Task 38583732

Name	JNK1_A28_A14_r0_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-1-5-RND6516_0
Workunit	31547796
Created	14 Dec 2025, 14:53:25 UTC
Sent	14 Dec 2025, 14:53:29 UTC
Report deadline	19 Dec 2025, 14:53:29 UTC
Received	14 Dec 2025, 19:21:16 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	53 min 31 sec
CPU time	23 min
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	637.93 MB
Peak swap size	17.25 GB
Peak disk usage	3.04 GB

Stderr output

<core_client_version>7.16.6</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2025-12-14 18:27:07 (2235553): wrapper (8.1.26018): starting
2025-12-14 18:27:50 (2235553): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 18:27:50 (2235553): wrapper: created child process 2235570
2025-12-14 18:27:53 (2235553): bin/python exited; CPU time 0.309472
2025-12-14 18:27:53 (2235553): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 18:27:53 (2235553): wrapper: created child process 2235574
2025-12-14 18:27:57 (2235553): bin/tar exited; CPU time 3.142702
2025-12-14 18:27:57 (2235553): wrapper: running bin/bash (run.sh)
2025-12-14 18:27:57 (2235553): wrapper: created child process 2235576
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/t11/Mo/2/slots/2/bin
+++ dirname /home/t11/Mo/2/slots/2/bin
++ local full_path_env=/home/t11/Mo/2/slots/2
+++ basename /home/t11/Mo/2/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/t11/Mo/2/slots/2
++ CONDA_PREFIX=/home/t11/Mo/2/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/t11/Mo/2/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/t11/Mo/2/slots/2/etc/conda/activate.d
++ '[' -d /home/t11/Mo/2/slots/2/etc/conda/activate.d ']'
+ export PATH=/home/t11/Mo/2/slots/2:/home/t11/Mo/2/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/t11/Mo/2/slots/2:/home/t11/Mo/2/slots/2/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/2/tmp
+ TMP=/home/t11/Mo/2/slots/2/tmp
+ mkdir -p /home/t11/Mo/2/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/t11/Mo/2/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>
]]>