Task 38598641
| Name | JNK1_A13_A12_r0_2-QUICO_ATM_GAFF2_NAGL_JNK1-1-6-RND9117_1 |
| Workunit | 31553739 |
| Created | 8 Apr 2026, 10:51:21 UTC |
| Sent | 8 Apr 2026, 10:51:46 UTC |
| Report deadline | 13 Apr 2026, 10:51:46 UTC |
| Received | 8 Apr 2026, 19:28:09 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 279481 |
| Run time | 8 hours 33 min 20 sec |
| CPU time | 8 hours 33 min 20 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 13,171.26 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 669.98 MB |
| Peak swap size | 13.40 GB |
| Peak disk usage | 3.07 GB |
Stderr output
<core_client_version>8.3.0</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-08 06:53:23 (1001800): wrapper (8.1.26018): starting
2026-04-08 06:53:50 (1001800): wrapper: running bin/python (bin/conda-unpack)
2026-04-08 06:53:50 (1001800): wrapper: created child process 1001802
2026-04-08 06:53:51 (1001800): bin/python exited; CPU time 0.277046
2026-04-08 06:53:51 (1001800): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-08 06:53:51 (1001800): wrapper: created child process 1001803
2026-04-08 06:53:54 (1001800): bin/tar exited; CPU time 2.454414
2026-04-08 06:53:54 (1001800): wrapper: running bin/bash (run.sh)
2026-04-08 06:53:54 (1001800): wrapper: created child process 1001805
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/psands/BOINC/slots/6/bin
+++ dirname /home/psands/BOINC/slots/6/bin
++ local full_path_env=/home/psands/BOINC/slots/6
+++ basename /home/psands/BOINC/slots/6
++ local env_name=6
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/psands/BOINC/slots/6
++ CONDA_PREFIX=/home/psands/BOINC/slots/6
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/psands/BOINC/slots/6/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(6) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/psands/BOINC/slots/6/etc/conda/activate.d
++ '[' -d /home/psands/BOINC/slots/6/etc/conda/activate.d ']'
+ export PATH=/home/psands/BOINC/slots/6:/home/psands/BOINC/slots/6/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/psands/BOINC/slots/6:/home/psands/BOINC/slots/6/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/psands/BOINC/slots/6/tmp
+ TMP=/home/psands/BOINC/slots/6/tmp
+ mkdir -p /home/psands/BOINC/slots/6/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/psands/BOINC/slots/6/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample does not exist.'
+ echo 'Install ATM and deps'
+ python -m pip list
+ python -m pip install pyaml -v
+ python -m pip install --no-dependencies atom-openmm -v
Running command pip subprocess to install build dependencies
Using pip 24.3.1 from /home/psands/BOINC/slots/6/lib/python3.11/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 4.3 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 /home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/bin
changing mode of /home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/bin/vcs-versioning to 755
changing mode of /home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/bin/setuptools-scm to 755
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
/home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/lib/python3.11/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
/home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/lib/python3.11/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)
/home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/lib/python3.11/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 /home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info
writing /home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/PKG-INFO
writing dependency_links to /home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/dependency_links.txt
writing entry points to /home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/entry_points.txt
writing requirements to /home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/requires.txt
writing top-level names to /home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/top_level.txt
writing manifest file '/home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/SOURCES.txt'
/home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/lib/python3.11/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 '/home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file '/home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm.egg-info/SOURCES.txt'
creating '/home/psands/BOINC/slots/6/tmp/pip-modern-metadata-dlp_l38h/atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
/home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/lib/python3.11/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/rbfe_structprep.py -> build/lib/atom_openmm
copying atom_openmm/__init__.py -> build/lib/atom_openmm
copying atom_openmm/async_re.py -> build/lib/atom_openmm
copying atom_openmm/openmm_async_re.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/local_openmm_transport.py -> build/lib/atom_openmm
copying atom_openmm/uwham.py -> build/lib/atom_openmm
copying atom_openmm/abfe_structprep.py -> build/lib/atom_openmm
copying atom_openmm/gibbs_sampling.py -> build/lib/atom_openmm
