Task 38622907

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-21 05:03:24 (559679): wrapper (8.1.26018): starting
2026-04-21 05:03:39 (559679): wrapper: running bin/python (bin/conda-unpack)
2026-04-21 05:03:39 (559679): wrapper: created child process 559696
2026-04-21 05:03:40 (559679): bin/python exited; CPU time 0.077653
2026-04-21 05:03:40 (559679): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-21 05:03:40 (559679): wrapper: created child process 559698
2026-04-21 05:03:42 (559679): bin/tar exited; CPU time 1.104778
2026-04-21 05:03:42 (559679): wrapper: running bin/bash (run.sh)
2026-04-21 05:03:42 (559679): wrapper: created child process 559700
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/40000/slots/0/bin
+++ dirname /home/maciek/BOINC/40000/slots/0/bin
++ local full_path_env=/home/maciek/BOINC/40000/slots/0
+++ basename /home/maciek/BOINC/40000/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/40000/slots/0
++ CONDA_PREFIX=/home/maciek/BOINC/40000/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/40000/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/40000/slots/0/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/40000/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/40000/slots/0:/home/maciek/BOINC/40000/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/40000/slots/0:/home/maciek/BOINC/40000/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/maciek/BOINC/40000/slots/0/tmp
+ TMP=/home/maciek/BOINC/40000/slots/0/tmp
+ mkdir -p /home/maciek/BOINC/40000/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/maciek/BOINC/40000/slots/0/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
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_A22_A08_input.yaml
+ python bin/rbfe_production QB_A22_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "/home/maciek/BOINC/40000/slots/0/bin/rbfe_production", line 8, in <module>
    sys.exit(rbfe_production())
             ^^^^^^^^^^^^^^^^^
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maciek/BOINC/40000/slots/0/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maciek/BOINC/40000/slots/0/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
2026-04-21 07:09:11 (559679): bin/bash exited; CPU time 8232.264599
2026-04-21 07:09:11 (559679): app exit status: 0x1
2026-04-21 07:09:11 (559679): called boinc_finish(195)

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra