Task 38580334
| Name | JNK1_A10_A05_r4_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-0-5-RND5400_1 |
| Workunit | 31545145 |
| Created | 11 Dec 2025, 14:28:04 UTC |
| Sent | 11 Dec 2025, 14:28:11 UTC |
| Report deadline | 16 Dec 2025, 14:28:11 UTC |
| Received | 17 Dec 2025, 16:56:28 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 619341 |
| Run time | 3 days 10 hours 46 min 20 sec |
| CPU time | 2 days 11 hours 1 min 26 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 14,902.89 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 871.34 MB |
| Peak swap size | 8.46 GB |
| Peak disk usage | 4.85 GB |
Stderr output
<core_client_version>8.0.2</core_client_version>
<![CDATA[
<stderr_txt>
22:32:54 (2308): wrapper (7.9.26016): starting
22:32:54 (2308): 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
22:33:02 (2308): Library/usr/bin/tar.exe exited; CPU time 0.000000
22:33:02 (2308): 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\20\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\20\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
Using cached 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)
Using cached 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\20\pip-build-env-u7kmuitl\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\20\pip-build-env-u7kmuitl\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\20\pip-build-env-u7kmuitl\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\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info
writing D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\PKG-INFO
writing dependency_links to D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\dependency_links.txt
writing entry points to D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\entry_points.txt
writing requirements to D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\requires.txt
writing top-level names to D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\top_level.txt
writing manifest file 'D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm.egg-info\SOURCES.txt'
creating 'D:\BOINC\Data\slots\20\pip-modern-metadata-m7vli7e5\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
D:\BOINC\Data\slots\20\pip-build-env-u7kmuitl\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\20\pip-wheel-iywa70z4\.tmp-vjsefykj\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\20\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) : {3835297} normal block at 0x0000019479CC13D0, 8 bytes long.
Data: < y > 00 00 C5 79 94 01 00 00
..\lib\diagnostics_win.cpp(417) : {3834026} normal block at 0x0000019479D9E820, 1080 bytes long.
Data: < > 94 1B 00 00 CD CD CD CD CC 03 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x0000019479CC1960, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
17:05:55 (6968): wrapper (7.9.26016): starting
17:05:55 (6968): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
×ÓĿ¼»òÎļþ D:\BOINC\Data\slots\20\tmp ÒѾ­´æÔÚ¡£
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3849980} normal block at 0x000001DF7AFD20F0, 8 bytes long.
Data: < | > 00 00 A0 7C DF 01 00 00
..\lib\diagnostics_win.cpp(417) : {3848709} normal block at 0x000001DF7D0F6D50, 1080 bytes long.
Data: <p6 L > 70 36 00 00 CD CD CD CD 4C 01 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x000001DF7AFD2810, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
17:05:05 (12936): wrapper (7.9.26016): starting
17:05:05 (12936): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
×ÓĿ¼»òÎļþ D:\BOINC\Data\slots\20\tmp ÒѾ­´æÔÚ¡£
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
03:32:09 (12936): C:/Windows/system32/cmd.exe exited; CPU time 28403.328125
03:32:09 (12936): called boinc_finish(0)
0 bytes in 0 Free Blocks.
176 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: 651345758 bytes.
Dumping objects ->
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{3850057} normal block at 0x000001E6D1262A90, 32 bytes long.
Data: <HOME=D:\BOINC\Da> 48 4F 4D 45 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61
{3850046} normal block at 0x000001E6D12627F0, 32 bytes long.
Data: <TMP=D:\BOINC\Dat> 54 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61 74
{3850035} normal block at 0x000001E6D1263030, 32 bytes long.
Data: <TEMP=D:\BOINC\Da> 54 45 4D 50 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61
{3850024} normal block at 0x000001E6D1261B30, 32 bytes long.
Data: <TMPDIR=D:\BOINC\> 54 4D 50 44 49 52 3D 44 3A 5C 42 4F 49 4E 43 5C
{3849993} normal block at 0x000001E6CF21B1E0, 48 bytes long.
Data: <PATH=D:\BOINC\Da> 50 41 54 48 3D 44 3A 5C 42 4F 49 4E 43 5C 44 61
..\api\boinc_api.cpp(309) : {3849980} normal block at 0x000001E6CF21F440, 8 bytes long.
Data: < > 00 00 1C CF E6 01 00 00
{3848710} normal block at 0x000001E6CF21F300, 8 bytes long.
Data: < " > 20 C1 22 D1 E6 01 00 00
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Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
{290} normal block at 0x000001E6CF205B60, 80 bytes long.
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Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55
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{255} normal block at 0x000001E6CF21F4E0, 16 bytes long.
Data: < " > 10 10 22 CF E6 01 00 00 00 00 00 00 00 00 00 00
{254} normal block at 0x000001E6CF21F350, 16 bytes long.
Data: < " > E8 0F 22 CF E6 01 00 00 00 00 00 00 00 00 00 00
{253} normal block at 0x000001E6CF216670, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{252} normal block at 0x000001E6CF21F800, 16 bytes long.
Data: < " > C0 0F 22 CF E6 01 00 00 00 00 00 00 00 00 00 00
{251} normal block at 0x000001E6CF220FC0, 992 bytes long.
Data: < ! pf! > 00 F8 21 CF E6 01 00 00 70 66 21 CF E6 01 00 00
{87} normal block at 0x000001E6CF216250, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{86} normal block at 0x000001E6CF215D10, 16 bytes long.
Data: < ! > 00 B1 21 CF E6 01 00 00 00 00 00 00 00 00 00 00
{85} normal block at 0x000001E6CF21B100, 40 bytes long.
Data: < ]! Pb! > 10 5D 21 CF E6 01 00 00 50 62 21 CF E6 01 00 00
{62} normal block at 0x000001E6CF2156D0, 16 bytes long.
Data: < -h > 80 EA 2D 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x000001E6CF216030, 16 bytes long.
Data: <@ -h > 40 E9 2D 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x000001E6CF215680, 16 bytes long.
Data: < W*h > F8 57 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{59} normal block at 0x000001E6CF2155E0, 16 bytes long.
Data: < W*h > D8 57 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{58} normal block at 0x000001E6CF215630, 16 bytes long.
Data: <P *h > 50 04 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{57} normal block at 0x000001E6CF215400, 16 bytes long.
Data: <0 *h > 30 04 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{56} normal block at 0x000001E6CF215900, 16 bytes long.
Data: < *h > E0 02 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{55} normal block at 0x000001E6CF215A90, 16 bytes long.
Data: < *h > 10 04 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{54} normal block at 0x000001E6CF215720, 16 bytes long.
Data: <p *h > 70 04 2A 68 F6 7F 00 00 00 00 00 00 00 00 00 00
{53} normal block at 0x000001E6CF215C70, 16 bytes long.
Data: < (h > 18 C0 28 68 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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