Task 38597245
| Name | p38_A08_A01_r0_2-QUICO_ATM_GAFF2_NAGL_p38-0-6-RND1977_0 |
| Workunit | 31553160 |
| Created | 8 Apr 2026, 7:44:46 UTC |
| Sent | 8 Apr 2026, 8:00:26 UTC |
| Report deadline | 13 Apr 2026, 8:00:26 UTC |
| Received | 9 Apr 2026, 14:41:24 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 651019 |
| Run time | 9 hours 23 min 26 sec |
| CPU time | 5 hours 9 min 59 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 2,182.86 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 632.55 MB |
| Peak swap size | 11.49 GB |
| Peak disk usage | 2.99 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-08 10:01:33 (548967): wrapper (8.1.26018): starting
2026-04-08 10:02:54 (548967): wrapper: running bin/python (bin/conda-unpack)
2026-04-08 10:02:54 (548967): wrapper: created child process 549125
2026-04-08 10:02:55 (548967): bin/python exited; CPU time 0.194626
2026-04-08 10:02:55 (548967): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-08 10:02:55 (548967): wrapper: created child process 549128
2026-04-08 10:02:59 (548967): bin/tar exited; CPU time 2.056026
2026-04-08 10:02:59 (548967): wrapper: running bin/bash (run.sh)
2026-04-08 10:02:59 (548967): wrapper: created child process 549137
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/config/slots/1/bin
+++ dirname /config/slots/1/bin
++ local full_path_env=/config/slots/1
+++ basename /config/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/config/slots/1
++ CONDA_PREFIX=/config/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/config/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/config/slots/1/etc/conda/activate.d
++ '[' -d /config/slots/1/etc/conda/activate.d ']'
+ export PATH=/config/slots/1:/config/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/config/slots/1:/config/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/config/slots/1/tmp
+ TMP=/config/slots/1/tmp
+ mkdir -p /config/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/config/slots/1/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 /config/slots/1/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 2.8 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 /config/slots/1/tmp/pip-build-env-jjrghuna/overlay/bin
changing mode of /config/slots/1/tmp/pip-build-env-jjrghuna/overlay/bin/vcs-versioning to 777
changing mode of /config/slots/1/tmp/pip-build-env-jjrghuna/overlay/bin/setuptools-scm to 777
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
/config/slots/1/tmp/pip-build-env-jjrghuna/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
/config/slots/1/tmp/pip-build-env-jjrghuna/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)
/config/slots/1/tmp/pip-build-env-jjrghuna/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 /config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info
writing /config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/PKG-INFO
writing dependency_links to /config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/dependency_links.txt
writing entry points to /config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/entry_points.txt
writing requirements to /config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/requires.txt
writing top-level names to /config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/top_level.txt
writing manifest file '/config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/SOURCES.txt'
/config/slots/1/tmp/pip-build-env-jjrghuna/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 '/config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file '/config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm.egg-info/SOURCES.txt'
creating '/config/slots/1/tmp/pip-modern-metadata-on6jgbyf/atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
/config/slots/1/tmp/pip-build-env-jjrghuna/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/temperatureRE_explicit.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_explicit.py -> build/lib/atom_openmm
copying atom_openmm/gibbs_sampling.py -> build/lib/atom_openmm
copying atom_openmm/rbfe_structprep.py -> build/lib/atom_openmm
copying atom_openmm/make_atm_system_from_rcpt_lig.py -> build/lib/atom_openmm
copying atom_openmm/transport.py -> build/lib/atom_openmm
copying atom_openmm/abfe_structprep.py -> build/lib/atom_openmm
copying atom_openmm/__init__.py -> build/lib/atom_openmm
copying atom_openmm/openmm_async_re.py -> build/lib/atom_openmm
copying atom_openmm/ommreplica.py -> build/lib/atom_openmm
copying atom_openmm/make_atm_system_from_amber.py -> build/lib/atom_openmm
copying atom_openmm/ommsystem.py -> build/lib/atom_openmm
copying atom_openmm/abfe_production.py -> build/lib/atom_openmm
copying atom_openmm/make_atm_system_from_pdb.py -> build/lib/atom_openmm
copying atom_openmm/async_re.py -> build/lib/atom_openmm
copying atom_openmm/ommworker.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
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/timer.py -> build/lib/atom_openmm/utils
copying atom_openmm/utils/singal_guard.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
/config/slots/1/tmp/pip-build-env-jjrghuna/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/temperatureRE_explicit.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_explicit.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/rbfe_structprep.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/transport.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/__init__.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/ommreplica.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/ommsystem.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/make_atm_system_from_pdb.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/ommworker.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
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/logging.conf -> 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/singal_guard.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/rbfe_production.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 '/config/slots/1/tmp/pip-wheel-nrq2bsac/.tmp-12zm8tyu/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_A08_A01_input.yaml
+ python bin/rbfe_production QB_A08_A01_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-08 19:16:19 (771): wrapper (8.1.26018): starting
2026-04-08 19:16:20 (771): wrapper: running bin/bash (run.sh)
2026-04-08 19:16:20 (771): wrapper: created child process 773
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/config/slots/1/bin
+++ dirname /config/slots/1/bin
++ local full_path_env=/config/slots/1
+++ basename /config/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/config/slots/1
++ CONDA_PREFIX=/config/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/config/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/config/slots/1/etc/conda/activate.d
++ '[' -d /config/slots/1/etc/conda/activate.d ']'
+ export PATH=/config/slots/1:/config/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/config/slots/1:/config/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/config/slots/1/tmp
+ TMP=/config/slots/1/tmp
+ mkdir -p /config/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/config/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A08_A01_input.yaml
+ python bin/rbfe_production QB_A08_A01_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Terminated
/config/slots/1/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown
warnings.warn('resource_tracker: There appear to be %d '
2026-04-09 16:39:41 (771): bin/bash exited; CPU time 18557.216260
2026-04-09 16:39:41 (771): app exit status: 0x8f
2026-04-09 16:39:41 (771): called boinc_finish(195)
</stderr_txt>
]]>
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