Task 38598877

Stderr output

<core_client_version>8.3.0</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-08 15:08:05 (23213): wrapper (8.1.26018): starting
2026-04-08 15:08:26 (23213): wrapper: running bin/python (bin/conda-unpack)
2026-04-08 15:08:26 (23213): wrapper: created child process 23217
2026-04-08 15:08:27 (23213): bin/python exited; CPU time 0.120179
2026-04-08 15:08:27 (23213): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-08 15:08:27 (23213): wrapper: created child process 23218
2026-04-08 15:08:28 (23213): bin/tar exited; CPU time 0.003516
2026-04-08 15:08:28 (23213): wrapper: running bin/bash (run.sh)
2026-04-08 15:08:28 (23213): wrapper: created child process 23220
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/28/bin
+++ dirname /var/lib/boinc/slots/28/bin
++ local full_path_env=/var/lib/boinc/slots/28
+++ basename /var/lib/boinc/slots/28
++ local env_name=28
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/28
++ CONDA_PREFIX=/var/lib/boinc/slots/28
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/28/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(28) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/28/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/28/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/28:/var/lib/boinc/slots/28/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/28:/var/lib/boinc/slots/28/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/28/tmp
+ TMP=/var/lib/boinc/slots/28/tmp
+ mkdir -p /var/lib/boinc/slots/28/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/28/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
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A27_A25_input.yaml
+ python bin/rbfe_production QB_A27_A25_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "/var/lib/boinc/slots/28/bin/rbfe_production", line 8, in <module>
    sys.exit(rbfe_production())
             ^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
    rx = openmm_job_RBFE(
         ^^^^^^^^^^^^^^^^
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 427, in __init__
    self.service_worker = ommworkercls(self.basename, service_ommsys, self.keywords, compute = False, logger = self.logger)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
    self.start_worker()
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 443, in start_worker
    self._openmm_worker_body()
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 198, in _openmm_worker_body
    self.ommsystem.create_system()
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/ommsystem.py", line 872, in create_system
    self.load_system()
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/atom_openmm/ommsystem.py", line 91, in load_system
    self.pdb = PDBFile(self.pdbtopfile)
               ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/var/lib/boinc/slots/28/lib/python3.11/site-packages/openmm/app/pdbfile.py", line 93, in __init__
    inputfile = open(file)
                ^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'QB_A27_A25.pdb'
2026-04-08 15:08:31 (23213): bin/bash exited; CPU time 3.069195
2026-04-08 15:08:31 (23213): app exit status: 0x1
2026-04-08 15:08:31 (23213): called boinc_finish(195)

</stderr_txt>
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