Task 38583901

Name JNK1_A20_A05_r4_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-1-5-RND7170_2
Workunit 31547653
Created 14 Dec 2025, 22:16:12 UTC
Sent 14 Dec 2025, 22:16:15 UTC
Report deadline 19 Dec 2025, 22:16:15 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 15 min 23 sec
CPU time 1 hours 13 min 35 sec
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 678.38 MB
Peak swap size 32.96 GB
Peak disk usage 3.13 GB

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2025-12-14 23:21:17 (64457): wrapper (8.1.26018): starting
2025-12-14 23:21:31 (64457): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 23:21:31 (64457): wrapper: created child process 64485
2025-12-14 23:21:32 (64457): bin/python exited; CPU time 0.056947
2025-12-14 23:21:32 (64457): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 23:21:32 (64457): wrapper: created child process 64486
2025-12-14 23:21:33 (64457): bin/tar exited; CPU time 0.702530
2025-12-14 23:21:33 (64457): wrapper: running bin/bash (run.sh)
2025-12-14 23:21:33 (64457): wrapper: created child process 64492
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/41000/slots/3/bin
+++ dirname /home/maciek/BOINC/41000/slots/3/bin
++ local full_path_env=/home/maciek/BOINC/41000/slots/3
+++ basename /home/maciek/BOINC/41000/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/41000/slots/3
++ CONDA_PREFIX=/home/maciek/BOINC/41000/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/41000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/41000/slots/3/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/41000/slots/3/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/41000/slots/3:/home/maciek/BOINC/41000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/41000/slots/3:/home/maciek/BOINC/41000/slots/3/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/3/tmp
+ TMP=/home/maciek/BOINC/41000/slots/3/tmp
+ mkdir -p /home/maciek/BOINC/41000/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:2,1,CUDA,,/home/maciek/BOINC/41000/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
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_A20_A05_input.yaml
+ python bin/rbfe_production QB_A20_A05_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
2025-12-15 08:49:14 (7734): wrapper (8.1.26018): starting
2025-12-15 08:49:14 (7734): wrapper: running bin/bash (run.sh)
2025-12-15 08:49:14 (7734): wrapper: created child process 7737
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/41000/slots/3/bin
+++ dirname /home/maciek/BOINC/41000/slots/3/bin
++ local full_path_env=/home/maciek/BOINC/41000/slots/3
+++ basename /home/maciek/BOINC/41000/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/41000/slots/3
++ CONDA_PREFIX=/home/maciek/BOINC/41000/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/41000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/41000/slots/3/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/41000/slots/3/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/41000/slots/3:/home/maciek/BOINC/41000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/41000/slots/3:/home/maciek/BOINC/41000/slots/3/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/3/tmp
+ TMP=/home/maciek/BOINC/41000/slots/3/tmp
+ mkdir -p /home/maciek/BOINC/41000/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/home/maciek/BOINC/41000/slots/3/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A05_input.yaml
+ python bin/rbfe_production QB_A20_A05_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.

</stderr_txt>
]]>


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