Task 38629745

Stderr output

<core_client_version>7.24.1</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-25 14:49:44 (557565): wrapper (8.1.26018): starting
2026-04-25 14:50:03 (557565): wrapper: running bin/python (bin/conda-unpack)
2026-04-25 14:50:03 (557565): wrapper: created child process 557581
2026-04-25 14:50:04 (557565): bin/python exited; CPU time 0.168986
2026-04-25 14:50:04 (557565): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-25 14:50:04 (557565): wrapper: created child process 557582
2026-04-25 14:50:06 (557565): bin/tar exited; CPU time 1.312108
2026-04-25 14:50:06 (557565): wrapper: running bin/bash (run.sh)
2026-04-25 14:50:06 (557565): wrapper: created child process 557587
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/0/bin
+++ dirname /var/lib/boinc-client/slots/0/bin
++ local full_path_env=/var/lib/boinc-client/slots/0
+++ basename /var/lib/boinc-client/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/0
++ CONDA_PREFIX=/var/lib/boinc-client/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/0/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/0/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/0:/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/0:/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/0/tmp
+ TMP=/var/lib/boinc-client/slots/0/tmp
+ mkdir -p /var/lib/boinc-client/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc-client/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
+ python -m pip install --no-dependencies atom-openmm -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2

bzip2: Data integrity error when decompressing.
	Input file = (stdin), output file = (stdout)

It is possible that the compressed file(s) have become corrupted.
You can use the -tvv option to test integrity of such files.

You can use the `bzip2recover' program to attempt to recover
data from undamaged sections of corrupted files.

tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now
+ true
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A26_input.yaml
+ python bin/rbfe_production QB_A11_A26_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 432, in __init__
    replica = OMMReplicaATM(i, self.basename, self.service_worker, self.logger, self.keywords)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/ommreplica.py", line 41, in __init__
    self.load_checkpoint()
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/ommreplica.py", line 79, in load_checkpoint
    self.worker.simulation.loadState(ckptfile)
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/openmm/app/simulation.py", line 363, in loadState
    self.context.setState(mm.XmlSerializer.deserialize(xml))
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/openmm/openmm.py", line 4068, in deserialize
    return XmlSerializer._deserializeState(inputString)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/openmm/openmm.py", line 4031, in _deserializeState
    return _openmm.XmlSerializer__deserializeState(inputString)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Unknown property 'z' in node '
		'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/var/lib/boinc-client/slots/0/bin/rbfe_production", line 8, in <module>
    sys.exit(rbfe_production())
             ^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 434, in __init__
    self._exit("Error when creating replica.")
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/async_re.py", line 69, in _exit
    self.checkpointJob()
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 48, in checkpointJob
    self.update_state_of_replica(repl)
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 86, in update_state_of_replica
    stateid = self.status[repl]['stateid_current']
              ^^^^^^^^^^^
  File "/var/lib/boinc-client/slots/0/lib/python3.11/site-packages/atom_openmm/async_re.py", line 131, in __getattribute__
    return object.__getattribute__(self,name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'openmm_job_RBFE' object has no attribute 'status'
2026-04-25 14:50:27 (557565): bin/bash exited; CPU time 17.990813
2026-04-25 14:50:27 (557565): app exit status: 0x1
2026-04-25 14:50:27 (557565): called boinc_finish(195)

</stderr_txt>
]]>

©2026 Universitat Pompeu Fabra