Task 38583598

Name	JNK1_A25_A38_r2_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-1-5-RND8318_0
Workunit	31547689
Created	14 Dec 2025, 9:53:19 UTC
Sent	14 Dec 2025, 9:53:22 UTC
Report deadline	19 Dec 2025, 9:53:22 UTC
Received	14 Dec 2025, 18:28:03 UTC
Server state	Over
Outcome	Computation error
Client state	Aborted by user
Exit status	203 (0x000000CB) EXIT_ABORTED_VIA_GUI
Computer ID	648010
Run time	3 hours 33 min 31 sec
CPU time	1 hours 30 min 54 sec
Validate state	Invalid
Credit	0.00
Device peak FLOPS	17,961.84 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	638.57 MB
Peak swap size	17.25 GB
Peak disk usage	3.07 GB

Stderr output

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2025-12-14 14:53:29 (2233045): wrapper (8.1.26018): starting
2025-12-14 14:54:16 (2233045): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 14:54:16 (2233045): wrapper: created child process 2233063
2025-12-14 14:54:18 (2233045): bin/python exited; CPU time 0.337602
2025-12-14 14:54:18 (2233045): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 14:54:18 (2233045): wrapper: created child process 2233065
2025-12-14 14:54:22 (2233045): bin/tar exited; CPU time 3.671730
2025-12-14 14:54:22 (2233045): wrapper: running bin/bash (run.sh)
2025-12-14 14:54:22 (2233045): wrapper: created child process 2233070
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/t11/Mo/2/slots/1/bin
+++ dirname /home/t11/Mo/2/slots/1/bin
++ local full_path_env=/home/t11/Mo/2/slots/1
+++ basename /home/t11/Mo/2/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/t11/Mo/2/slots/1
++ CONDA_PREFIX=/home/t11/Mo/2/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/t11/Mo/2/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/t11/Mo/2/slots/1/etc/conda/activate.d
++ '[' -d /home/t11/Mo/2/slots/1/etc/conda/activate.d ']'
+ export PATH=/home/t11/Mo/2/slots/1:/home/t11/Mo/2/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/t11/Mo/2/slots/1:/home/t11/Mo/2/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/t11/Mo/2/slots/1/tmp
+ TMP=/home/t11/Mo/2/slots/1/tmp
+ mkdir -p /home/t11/Mo/2/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/t11/Mo/2/slots/1/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_A25_A38_input.yaml
+ python bin/rbfe_production QB_A25_A38_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.

</stderr_txt>
]]>