Task 38598506
| Name | MCL1_A09_A40_r0_5-QUICO_ATM_GAFF2_NAGL_MCL1-1-6-RND1545_2 |
| Workunit | 31553683 |
| Created | 8 Apr 2026, 10:06:16 UTC |
| Sent | 8 Apr 2026, 10:06:49 UTC |
| Report deadline | 13 Apr 2026, 10:06:49 UTC |
| Received | 8 Apr 2026, 20:18:59 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 626176 |
| Run time | 9 hours 33 min 33 sec |
| CPU time | 7 hours 12 min 35 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 3,940.98 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 422.07 MB |
| Peak swap size | 3.39 GB |
| Peak disk usage | 2.91 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
03:11:13 (3440): wrapper (7.9.26016): starting
03:11:13 (3440): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A09_A40_0.pdb
QB_A09_A40_0.xml
QB_A09_A40.inpcrd
QB_A09_A40_input.yaml
QB_A09_A40.pdb
QB_A09_A40.prmtop
QB_A09_A40_sys.xml
run.bat
run.sh
03:11:14 (3440): Library/usr/bin/tar.exe exited; CPU time 0.000000
03:11:14 (3440): 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:\ProgramData1\slots\2\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:\ProgramData1\slots\2\Lib\site-packages\pip (python 3.11)
Collecting setuptools
Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/9d/76/f789f7a86709c6b087c5a2f52f911838cad707cc613162401badc665acfe/setuptools-82.0.1-py3-none-any.whl.metadata
Downloading setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
Collecting setuptools-scm>=8
Obtaining dependency information for setuptools-scm>=8 from https://files.pythonhosted.org/packages/5c/e1/342c4434df56aa537f6ce7647eefee521d96fbb828b08acd709865767652/setuptools_scm-10.0.5-py3-none-any.whl.metadata
Downloading setuptools_scm-10.0.5-py3-none-any.whl.metadata (6.5 kB)
Collecting vcs-versioning>=1.0.0.dev0 (from setuptools-scm>=8)
Obtaining dependency information for vcs-versioning>=1.0.0.dev0 from https://files.pythonhosted.org/packages/e6/60/73603fbcdbe5e803855bcce4414f94eaeed449083bd8183e67161af78188/vcs_versioning-1.1.1-py3-none-any.whl.metadata
Downloading vcs_versioning-1.1.1-py3-none-any.whl.metadata (1.6 kB)
Collecting packaging>=20 (from setuptools-scm>=8)
Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl.metadata
Downloading packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
---------------------------------------- 1.0/1.0 MB 6.8 MB/s eta 0:00:00
Downloading setuptools_scm-10.0.5-py3-none-any.whl (21 kB)
Downloading packaging-26.0-py3-none-any.whl (74 kB)
Downloading vcs_versioning-1.1.1-py3-none-any.whl (79 kB)
Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
Creating D:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Scripts
Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1
Running command Getting requirements to build wheel
D:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
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
D:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
return get_active_overrides().subprocess_timeout
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:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
running dist_info
creating D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info
writing D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\PKG-INFO
writing dependency_links to D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\dependency_links.txt
writing entry points to D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\entry_points.txt
writing requirements to D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\requires.txt
writing top-level names to D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\top_level.txt
writing manifest file 'D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\SOURCES.txt'
D:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
return get_active_overrides().subprocess_timeout
listing git files failed - pretending there aren't any
reading manifest file 'D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm.egg-info\SOURCES.txt'
creating 'D:\ProgramData1\slots\2\pip-modern-metadata-d2_ykthn\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
D:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
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
D:\ProgramData1\slots\2\pip-build-env-c2yc6or8\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
return get_active_overrides().subprocess_timeout
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:\\ProgramData1\\slots\\2\\pip-wheel-eaeg6kst\\.tmp-9kr9nlvg\\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:\ProgramData1\slots\2\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
13:17:47 (3440): C:/Windows/system32/cmd.exe exited; CPU time 25955.984375
13:17:47 (3440): called boinc_finish(0)
0 bytes in 0 Free Blocks.
456 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: 372689143 bytes.
Dumping objects ->
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{257} normal block at 0x0000020487FF82E0, 16 bytes long.
Data: < …ÿ‡ > 08 85 FF 87 04 02 00 00 00 00 00 00 00 00 00 00
{256} normal block at 0x0000020487FF3E80, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{255} normal block at 0x0000020487FF8240, 16 bytes long.
Data: <à„ÿ‡ > E0 84 FF 87 04 02 00 00 00 00 00 00 00 00 00 00
{254} normal block at 0x0000020487FF84E0, 992 bytes long.
Data: <@‚ÿ‡ >ÿ‡ > 40 82 FF 87 04 02 00 00 80 3E FF 87 04 02 00 00
{90} normal block at 0x0000020487FF36A0, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{89} normal block at 0x0000020487FEFCA0, 16 bytes long.
Data: <`Âý‡ > 60 C2 FD 87 04 02 00 00 00 00 00 00 00 00 00 00
{88} normal block at 0x0000020487FDC260, 40 bytes long.
Data: < üþ‡  6ÿ‡ > A0 FC FE 87 04 02 00 00 A0 36 FF 87 04 02 00 00
{67} normal block at 0x0000020487FF0470, 16 bytes long.
Data: < ê#_ö > 80 EA 23 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x0000020487FEFB10, 16 bytes long.
Data: <@é#_ö > 40 E9 23 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x0000020487FEFD40, 16 bytes long.
Data: <øW _ö > F8 57 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x0000020487FF0420, 16 bytes long.
Data: <ØW _ö > D8 57 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x0000020487FF0790, 16 bytes long.
Data: <P _ö > 50 04 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x0000020487FEFDE0, 16 bytes long.
Data: <0 _ö > 30 04 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x0000020487FF0060, 16 bytes long.
Data: <à _ö > E0 02 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x0000020487FF02E0, 16 bytes long.
Data: < _ö > 10 04 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{59} normal block at 0x0000020487FF0560, 16 bytes long.
Data: <p _ö > 70 04 20 5F F6 7F 00 00 00 00 00 00 00 00 00 00
{58} normal block at 0x0000020487FF0740, 16 bytes long.
Data: < À _ö > 18 C0 1E 5F F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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