Task 38582871

Name	JNK1_A01_A04_r0_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-4-5-RND3580_0
Workunit	31547105
Created	13 Dec 2025, 13:43:23 UTC
Sent	13 Dec 2025, 13:43:35 UTC
Report deadline	18 Dec 2025, 13:43:35 UTC
Received	13 Dec 2025, 15:59:40 UTC
Server state	Over
Outcome	Success
Client state	Done
Exit status	0 (0x00000000)
Computer ID	628374
Run time	2 hours 16 min 5 sec
CPU time	2 hours 29 min 19 sec
Validate state	Valid
Credit	750,000.00
Device peak FLOPS	84,054.54 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	659.18 MB
Peak swap size	33.21 GB
Peak disk usage	3.59 GB

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-13 14:44:12 (19991): wrapper (8.1.26018): starting
2025-12-13 14:44:26 (19991): wrapper: running bin/python (bin/conda-unpack)
2025-12-13 14:44:26 (19991): wrapper: created child process 20021
2025-12-13 14:44:27 (19991): bin/python exited; CPU time 0.061056
2025-12-13 14:44:27 (19991): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-13 14:44:27 (19991): wrapper: created child process 20022
2025-12-13 14:44:28 (19991): bin/tar exited; CPU time 0.820102
2025-12-13 14:44:28 (19991): wrapper: running bin/bash (run.sh)
2025-12-13 14:44:28 (19991): wrapper: created child process 20024
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/40000/slots/2/bin
+++ dirname /home/maciek/BOINC/40000/slots/2/bin
++ local full_path_env=/home/maciek/BOINC/40000/slots/2
+++ basename /home/maciek/BOINC/40000/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/40000/slots/2
++ CONDA_PREFIX=/home/maciek/BOINC/40000/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/40000/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/40000/slots/2/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/40000/slots/2/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/40000/slots/2:/home/maciek/BOINC/40000/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/40000/slots/2:/home/maciek/BOINC/40000/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/40000/slots/2/tmp
+ TMP=/home/maciek/BOINC/40000/slots/2/tmp
+ mkdir -p /home/maciek/BOINC/40000/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/maciek/BOINC/40000/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_A01_A04_input.yaml
+ python bin/rbfe_production QB_A01_A04_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
+ echo 'Save output'
+ tar cjvf output.tar.bz2 run.log stderr.txt r0/QB_A01_A04.out r1/QB_A01_A04.out r10/QB_A01_A04.out r11/QB_A01_A04.out r12/QB_A01_A04.out r13/QB_A01_A04.out r14/QB_A01_A04.out r15/QB_A01_A04.out r16/QB_A01_A04.out r17/QB_A01_A04.out r18/QB_A01_A04.out r19/QB_A01_A04.out r2/QB_A01_A04.out r20/QB_A01_A04.out r21/QB_A01_A04.out r3/QB_A01_A04.out r4/QB_A01_A04.out r5/QB_A01_A04.out r6/QB_A01_A04.out r7/QB_A01_A04.out r8/QB_A01_A04.out r9/QB_A01_A04.out 'r*/*.dcd' r0/QB_A01_A04.xtc r1/QB_A01_A04.xtc r10/QB_A01_A04.xtc r11/QB_A01_A04.xtc r12/QB_A01_A04.xtc r13/QB_A01_A04.xtc r14/QB_A01_A04.xtc r15/QB_A01_A04.xtc r16/QB_A01_A04.xtc r17/QB_A01_A04.xtc r18/QB_A01_A04.xtc r19/QB_A01_A04.xtc r2/QB_A01_A04.xtc r20/QB_A01_A04.xtc r21/QB_A01_A04.xtc r3/QB_A01_A04.xtc r4/QB_A01_A04.xtc r5/QB_A01_A04.xtc r6/QB_A01_A04.xtc r7/QB_A01_A04.xtc r8/QB_A01_A04.xtc r9/QB_A01_A04.xtc
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
+ true
+ echo 'Save restart'
+ tar cjvf restart.tar.bz2 r0/checkpoint.xml r1/checkpoint.xml r10/checkpoint.xml r11/checkpoint.xml r12/checkpoint.xml r13/checkpoint.xml r14/checkpoint.xml r15/checkpoint.xml r16/checkpoint.xml r17/checkpoint.xml r18/checkpoint.xml r19/checkpoint.xml r2/checkpoint.xml r20/checkpoint.xml r21/checkpoint.xml r3/checkpoint.xml r4/checkpoint.xml r5/checkpoint.xml r6/checkpoint.xml r7/checkpoint.xml r8/checkpoint.xml r9/checkpoint.xml
2025-12-13 16:58:40 (19991): bin/bash exited; CPU time 8792.423439
2025-12-13 16:58:40 (19991): called boinc_finish(0)

</stderr_txt>
]]>