Task 38601394
| Name | p38_A27_A25_r0_2-QUICO_ATM_GAFF2_NAGL_p38-0-6-RND9849_7 |
| Workunit | 31553375 |
| Created | 9 Apr 2026, 13:09:05 UTC |
| Sent | 9 Apr 2026, 13:09:13 UTC |
| Report deadline | 14 Apr 2026, 13:09:13 UTC |
| Received | 9 Apr 2026, 13:15:10 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 637038 |
| Run time | 37 sec |
| CPU time | |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 6,345.96 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 5.03 MB |
| Peak swap size | 13.16 MB |
| Peak disk usage | 1.44 GB |
Stderr output
<core_client_version>8.3.0</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-09 09:14:27 (1453645): wrapper (8.1.26018): starting
2026-04-09 09:14:56 (1453645): wrapper: running bin/python (bin/conda-unpack)
2026-04-09 09:14:56 (1453645): wrapper: created child process 1453678
2026-04-09 09:14:57 (1453645): bin/python exited; CPU time 0.249948
2026-04-09 09:14:57 (1453645): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-09 09:14:57 (1453645): wrapper: created child process 1453681
2026-04-09 09:14:58 (1453645): bin/tar exited; CPU time 0.000000
2026-04-09 09:14:58 (1453645): wrapper: running bin/bash (run.sh)
2026-04-09 09:14:58 (1453645): wrapper: created child process 1453687
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/whitlerd/Desktop/BOINC/slots/7/bin
+++ dirname /home/whitlerd/Desktop/BOINC/slots/7/bin
++ local full_path_env=/home/whitlerd/Desktop/BOINC/slots/7
+++ basename /home/whitlerd/Desktop/BOINC/slots/7
++ local env_name=7
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/whitlerd/Desktop/BOINC/slots/7
++ CONDA_PREFIX=/home/whitlerd/Desktop/BOINC/slots/7
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/whitlerd/Desktop/BOINC/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(7) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/whitlerd/Desktop/BOINC/slots/7/etc/conda/activate.d
++ '[' -d /home/whitlerd/Desktop/BOINC/slots/7/etc/conda/activate.d ']'
+ export PATH=/home/whitlerd/Desktop/BOINC/slots/7:/home/whitlerd/Desktop/BOINC/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/whitlerd/Desktop/BOINC/slots/7:/home/whitlerd/Desktop/BOINC/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/whitlerd/Desktop/BOINC/slots/7/tmp
+ TMP=/home/whitlerd/Desktop/BOINC/slots/7/tmp
+ mkdir -p /home/whitlerd/Desktop/BOINC/slots/7/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/home/whitlerd/Desktop/BOINC/slots/7/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 "/home/whitlerd/Desktop/BOINC/slots/7/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/home/whitlerd/Desktop/BOINC/slots/7/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
rx = openmm_job_RBFE(
^^^^^^^^^^^^^^^^
File "/home/whitlerd/Desktop/BOINC/slots/7/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 "/home/whitlerd/Desktop/BOINC/slots/7/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
self.start_worker()
File "/home/whitlerd/Desktop/BOINC/slots/7/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 443, in start_worker
self._openmm_worker_body()
File "/home/whitlerd/Desktop/BOINC/slots/7/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 198, in _openmm_worker_body
self.ommsystem.create_system()
File "/home/whitlerd/Desktop/BOINC/slots/7/lib/python3.11/site-packages/atom_openmm/ommsystem.py", line 872, in create_system
self.load_system()
File "/home/whitlerd/Desktop/BOINC/slots/7/lib/python3.11/site-packages/atom_openmm/ommsystem.py", line 91, in load_system
self.pdb = PDBFile(self.pdbtopfile)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/whitlerd/Desktop/BOINC/slots/7/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'
2026-04-09 09:15:03 (1453645): bin/bash exited; CPU time 5.286787
2026-04-09 09:15:03 (1453645): app exit status: 0x1
2026-04-09 09:15:03 (1453645): called boinc_finish(195)
</stderr_txt>
]]>
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