Task 38580534
| Name | JNK1_A10_A05_r0_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-0-5-RND4924_0 |
| Workunit | 31545276 |
| Created | 11 Dec 2025, 16:04:48 UTC |
| Sent | 11 Dec 2025, 16:04:52 UTC |
| Report deadline | 16 Dec 2025, 16:04:52 UTC |
| Received | 11 Dec 2025, 21:53:21 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 616596 |
| Run time | 5 hours 27 min 4 sec |
| CPU time | 5 hours 27 min 4 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 15,212.24 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 677.91 MB |
| Peak swap size | 3.82 GB |
| Peak disk usage | 3.51 GB |
Stderr output
<core_client_version>8.0.2</core_client_version>
<![CDATA[
<stderr_txt>
11:06:29 (37388): wrapper (7.9.26016): starting
11:06:29 (37388): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A10_A05_0.pdb
QB_A10_A05_0.xml
QB_A10_A05_equil.pdb
QB_A10_A05.inpcrd
QB_A10_A05_input.yaml
QB_A10_A05_mdlambda.pdb
QB_A10_A05_min.pdb
QB_A10_A05_npt.pdb
QB_A10_A05_out_merged_nowater.pdb
QB_A10_A05.pdb
QB_A10_A05.prmtop
QB_A10_A05_sys.xml
QB_A10_A05_therm.pdb
run.bat
run.sh
11:06:53 (37388): Library/usr/bin/tar.exe exited; CPU time 0.171875
11:06:53 (37388): 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 'R:\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 R:\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 30.3 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 R:\ProgramData\BOINC\slots\0\pip-build-env-_luv6xiv\overlay\Scripts
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
R:\ProgramData\BOINC\slots\0\pip-build-env-_luv6xiv\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)
R:\ProgramData\BOINC\slots\0\pip-build-env-_luv6xiv\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 R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info
writing R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\PKG-INFO
writing dependency_links to R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\dependency_links.txt
writing entry points to R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\entry_points.txt
writing requirements to R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\requires.txt
writing top-level names to R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\top_level.txt
writing manifest file 'R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm.egg-info\SOURCES.txt'
creating 'R:\ProgramData\BOINC\slots\0\pip-modern-metadata-8jeppb82\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
R:\ProgramData\BOINC\slots\0\pip-build-env-_luv6xiv\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 'R:\ProgramData\BOINC\slots\0\pip-wheel-tddmueuh\.tmp-cg5simhs\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 'R:\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.
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
16:40:43 (37388): C:/Windows/system32/cmd.exe exited; CPU time 19624.328125
16:40:43 (37388): 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: 343369691 bytes.
Dumping objects ->
{3835295} normal block at 0x000001E58DB202E0, 48 bytes long.
Data: <PATH=R:\ProgramD> 50 41 54 48 3D 52 3A 5C 50 72 6F 67 72 61 6D 44
{3835284} normal block at 0x000001E58DB20F90, 48 bytes long.
Data: <HOME=R:\ProgramD> 48 4F 4D 45 3D 52 3A 5C 50 72 6F 67 72 61 6D 44
{3835273} normal block at 0x000001E58DB20BA0, 48 bytes long.
Data: <TMP=R:\ProgramDa> 54 4D 50 3D 52 3A 5C 50 72 6F 67 72 61 6D 44 61
{3835262} normal block at 0x000001E58DB20D60, 48 bytes long.
Data: <TEMP=R:\ProgramD> 54 45 4D 50 3D 52 3A 5C 50 72 6F 67 72 61 6D 44
{3835251} normal block at 0x000001E58BE52FD0, 48 bytes long.
Data: <TMPDIR=R:\Progra> 54 4D 50 44 49 52 3D 52 3A 5C 50 72 6F 67 72 61
{3835220} normal block at 0x000001E58DB6E420, 64 bytes long.
Data: <PATH=R:\ProgramD> 50 41 54 48 3D 52 3A 5C 50 72 6F 67 72 61 6D 44
..\api\boinc_api.cpp(309) : {3835207} normal block at 0x000001E58BE4D870, 8 bytes long.
Data: < á‹å > 00 00 E1 8B E5 01 00 00
{3833959} normal block at 0x000001E58BE4DC30, 8 bytes long.
Data: <À~¿ å > C0 7E BF 8D E5 01 00 00
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x000001E58BE465D0, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
{296} normal block at 0x000001E58BE44B20, 80 bytes long.
Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C
{295} normal block at 0x000001E58BE59000, 16 bytes long.
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{291} normal block at 0x000001E58BE590F0, 16 bytes long.
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{290} normal block at 0x000001E58BE59690, 16 bytes long.
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{289} normal block at 0x000001E58BE59410, 16 bytes long.
Data: <Pό܌ > 50 9C E5 8B E5 01 00 00 00 00 00 00 00 00 00 00
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{280} normal block at 0x000001E58BE58920, 16 bytes long.
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{268} normal block at 0x000001E58BE588D0, 16 bytes long.
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{267} normal block at 0x000001E58BE58AB0, 16 bytes long.
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{266} normal block at 0x000001E58BE58A60, 16 bytes long.
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{265} normal block at 0x000001E58BE59280, 16 bytes long.
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{263} normal block at 0x000001E58BE58FB0, 16 bytes long.
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{262} normal block at 0x000001E58BE52E80, 40 bytes long.
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{260} normal block at 0x000001E58BE58A10, 16 bytes long.
Data: < šå‹å > 18 9A E5 8B E5 01 00 00 00 00 00 00 00 00 00 00
{259} normal block at 0x000001E58BE549E0, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
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{257} normal block at 0x000001E58BE599F0, 992 bytes long.
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{93} normal block at 0x000001E58BE54920, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{92} normal block at 0x000001E58BE4D910, 16 bytes long.
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{91} normal block at 0x000001E58BE52BE0, 40 bytes long.
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{70} normal block at 0x000001E58BE4DE10, 16 bytes long.
Data: < êe·ö > 80 EA 65 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{69} normal block at 0x000001E58BE4E4F0, 16 bytes long.
Data: <@ée·ö > 40 E9 65 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x000001E58BE4D820, 16 bytes long.
Data: <øWb·ö > F8 57 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x000001E58BE4E4A0, 16 bytes long.
Data: <ØWb·ö > D8 57 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x000001E58BE4DB90, 16 bytes long.
Data: <P b·ö > 50 04 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x000001E58BE4E270, 16 bytes long.
Data: <0 b·ö > 30 04 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x000001E58BE4DB40, 16 bytes long.
Data: <à b·ö > E0 02 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x000001E58BE4E400, 16 bytes long.
Data: < b·ö > 10 04 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x000001E58BE4E220, 16 bytes long.
Data: <p b·ö > 70 04 62 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x000001E58BE4E3B0, 16 bytes long.
Data: < À`·ö > 18 C0 60 B7 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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