Task 38674120
| Name | test_237-GPUGRID_TEST_ATM_40STEP_20261023-18-40-RND0196_0 |
| Workunit | 31616169 |
| Created | 26 Oct 2026, 4:21:57 UTC |
| Sent | 26 Oct 2026, 4:22:01 UTC |
| Report deadline | 31 Oct 2026, 4:22:01 UTC |
| Received | 26 Oct 2026, 5:29:45 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 654935 |
| Run time | 48 min 40 sec |
| CPU time | 27 min 19 sec |
| Validate state | Valid |
| Credit | 60,000.00 |
| Device peak FLOPS | 19,172.90 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 722.43 MB |
| Peak swap size | 47.17 GB |
| Peak disk usage | 3.01 GB |
Stderr output
<core_client_version>7.24.1</core_client_version>
<![CDATA[
<stderr_txt>
2026-10-26 04:40:47 (3493378): wrapper (8.1.26018): starting
2026-10-26 04:41:29 (3493378): wrapper: running bin/python (bin/conda-unpack)
2026-10-26 04:41:29 (3493378): wrapper: created child process 3495180
2026-10-26 04:41:31 (3493378): bin/python exited; CPU time 0.337610
2026-10-26 04:41:31 (3493378): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-10-26 04:41:31 (3493378): wrapper: created child process 3495208
2026-10-26 04:41:34 (3493378): bin/tar exited; CPU time 1.181351
2026-10-26 04:41:34 (3493378): wrapper: running bin/bash (run.sh)
2026-10-26 04:41:34 (3493378): wrapper: created child process 3495357
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/workspace/slots/5/bin
+++ dirname /workspace/slots/5/bin
++ local full_path_env=/workspace/slots/5
+++ basename /workspace/slots/5
++ local env_name=5
++ '[' -n '' ']'
++ export CONDA_PREFIX=/workspace/slots/5
++ CONDA_PREFIX=/workspace/slots/5
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/workspace/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(5) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/workspace/slots/5/etc/conda/activate.d
++ '[' -d /workspace/slots/5/etc/conda/activate.d ']'
+ export PATH=/workspace/slots/5:/workspace/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/workspace/slots/5:/workspace/slots/5/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/workspace/slots/5/tmp
+ TMP=/workspace/slots/5/tmp
+ mkdir -p /workspace/slots/5/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/workspace/slots/5/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==26.2.1 -v
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ python -m pip install --no-dependencies atom-openmm==8.4.0 -v
Running command pip subprocess to install build dependencies
Using pip 24.3.1 from /workspace/slots/5/lib/python3.11/site-packages/pip (python 3.11)
Collecting setuptools
Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/ef/55/6dc6d6bb953bdfc52519a0059592c52b6e3b8ad51cf8256dffceb55b0610/setuptools-84.2.1-py3-none-any.whl.metadata
Downloading setuptools-84.2.1-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/da/f5/54538a1f17ea753c42b0928dc2e62986d463f8c393340b9a1e602f2d4dd9/setuptools_scm-10.3.4-py3-none-any.whl.metadata
Downloading setuptools_scm-10.3.4-py3-none-any.whl.metadata (6.7 kB)
Collecting vcs-versioning<3,>=2.5.0.dev0 (from setuptools-scm>=8)
Obtaining dependency information for vcs-versioning<3,>=2.5.0.dev0 from https://files.pythonhosted.org/packages/73/1d/ad4064bf12f4503bf61e65d74c93c523672776d25ee0a06aaf42ae09ef3f/vcs_versioning-2.6.0-py3-none-any.whl.metadata
Downloading vcs_versioning-2.6.0-py3-none-any.whl.metadata (1.7 kB)
Collecting packaging>=20 (from setuptools-scm>=8)
Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/63/34/ba1c580383c9eada3711951fef0795c80b829a078d72188184bcab9dd527/packaging-26.3-py3-none-any.whl.metadata
Downloading packaging-26.3-py3-none-any.whl.metadata (3.5 kB)
Downloading setuptools-84.2.1-py3-none-any.whl (876 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 876.3/876.3 kB 24.5 MB/s eta 0:00:00
Downloading setuptools_scm-10.3.4-py3-none-any.whl (33 kB)
Downloading packaging-26.3-py3-none-any.whl (129 kB)
Downloading vcs_versioning-2.6.0-py3-none-any.whl (123 kB)
Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
Creating /workspace/slots/5/tmp/pip-build-env-iuaiqv7p/overlay/bin
changing mode of /workspace/slots/5/tmp/pip-build-env-iuaiqv7p/overlay/bin/vcs-versioning to 775
changing mode of /workspace/slots/5/tmp/pip-build-env-iuaiqv7p/overlay/bin/setuptools-scm to 775
Successfully installed packaging-26.3 setuptools-84.2.1 setuptools-scm-10.3.4 vcs-versioning-2.6.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
Running command Getting requirements to build wheel
/workspace/slots/5/tmp/pip-build-env-iuaiqv7p/overlay/lib/python3.11/site-packages/setuptools_scm/_integration/version_inference.py:236: 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
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)
/workspace/slots/5/tmp/pip-build-env-iuaiqv7p/overlay/lib/python3.11/site-packages/setuptools_scm/_integration/version_inference.py:236: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
running dist_info
creating /workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info
writing /workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/PKG-INFO
writing dependency_links to /workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/dependency_links.txt
writing entry points to /workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/entry_points.txt
writing requirements to /workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/requires.txt
writing top-level names to /workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/top_level.txt
writing manifest file '/workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/SOURCES.txt'
reading manifest file '/workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file '/workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm.egg-info/SOURCES.txt'
creating '/workspace/slots/5/tmp/pip-modern-metadata-c8wywl2l/atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
/workspace/slots/5/tmp/pip-build-env-iuaiqv7p/overlay/lib/python3.11/site-packages/setuptools_scm/_integration/version_inference.py:236: 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/__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
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 '/workspace/slots/5/tmp/pip-wheel-3sbusg99/.tmp-puvnw0co/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
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_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_A34_A12.out r1/QB_A34_A12.out r10/QB_A34_A12.out r11/QB_A34_A12.out r12/QB_A34_A12.out r13/QB_A34_A12.out r14/QB_A34_A12.out r15/QB_A34_A12.out r16/QB_A34_A12.out r17/QB_A34_A12.out r18/QB_A34_A12.out r19/QB_A34_A12.out r2/QB_A34_A12.out r20/QB_A34_A12.out r21/QB_A34_A12.out r3/QB_A34_A12.out r4/QB_A34_A12.out r5/QB_A34_A12.out r6/QB_A34_A12.out r7/QB_A34_A12.out r8/QB_A34_A12.out r9/QB_A34_A12.out 'r*/*.dcd' 'r*/*.xtc'
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: r*/*.xtc: 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
2026-10-26 05:29:26 (3493378): bin/bash exited; CPU time 1594.642458
2026-10-26 05:29:26 (3493378): called boinc_finish(0)
</stderr_txt>
]]>
©2026 Universitat Pompeu Fabra