Task 38583639
| Name | JNK1_A20_A33_r1_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-0-5-RND2636_4 |
| Workunit | 31545192 |
| Created | 14 Dec 2025, 11:35:44 UTC |
| Sent | 14 Dec 2025, 11:35:48 UTC |
| Report deadline | 19 Dec 2025, 11:35:48 UTC |
| Received | 14 Dec 2025, 19:17:27 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 645867 |
| Run time | 4 hours 15 min 33 sec |
| CPU time | 2 hours 17 min 51 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 4,230.94 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 671.07 MB |
| Peak swap size | 16.34 GB |
| Peak disk usage | 3.01 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2025-12-14 09:00:06 (33031): wrapper (8.1.26018): starting
2025-12-14 09:00:49 (33031): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 09:00:49 (33031): wrapper: created child process 33131
2025-12-14 09:01:04 (33031): bin/python exited; CPU time 0.564760
2025-12-14 09:01:04 (33031): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 09:01:04 (33031): wrapper: created child process 33136
2025-12-14 09:01:15 (33031): bin/tar exited; CPU time 8.182521
2025-12-14 09:01:17 (33031): wrapper: running bin/bash (run.sh)
2025-12-14 09:01:17 (33031): wrapper: created child process 33204
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/3/bin
+++ dirname /var/lib/boinc/slots/3/bin
++ local full_path_env=/var/lib/boinc/slots/3
+++ basename /var/lib/boinc/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/3
++ CONDA_PREFIX=/var/lib/boinc/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/3/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/3/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/3/tmp
+ TMP=/var/lib/boinc/slots/3/tmp
+ mkdir -p /var/lib/boinc/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/3/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 /var/lib/boinc/slots/3/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 17.1 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 /var/lib/boinc/slots/3/tmp/pip-build-env-t963txkh/overlay/bin
changing mode of /var/lib/boinc/slots/3/tmp/pip-build-env-t963txkh/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
/var/lib/boinc/slots/3/tmp/pip-build-env-t963txkh/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)
/var/lib/boinc/slots/3/tmp/pip-build-env-t963txkh/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 /var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info
writing /var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/PKG-INFO
writing dependency_links to /var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/dependency_links.txt
writing entry points to /var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/entry_points.txt
writing requirements to /var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/requires.txt
writing top-level names to /var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/top_level.txt
writing manifest file '/var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file '/var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file '/var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm.egg-info/SOURCES.txt'
creating '/var/lib/boinc/slots/3/tmp/pip-modern-metadata-zif2lukd/atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
/var/lib/boinc/slots/3/tmp/pip-build-env-t963txkh/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/ommsystem.py -> build/lib/atom_openmm
copying atom_openmm/__init__.py -> build/lib/atom_openmm
copying atom_openmm/transport.py -> build/lib/atom_openmm
copying atom_openmm/abfe_production.py -> build/lib/atom_openmm
copying atom_openmm/rbfe_explicit.py -> build/lib/atom_openmm
copying atom_openmm/ommworker.py -> build/lib/atom_openmm
copying atom_openmm/temperatureRE_explicit.py -> build/lib/atom_openmm
copying atom_openmm/gibbs_sampling.py -> build/lib/atom_openmm
copying atom_openmm/make_atm_system_from_pdb.py -> build/lib/atom_openmm
copying atom_openmm/ommreplica.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/uwham.py -> build/lib/atom_openmm
copying atom_openmm/openmm_async_re.py -> build/lib/atom_openmm
copying atom_openmm/async_re.py -> build/lib/atom_openmm
copying atom_openmm/abfe_explicit.py -> build/lib/atom_openmm
copying atom_openmm/make_atm_system_from_amber.py -> build/lib/atom_openmm
copying atom_openmm/local_openmm_transport.py -> build/lib/atom_openmm
copying atom_openmm/abfe_structprep.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/__init__.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/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
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/ommsystem.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/transport.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_explicit.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/temperatureRE_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/make_atm_system_from_pdb.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/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
creating 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/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/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/uwham.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/async_re.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/make_atm_system_from_amber.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/abfe_structprep.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
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 '/var/lib/boinc/slots/3/tmp/pip-wheel-ezxu3bqi/.tmp-83qzzikk/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_A20_A33_input.yaml
+ python bin/rbfe_production QB_A20_A33_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/lib/boinc/slots/3/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 212, in _update_replica
pot = job['openmm_worker'].get_energy()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/openmm/openmm.py", line 15506, in getState
state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Particle coordinate is NaN. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan
2025-12-14 13:15:39 (33031): bin/bash exited; CPU time 5791.806947
2025-12-14 13:15:39 (33031): app exit status: 0x1
2025-12-14 13:15:39 (33031): called boinc_finish(195)
</stderr_txt>
]]>
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