Task 38583614

Name JNK1_A31_A38_r1_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-3-5-RND9115_0
Workunit 31547703
Created 14 Dec 2025, 10:18:26 UTC
Sent 14 Dec 2025, 10:18:37 UTC
Report deadline 19 Dec 2025, 10:18:37 UTC
Received 17 Dec 2025, 21:35:48 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 637789
Run time 12 hours 17 min 49 sec
CPU time 12 hours 17 min 49 sec
Validate state Valid
Credit 750,000.00
Device peak FLOPS 2,906.89 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
windows_x86_64
Peak working set size 706.96 MB
Peak swap size 14.22 GB
Peak disk usage 3.66 GB

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<stderr_txt>
06:09:32 (4352): wrapper (7.9.26016): starting
06:09:32 (4352): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A31_A38_0.pdb
QB_A31_A38_0.xml
QB_A31_A38_equil.pdb
QB_A31_A38.inpcrd
QB_A31_A38_input.yaml
QB_A31_A38_mdlambda.pdb
QB_A31_A38_min.pdb
QB_A31_A38_npt.pdb
QB_A31_A38_out_merged_nowater.pdb
QB_A31_A38.pdb
QB_A31_A38.prmtop
QB_A31_A38_sys.xml
QB_A31_A38_therm.pdb
run.bat
run.sh
06:09:35 (4352): Library/usr/bin/tar.exe exited; CPU time 0.000000
06:09:35 (4352): 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\10\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\10\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 20.4 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\10\pip-build-env-xhonkizm\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\10\pip-build-env-xhonkizm\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\10\pip-build-env-xhonkizm\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\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\10\pip-modern-metadata-cl491y7x\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\10\pip-build-env-xhonkizm\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\10\pip-wheel-6975j7au\.tmp-ajuqxdu9\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\10\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) : {3835107} normal block at 0x000001E0476FBE50, 8 bytes long.
 Data: <  dG    > 00 00 64 47 E0 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833948} normal block at 0x000001E0477DE910, 1080 bytes long.
 Data: <                > B8 0D 00 00 CD CD CD CD E0 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {306} normal block at 0x000001E047704EE0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
15:27:22 (22996): wrapper (7.9.26016): starting
15:27:22 (22996): 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\10\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
21:41:17 (22996): C:/Windows/system32/cmd.exe exited; CPU time 22588.796875
21:41:17 (22996): 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: 404503741 bytes.
Dumping objects ->
{1546} normal block at 0x000002124E9EC970, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1535} normal block at 0x000002124E9EC820, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1524} normal block at 0x000002124E9EC7B0, 48 bytes long.
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{1513} normal block at 0x000002124E9EC660, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1502} normal block at 0x000002124E9EC900, 48 bytes long.
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{1471} normal block at 0x000002124E9F2800, 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) : {1458} normal block at 0x000002124E9E8460, 8 bytes long.
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{300} normal block at 0x000002124E9E7E20, 8 bytes long.
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{291} normal block at 0x000002124E9EDA60, 80 bytes long.
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{290} normal block at 0x000002124E9E7D30, 16 bytes long.
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{289} normal block at 0x000002124E9E7CE0, 16 bytes long.
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{253} normal block at 0x000002124E9ED850, 16 bytes long.
 Data: < < N            > A0 3C 9F 4E 12 02 00 00 00 00 00 00 00 00 00 00 
{252} normal block at 0x000002124E9F3CA0, 992 bytes long.
 Data: <P  N       N    > 50 D8 9E 4E 12 02 00 00 D0 E8 9E 4E 12 02 00 00 
{88} normal block at 0x000002124E9EE450, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{87} normal block at 0x000002124E9E8140, 16 bytes long.
 Data: <   N            > 80 C5 9E 4E 12 02 00 00 00 00 00 00 00 00 00 00 
{86} normal block at 0x000002124E9EC580, 40 bytes long.
 Data: <@  N    P  N    > 40 81 9E 4E 12 02 00 00 50 E4 9E 4E 12 02 00 00 
{65} normal block at 0x000002124E9E7880, 16 bytes long.
 Data: <   P            > 80 EA 96 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x000002124E9E7A60, 16 bytes long.
 Data: <@  P            > 40 E9 96 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000002124E9E8550, 16 bytes long.
 Data: < W P            > F8 57 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000002124E9E8370, 16 bytes long.
 Data: < W P            > D8 57 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000002124E9E7A10, 16 bytes long.
 Data: <P  P            > 50 04 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000002124E9E8500, 16 bytes long.
 Data: <0  P            > 30 04 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000002124E9E8320, 16 bytes long.
 Data: <   P            > E0 02 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000002124E9E84B0, 16 bytes long.
 Data: <   P            > 10 04 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x000002124E9E80F0, 16 bytes long.
 Data: <p  P            > 70 04 93 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x000002124E9E82D0, 16 bytes long.
 Data: <   P            > 18 C0 91 50 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>


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