data: <0 > 30 04 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x00000185A6CFDEB0, 16 bytes long.
Data: < > E0 02 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x00000185A6CFDB40, 16 bytes long.
Data: < > 10 04 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x00000185A6CFD320, 16 bytes long.
Data: <p > 70 04 9A 80 F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x00000185A6CFDAA0, 16 bytes long.
Data: < > 18 C0 98 80 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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