Task 38584003

Name	JNK1_A28_A14_r3_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-1-5-RND7007_2
Workunit	31547237
Created	15 Dec 2025, 7:54:49 UTC
Sent	15 Dec 2025, 7:54:54 UTC
Report deadline	20 Dec 2025, 7:54:54 UTC
Received	15 Dec 2025, 16:52:41 UTC
Server state	Over
Outcome	Computation error
Client state	Aborted by user
Exit status	203 (0x000000CB) EXIT_ABORTED_VIA_GUI
Computer ID	634307
Run time	6 hours 3 min 5 sec
CPU time	1 hours 11 min
Validate state	Invalid
Credit	0.00
Device peak FLOPS	14,135.72 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	682.84 MB
Peak swap size	32.96 GB
Peak disk usage	3.10 GB

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2025-12-15 09:01:10 (11206): wrapper (8.1.26018): starting
2025-12-15 09:01:25 (11206): wrapper: running bin/python (bin/conda-unpack)
2025-12-15 09:01:25 (11206): wrapper: created child process 11236
2025-12-15 09:01:26 (11206): bin/python exited; CPU time 0.050792
2025-12-15 09:01:26 (11206): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-15 09:01:26 (11206): wrapper: created child process 11241
2025-12-15 09:01:27 (11206): bin/tar exited; CPU time 0.688359
2025-12-15 09:01:27 (11206): wrapper: running bin/bash (run.sh)
2025-12-15 09:01:27 (11206): wrapper: created child process 11243
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/41000/slots/2/bin
+++ dirname /home/maciek/BOINC/41000/slots/2/bin
++ local full_path_env=/home/maciek/BOINC/41000/slots/2
+++ basename /home/maciek/BOINC/41000/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/41000/slots/2
++ CONDA_PREFIX=/home/maciek/BOINC/41000/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/41000/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/41000/slots/2/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/41000/slots/2/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/41000/slots/2:/home/maciek/BOINC/41000/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/41000/slots/2:/home/maciek/BOINC/41000/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/maciek/BOINC/41000/slots/2/tmp
+ TMP=/home/maciek/BOINC/41000/slots/2/tmp
+ mkdir -p /home/maciek/BOINC/41000/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:2,1,CUDA,,/home/maciek/BOINC/41000/slots/2/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_A28_A14_input.yaml
+ python bin/rbfe_production QB_A28_A14_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.

</stderr_txt>
]]>