Task 38583879
| Name | PFKFB3_A12_A35_r0_5-QUICO_ATM_GAFF2_LOMAP_PFKFB3-3-5-RND8678_0 |
| Workunit | 31547889 |
| Created | 14 Dec 2025, 21:09:17 UTC |
| Sent | 14 Dec 2025, 21:09:24 UTC |
| Report deadline | 19 Dec 2025, 21:09:24 UTC |
| Received | 17 Dec 2025, 18:43:04 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 643038 |
| Run time | 12 hours 26 min 28 sec |
| CPU time | 11 hours 37 min 9 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 2,910.89 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 796.67 MB |
| Peak swap size | 8.34 GB |
| Peak disk usage | 3.68 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
16:37:15 (7276): wrapper (7.9.26016): starting
16:37:15 (7276): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A12_A35_0.pdb
QB_A12_A35_0.xml
QB_A12_A35_equil.pdb
QB_A12_A35.inpcrd
QB_A12_A35_input.yaml
QB_A12_A35_mdlambda.pdb
QB_A12_A35_min.pdb
QB_A12_A35_npt.pdb
QB_A12_A35.pdb
QB_A12_A35.prmtop
QB_A12_A35_sys.xml
QB_A12_A35_therm.pdb
run.bat
run.sh
16:37:17 (7276): Library/usr/bin/tar.exe exited; CPU time 0.000000
16:37:17 (7276): 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\18\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\18\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
Downloading 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 12.0 MB/s eta 0:00:00
Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
Downloading packaging-25.0-py3-none-any.whl (66 kB)
Installing collected packages: setuptools, packaging, setuptools-scm
Creating C:\ProgramData\BOINC\slots\18\pip-build-env-k09nt0yi\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\18\pip-build-env-k09nt0yi\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\18\pip-build-env-k09nt0yi\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\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\18\pip-modern-metadata-oqlqabmn\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\18\pip-build-env-k09nt0yi\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\18\pip-wheel-y003n0yn\.tmp-b93thn68\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\18\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) : {3835434} normal block at 0x00000254FE74E730, 8 bytes long.
Data: < T > 00 00 C0 FE 54 02 00 00
..\lib\diagnostics_win.cpp(417) : {3833956} normal block at 0x00000254FE82EA00, 1080 bytes long.
Data: < j > F4 6A 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {310} normal block at 0x00000254FE746640, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
15:30:44 (19048): wrapper (7.9.26016): starting
15:30:44 (19048): 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\18\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1781} normal block at 0x0000022B48495490, 8 bytes long.
Data: < EH+ > 00 00 45 48 2B 02 00 00
..\lib\diagnostics_win.cpp(417) : {303} normal block at 0x0000022B484966E0, 1080 bytes long.
Data: < F > B4 46 00 00 CD CD CD CD A8 01 00 00 00 00 00 00
Object dump complete.
15:45:06 (21204): wrapper (7.9.26016): starting
15:45:06 (21204): 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\18\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
19:17:13 (21204): C:/Windows/system32/cmd.exe exited; CPU time 11936.156250
19:17:13 (21204): called boinc_finish(0)
0 bytes in 0 Free Blocks.
536 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: 207600477 bytes.
Dumping objects ->
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{1837} normal block at 0x00000267935C4920, 48 bytes long.
Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
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Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61
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Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1784} normal block at 0x00000267935AD0C0, 140 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) : {1781} normal block at 0x00000267935C5530, 8 bytes long.
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Data: < c\ g > 10 63 5C 93 67 02 00 00 00 00 00 00 00 00 00 00
{259} normal block at 0x00000267935C5FD0, 16 bytes long.
Data: < b\ g > E8 62 5C 93 67 02 00 00 00 00 00 00 00 00 00 00
{258} normal block at 0x00000267935C09B0, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{257} normal block at 0x00000267935C5940, 16 bytes long.
Data: < b\ g > C0 62 5C 93 67 02 00 00 00 00 00 00 00 00 00 00
{256} normal block at 0x00000267935C62C0, 992 bytes long.
Data: <@Y\ g \ g > 40 59 5C 93 67 02 00 00 B0 09 5C 93 67 02 00 00
{92} normal block at 0x00000267935C07D0, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{91} normal block at 0x00000267935BD3A0, 16 bytes long.
Data: < Z g > D0 DD 5A 93 67 02 00 00 00 00 00 00 00 00 00 00
{90} normal block at 0x00000267935ADDD0, 40 bytes long.
Data: < [ g \ g > A0 D3 5B 93 67 02 00 00 D0 07 5C 93 67 02 00 00
{69} normal block at 0x00000267935BD1C0, 16 bytes long.
Data: < p > 80 EA 70 BC F6 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x00000267935BD530, 16 bytes long.
Data: <@ p > 40 E9 70 BC F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x00000267935BDD00, 16 bytes long.
Data: < Wm > F8 57 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x00000267935BD490, 16 bytes long.
Data: < Wm > D8 57 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x00000267935BDDF0, 16 bytes long.
Data: <P m > 50 04 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x00000267935BDC10, 16 bytes long.
Data: <0 m > 30 04 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x00000267935BD850, 16 bytes long.
Data: < m > E0 02 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x00000267935BD4E0, 16 bytes long.
Data: < m > 10 04 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x00000267935BD620, 16 bytes long.
Data: <p m > 70 04 6D BC F6 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x00000267935BD300, 16 bytes long.
Data: < k > 18 C0 6B BC F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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