copying atom_openmm/ommsystem.py -> build/lib/atom_openmm
copying atom_openmm/rbfe_explicit.py -> build/lib/atom_openmm
copying atom_openmm/abfe_production.py -> build/lib/atom_openmm
copying atom_openmm/rbfe_production.py -> build/lib/atom_openmm
copying atom_openmm/ommworker.py -> build/lib/atom_openmm
copying atom_openmm/abfe_explicit.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/make_atm_system_from_amber.py -> build/lib/atom_openmm
creating 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
copying atom_openmm/utils/singal_guard.py -> 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
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
/home/psands/BOINC/slots/6/tmp/pip-build-env-vg6tzawd/overlay/lib/python3.11/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.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/atom_openmm
copying build/lib/atom_openmm/rbfe_structprep.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/__init__.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/async_re.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/openmm_async_re.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/make_atm_system_from_pdb.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/make_atm_system_from_rcpt_lig.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/ommreplica.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/local_openmm_transport.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/uwham.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/abfe_structprep.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/gibbs_sampling.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/ommsystem.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/rbfe_explicit.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/abfe_production.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/rbfe_production.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/ommworker.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
creating build/bdist.linux-x86_64/wheel/atom_openmm/utils
copying build/lib/atom_openmm/utils/timer.py -> build/bdist.linux-x86_64/wheel/./atom_openmm/utils
copying build/lib/atom_openmm/utils/__init__.py -> build/bdist.linux-x86_64/wheel/./atom_openmm/utils
copying build/lib/atom_openmm/utils/singal_guard.py -> build/bdist.linux-x86_64/wheel/./atom_openmm/utils
copying build/lib/atom_openmm/utils/AtomUtils.py -> build/bdist.linux-x86_64/wheel/./atom_openmm/utils
copying build/lib/atom_openmm/utils/config.py -> build/bdist.linux-x86_64/wheel/./atom_openmm/utils
copying build/lib/atom_openmm/utils/logging.conf -> build/bdist.linux-x86_64/wheel/./atom_openmm/utils
copying build/lib/atom_openmm/abfe_explicit.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/temperatureRE_explicit.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/transport.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/make_atm_system_from_amber.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
running install_egg_info
Copying atom_openmm.egg-info to build/bdist.linux-x86_64/wheel/./atom_openmm-8.4.0-py3.11.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/atom_openmm-8.4.0.dist-info/WHEEL
creating '/home/psands/BOINC/slots/6/tmp/pip-wheel-jtar1esd/.tmp-dm6_7kzo/atom_openmm-8.4.0-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/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.linux-x86_64/wheel
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A13_A12_input.yaml
+ python bin/rbfe_production QB_A13_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
+ echo 'Save output'
+ tar cjvf output.tar.bz2 run.log stderr.txt r0/QB_A13_A12.out r1/QB_A13_A12.out r10/QB_A13_A12.out r11/QB_A13_A12.out r12/QB_A13_A12.out r13/QB_A13_A12.out r14/QB_A13_A12.out r15/QB_A13_A12.out r16/QB_A13_A12.out r17/QB_A13_A12.out r18/QB_A13_A12.out r19/QB_A13_A12.out r2/QB_A13_A12.out r20/QB_A13_A12.out r21/QB_A13_A12.out r3/QB_A13_A12.out r4/QB_A13_A12.out r5/QB_A13_A12.out r6/QB_A13_A12.out r7/QB_A13_A12.out r8/QB_A13_A12.out r9/QB_A13_A12.out 'r*/*.dcd' r0/QB_A13_A12.xtc r1/QB_A13_A12.xtc r10/QB_A13_A12.xtc r11/QB_A13_A12.xtc r12/QB_A13_A12.xtc r13/QB_A13_A12.xtc r14/QB_A13_A12.xtc r15/QB_A13_A12.xtc r16/QB_A13_A12.xtc r17/QB_A13_A12.xtc r18/QB_A13_A12.xtc r19/QB_A13_A12.xtc r2/QB_A13_A12.xtc r20/QB_A13_A12.xtc r21/QB_A13_A12.xtc r3/QB_A13_A12.xtc r4/QB_A13_A12.xtc r5/QB_A13_A12.xtc r6/QB_A13_A12.xtc r7/QB_A13_A12.xtc r8/QB_A13_A12.xtc r9/QB_A13_A12.xtc
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
+ true
+ echo 'Save restart'
+ tar cjvf restart.tar.bz2 r0/checkpoint.xml r1/checkpoint.xml r10/checkpoint.xml r11/checkpoint.xml r12/checkpoint.xml r13/checkpoint.xml r14/checkpoint.xml r15/checkpoint.xml r16/checkpoint.xml r17/checkpoint.xml r18/checkpoint.xml r19/checkpoint.xml r2/checkpoint.xml r20/checkpoint.xml r21/checkpoint.xml r3/checkpoint.xml r4/checkpoint.xml r5/checkpoint.xml r6/checkpoint.xml r7/checkpoint.xml r8/checkpoint.xml r9/checkpoint.xml
2026-04-08 15:26:14 (1001800): bin/bash exited; CPU time 30785.708266
2026-04-08 15:26:14 (1001800): called boinc_finish(0)
</stderr_txt>
]]>
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