Task 38580569

Stderr output

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-11 18:49:58 (2180407): wrapper (8.1.26018): starting
2025-12-11 18:50:49 (2180407): wrapper: running bin/python (bin/conda-unpack)
2025-12-11 18:50:49 (2180407): wrapper: created child process 2180437
2025-12-11 18:50:51 (2180407): bin/python exited; CPU time 0.415087
2025-12-11 18:50:51 (2180407): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-11 18:50:51 (2180407): wrapper: created child process 2180438
2025-12-11 18:50:55 (2180407): bin/tar exited; CPU time 3.459384
2025-12-11 18:50:55 (2180407): wrapper: running bin/bash (run.sh)
2025-12-11 18:50:55 (2180407): wrapper: created child process 2180441
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/t11/Mo/2/slots/2/bin
+++ dirname /home/t11/Mo/2/slots/2/bin
++ local full_path_env=/home/t11/Mo/2/slots/2
+++ basename /home/t11/Mo/2/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/t11/Mo/2/slots/2
++ CONDA_PREFIX=/home/t11/Mo/2/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/t11/Mo/2/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/t11/Mo/2/slots/2/etc/conda/activate.d
++ '[' -d /home/t11/Mo/2/slots/2/etc/conda/activate.d ']'
+ export PATH=/home/t11/Mo/2/slots/2:/home/t11/Mo/2/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/t11/Mo/2/slots/2:/home/t11/Mo/2/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/t11/Mo/2/slots/2/tmp
+ TMP=/home/t11/Mo/2/slots/2/tmp
+ mkdir -p /home/t11/Mo/2/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/t11/Mo/2/slots/2/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
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 -v
  Running command pip subprocess to install build dependencies
  Using pip 24.3.1 from /home/t11/Mo/2/slots/2/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
    Using cached 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
    Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
  Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
  Using cached packaging-25.0-py3-none-any.whl (66 kB)
  Installing collected packages: setuptools, packaging, setuptools-scm
    Creating /home/t11/Mo/2/slots/2/tmp/pip-build-env-vejd1gay/overlay/bin
    changing mode of /home/t11/Mo/2/slots/2/tmp/pip-build-env-vejd1gay/overlay/bin/setuptools-scm to 755
  Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
  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
  /home/t11/Mo/2/slots/2/tmp/pip-build-env-vejd1gay/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)
  /home/t11/Mo/2/slots/2/tmp/pip-build-env-vejd1gay/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 /home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info
  writing /home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/PKG-INFO
  writing dependency_links to /home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/dependency_links.txt
  writing entry points to /home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/entry_points.txt
  writing requirements to /home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/requires.txt
  writing top-level names to /home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/top_level.txt
  writing manifest file '/home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file '/home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file '/home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm.egg-info/SOURCES.txt'
  creating '/home/t11/Mo/2/slots/2/tmp/pip-modern-metadata-h72hopb1/atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  /home/t11/Mo/2/slots/2/tmp/pip-build-env-vejd1gay/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/local_openmm_transport.py -> build/lib/atom_openmm
  copying atom_openmm/abfe_structprep.py -> build/lib/atom_openmm
  copying atom_openmm/ommworker.py -> build/lib/atom_openmm
  copying atom_openmm/make_atm_system_from_pdb.py -> build/lib/atom_openmm
  copying atom_openmm/rbfe_structprep.py -> build/lib/atom_openmm
  copying atom_openmm/gibbs_sampling.py -> build/lib/atom_openmm
  copying atom_openmm/rbfe_production.py -> build/lib/atom_openmm
  copying atom_openmm/async_re.py -> build/lib/atom_openmm
  copying atom_openmm/ommsystem.py -> build/lib/atom_openmm
  copying atom_openmm/ommreplica.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/make_atm_system_from_amber.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/abfe_explicit.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/make_atm_system_from_rcpt_lig.py -> build/lib/atom_openmm
  copying atom_openmm/__init__.py -> build/lib/atom_openmm
  creating 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/config.py -> 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
  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/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/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/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/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/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/make_atm_system_from_pdb.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/gibbs_sampling.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/async_re.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/ommreplica.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/make_atm_system_from_amber.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/abfe_explicit.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/openmm_async_re.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/__init__.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/t11/Mo/2/slots/2/tmp/pip-wheel-n79wno8y/.tmp-zpqon1wb/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_A20_A01_input.yaml
+ python bin/rbfe_production QB_A20_A01_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_A20_A01.out r1/QB_A20_A01.out r10/QB_A20_A01.out r11/QB_A20_A01.out r12/QB_A20_A01.out r13/QB_A20_A01.out r14/QB_A20_A01.out r15/QB_A20_A01.out r16/QB_A20_A01.out r17/QB_A20_A01.out r18/QB_A20_A01.out r19/QB_A20_A01.out r2/QB_A20_A01.out r20/QB_A20_A01.out r21/QB_A20_A01.out r3/QB_A20_A01.out r4/QB_A20_A01.out r5/QB_A20_A01.out r6/QB_A20_A01.out r7/QB_A20_A01.out r8/QB_A20_A01.out r9/QB_A20_A01.out 'r*/*.dcd' r0/QB_A20_A01.xtc r1/QB_A20_A01.xtc r10/QB_A20_A01.xtc r11/QB_A20_A01.xtc r12/QB_A20_A01.xtc r13/QB_A20_A01.xtc r14/QB_A20_A01.xtc r15/QB_A20_A01.xtc r16/QB_A20_A01.xtc r17/QB_A20_A01.xtc r18/QB_A20_A01.xtc r19/QB_A20_A01.xtc r2/QB_A20_A01.xtc r20/QB_A20_A01.xtc r21/QB_A20_A01.xtc r3/QB_A20_A01.xtc r4/QB_A20_A01.xtc r5/QB_A20_A01.xtc r6/QB_A20_A01.xtc r7/QB_A20_A01.xtc r8/QB_A20_A01.xtc r9/QB_A20_A01.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
2025-12-11 23:12:13 (2180407): bin/bash exited; CPU time 15770.868599
2025-12-11 23:12:13 (2180407): called boinc_finish(0)

</stderr_txt>
]]>

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