Task 38598571
| Name | TYK2_A12_A05_r0_1-QUICO_ATM_GAFF2_NAGL_TYK2-3-5-RND6011_4 |
| Workunit | 31553685 |
| Created | 8 Apr 2026, 10:24:52 UTC |
| Sent | 8 Apr 2026, 10:24:56 UTC |
| Report deadline | 13 Apr 2026, 10:24:56 UTC |
| Received | 8 Apr 2026, 15:27:46 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 606097 |
| Run time | 4 hours 33 min 32 sec |
| CPU time | 4 hours 29 min 4 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 5,627.77 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 658.76 MB |
| Peak swap size | 11.66 GB |
| Peak disk usage | 3.04 GB |
Stderr output
<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-04-08 05:52:37 (11830): wrapper (8.1.26018): starting
2026-04-08 05:53:05 (11830): wrapper: running bin/python (bin/conda-unpack)
2026-04-08 05:53:05 (11830): wrapper: created child process 11834
2026-04-08 05:53:06 (11830): bin/python exited; CPU time 0.317192
2026-04-08 05:53:06 (11830): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-08 05:53:06 (11830): wrapper: created child process 11835
2026-04-08 05:53:08 (11830): bin/tar exited; CPU time 1.294585
2026-04-08 05:53:08 (11830): wrapper: running bin/bash (run.sh)
2026-04-08 05:53:08 (11830): wrapper: created child process 11837
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/3/bin
+++ dirname /var/lib/boinc/slots/3/bin
++ local full_path_env=/var/lib/boinc/slots/3
+++ basename /var/lib/boinc/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/3
++ CONDA_PREFIX=/var/lib/boinc/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/3/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/3/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/3/tmp
+ TMP=/var/lib/boinc/slots/3/tmp
+ mkdir -p /var/lib/boinc/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/3/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_A12_A05_input.yaml
+ python bin/rbfe_production QB_A12_A05_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/lib/boinc/slots/3/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/local_openmm_transport.py", line 212, in _update_replica
pot = job['openmm_worker'].get_energy()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc/slots/3/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
2026-04-08 10:26:07 (11830): bin/bash exited; CPU time 16142.419259
2026-04-08 10:26:07 (11830): app exit status: 0x1
2026-04-08 10:26:07 (11830): called boinc_finish(195)
</stderr_txt>
]]>
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