Task 38644506

Name	p38_3_A27_A31_r0_2-QUICO_ATM_OpenFF_NAGL_p38_3-4-6-RND2671_0
Workunit	31590041
Created	8 May 2026, 19:54:38 UTC
Sent	8 May 2026, 19:54:39 UTC
Report deadline	13 May 2026, 19:54:39 UTC
Received	9 May 2026, 10:36:33 UTC
Server state	Over
Outcome	Success
Client state	Done
Exit status	0 (0x00000000)
Computer ID	628374
Run time	3 hours 40 min 14 sec
CPU time	3 hours 40 min 14 sec
Validate state	Valid
Credit	750,000.00
Device peak FLOPS	32,842.94 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	620.68 MB
Peak swap size	32.98 GB
Peak disk usage	3.04 GB

Stderr output

<core_client_version>8.2.13</core_client_version>
<![CDATA[
<stderr_txt>
2026-05-08 23:34:53 (176896): wrapper (8.1.26018): starting
2026-05-08 23:35:07 (176896): wrapper: running bin/python (bin/conda-unpack)
2026-05-08 23:35:07 (176896): wrapper: created child process 176942
2026-05-08 23:35:08 (176896): bin/python exited; CPU time 0.050440
2026-05-08 23:35:08 (176896): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-05-08 23:35:08 (176896): wrapper: created child process 176943
2026-05-08 23:35:09 (176896): bin/tar exited; CPU time 0.429919
2026-05-08 23:35:09 (176896): wrapper: running bin/bash (run.sh)
2026-05-08 23:35:09 (176896): wrapper: created child process 176954
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/40000/slots/8/bin
+++ dirname /home/maciek/BOINC/40000/slots/8/bin
++ local full_path_env=/home/maciek/BOINC/40000/slots/8
+++ basename /home/maciek/BOINC/40000/slots/8
++ local env_name=8
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/40000/slots/8
++ CONDA_PREFIX=/home/maciek/BOINC/40000/slots/8
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/40000/slots/8/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(8) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/40000/slots/8/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/40000/slots/8/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/40000/slots/8:/home/maciek/BOINC/40000/slots/8/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/40000/slots/8:/home/maciek/BOINC/40000/slots/8/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/8/tmp
+ TMP=/home/maciek/BOINC/40000/slots/8/tmp
+ mkdir -p /home/maciek/BOINC/40000/slots/8/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/maciek/BOINC/40000/slots/8/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_A27_A31_input.yaml
+ python bin/rbfe_production QB_A27_A31_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_A27_A31.out r1/QB_A27_A31.out r10/QB_A27_A31.out r11/QB_A27_A31.out r12/QB_A27_A31.out r13/QB_A27_A31.out r14/QB_A27_A31.out r15/QB_A27_A31.out r16/QB_A27_A31.out r17/QB_A27_A31.out r18/QB_A27_A31.out r19/QB_A27_A31.out r2/QB_A27_A31.out r20/QB_A27_A31.out r21/QB_A27_A31.out r3/QB_A27_A31.out r4/QB_A27_A31.out r5/QB_A27_A31.out r6/QB_A27_A31.out r7/QB_A27_A31.out r8/QB_A27_A31.out r9/QB_A27_A31.out r0/QB_A27_A31.xtc r1/QB_A27_A31.xtc r10/QB_A27_A31.xtc r11/QB_A27_A31.xtc r12/QB_A27_A31.xtc r13/QB_A27_A31.xtc r14/QB_A27_A31.xtc r15/QB_A27_A31.xtc r16/QB_A27_A31.xtc r17/QB_A27_A31.xtc r18/QB_A27_A31.xtc r19/QB_A27_A31.xtc r2/QB_A27_A31.xtc r20/QB_A27_A31.xtc r21/QB_A27_A31.xtc r3/QB_A27_A31.xtc r4/QB_A27_A31.xtc r5/QB_A27_A31.xtc r6/QB_A27_A31.xtc r7/QB_A27_A31.xtc r8/QB_A27_A31.xtc r9/QB_A27_A31.xtc
tar: run.log: file changed as we read it
+ 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
2026-05-09 03:08:53 (176896): bin/bash exited; CPU time 13111.035726
2026-05-09 03:08:53 (176896): called boinc_finish(0)

</stderr_txt>
]]>