Task 38584606
| Name | PFKFB3_A01_A03_r0_2-QUICO_ATM_GAFF2_LOMAP_PFKFB3-3-5-RND3997_0 |
| Workunit | 31548156 |
| Created | 17 Dec 2025, 19:11:35 UTC |
| Sent | 17 Dec 2025, 19:11:36 UTC |
| Report deadline | 22 Dec 2025, 19:11:36 UTC |
| Received | 18 Dec 2025, 9:59:49 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 628564 |
| Run time | 8 hours 52 min 50 sec |
| CPU time | 8 hours 45 min 21 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 13,177.75 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 729.04 MB |
| Peak swap size | 12.55 GB |
| Peak disk usage | 3.68 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-18 02:05:55 (1411584): wrapper (8.1.26018): starting
2025-12-18 02:07:00 (1411584): wrapper: running bin/python (bin/conda-unpack)
2025-12-18 02:07:00 (1411584): wrapper: created child process 1412910
2025-12-18 02:07:04 (1411584): bin/python exited; CPU time 0.089090
2025-12-18 02:07:04 (1411584): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-18 02:07:04 (1411584): wrapper: created child process 1413005
2025-12-18 02:07:06 (1411584): bin/tar exited; CPU time 0.699054
2025-12-18 02:07:06 (1411584): wrapper: running bin/bash (run.sh)
2025-12-18 02:07:06 (1411584): wrapper: created child process 1413043
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/run/media/boinc/GAMY/slots/8/bin
+++ dirname /run/media/boinc/GAMY/slots/8/bin
++ local full_path_env=/run/media/boinc/GAMY/slots/8
+++ basename /run/media/boinc/GAMY/slots/8
++ local env_name=8
++ '[' -n '' ']'
++ export CONDA_PREFIX=/run/media/boinc/GAMY/slots/8
++ CONDA_PREFIX=/run/media/boinc/GAMY/slots/8
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/run/media/boinc/GAMY/slots/8/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(8) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/run/media/boinc/GAMY/slots/8/etc/conda/activate.d
++ '[' -d /run/media/boinc/GAMY/slots/8/etc/conda/activate.d ']'
+ export PATH=/run/media/boinc/GAMY/slots/8:/run/media/boinc/GAMY/slots/8/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/run/media/boinc/GAMY/slots/8:/run/media/boinc/GAMY/slots/8/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/run/media/boinc/GAMY/slots/8/tmp
+ TMP=/run/media/boinc/GAMY/slots/8/tmp
+ mkdir -p /run/media/boinc/GAMY/slots/8/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/run/media/boinc/GAMY/slots/8/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample does not exist.'
+ echo 'Install ATM and deps'
+ python -m pip list
WARNING: The directory '/var/lib/boinc/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
+ python -m pip install pyaml -v
WARNING: The directory '/var/lib/boinc/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
+ python -m pip install --no-dependencies atom-openmm -v
WARNING: The directory '/var/lib/boinc/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
Running command pip subprocess to install build dependencies
WARNING: The directory '/var/lib/boinc/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
Using pip 24.3.1 from /run/media/boinc/GAMY/slots/8/lib/python3.11/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 29.3 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 /run/media/boinc/GAMY/slots/8/tmp/pip-build-env-i0vl7fjl/overlay/bin
changing mode of /run/media/boinc/GAMY/slots/8/tmp/pip-build-env-i0vl7fjl/overlay/bin/setuptools-scm to 755
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
/run/media/boinc/GAMY/slots/8/tmp/pip-build-env-i0vl7fjl/overlay/lib/python3.11/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)
/run/media/boinc/GAMY/slots/8/tmp/pip-build-env-i0vl7fjl/overlay/lib/python3.11/site-packages/setuptools_scm/_integration/version_inference.py:51: UserWarning: version of None already set
warnings.warn(self.message)
running dist_info
creating /run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info
writing /run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/PKG-INFO
writing dependency_links to /run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/dependency_links.txt
writing entry points to /run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/entry_points.txt
writing requirements to /run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/requires.txt
writing top-level names to /run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/top_level.txt
writing manifest file '/run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file '/run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file '/run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm.egg-info/SOURCES.txt'
creating '/run/media/boinc/GAMY/slots/8/tmp/pip-modern-metadata-zz5d9048/atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
/run/media/boinc/GAMY/slots/8/tmp/pip-build-env-i0vl7fjl/overlay/lib/python3.11/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/__init__.py -> 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
creating build/lib/atom_openmm/utils
copying atom_openmm/utils/AtomUtils.py -> build/lib/atom_openmm/utils
copying atom_openmm/utils/__init__.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
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.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/__init__.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/abfe_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/abfe_structprep.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/gibbs_sampling.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/make_atm_system_from_amber.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/ommsystem.py -> build/bdist.linux-x86_64/wheel/./atom_openmm
copying build/lib/atom_openmm/ommworker.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/rbfe_explicit.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/rbfe_structprep.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/uwham.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/AtomUtils.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/config.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/timer.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
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 '/run/media/boinc/GAMY/slots/8/tmp/pip-wheel-4k4idc2e/.tmp-l6k4xnmc/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
WARNING: The directory '/var/lib/boinc/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A01_A03_input.yaml
+ python bin/rbfe_production QB_A01_A03_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_A01_A03.out r1/QB_A01_A03.out r10/QB_A01_A03.out r11/QB_A01_A03.out r12/QB_A01_A03.out r13/QB_A01_A03.out r14/QB_A01_A03.out r15/QB_A01_A03.out r16/QB_A01_A03.out r17/QB_A01_A03.out r18/QB_A01_A03.out r19/QB_A01_A03.out r2/QB_A01_A03.out r20/QB_A01_A03.out r21/QB_A01_A03.out r3/QB_A01_A03.out r4/QB_A01_A03.out r5/QB_A01_A03.out r6/QB_A01_A03.out r7/QB_A01_A03.out r8/QB_A01_A03.out r9/QB_A01_A03.out 'r*/*.dcd' r0/QB_A01_A03.xtc r1/QB_A01_A03.xtc r10/QB_A01_A03.xtc r11/QB_A01_A03.xtc r12/QB_A01_A03.xtc r13/QB_A01_A03.xtc r14/QB_A01_A03.xtc r15/QB_A01_A03.xtc r16/QB_A01_A03.xtc r17/QB_A01_A03.xtc r18/QB_A01_A03.xtc r19/QB_A01_A03.xtc r2/QB_A01_A03.xtc r20/QB_A01_A03.xtc r21/QB_A01_A03.xtc r3/QB_A01_A03.xtc r4/QB_A01_A03.xtc r5/QB_A01_A03.xtc r6/QB_A01_A03.xtc r7/QB_A01_A03.xtc r8/QB_A01_A03.xtc r9/QB_A01_A03.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
2025-12-18 10:59:03 (1411584): bin/bash exited; CPU time 31520.242526
2025-12-18 10:59:03 (1411584): called boinc_finish(0)
</stderr_txt>
]]>
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