Task 38603063

Name	BACE_A18_A07_r0_4-QUICO_ATM_GAFF2_NAGL_BACE-2-6-RND3749_0
Workunit	31557379
Created	10 Apr 2026, 11:38:23 UTC
Sent	10 Apr 2026, 11:38:29 UTC
Report deadline	15 Apr 2026, 11:38:29 UTC
Received	10 Apr 2026, 16:39:36 UTC
Server state	Over
Outcome	Success
Client state	Done
Exit status	0 (0x00000000)
Computer ID	651884
Run time	5 hours 1 min 7 sec
CPU time	5 hours 45 min 4 sec
Validate state	Valid
Credit	750,000.00
Device peak FLOPS	5,096.24 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	686.04 MB
Peak swap size	57.27 GB
Peak disk usage	3.01 GB
Stderr output

<core_client_version>7.24.1</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-10 11:44:07 (16828): wrapper (8.1.26018): starting
2026-04-10 11:44:39 (16828): wrapper: running bin/python (bin/conda-unpack)
2026-04-10 11:44:39 (16828): wrapper: created child process 16831
2026-04-10 11:44:41 (16828): bin/python exited; CPU time 0.330335
2026-04-10 11:44:41 (16828): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-10 11:44:41 (16828): wrapper: created child process 16832
2026-04-10 11:44:42 (16828): bin/tar exited; CPU time 0.924390
2026-04-10 11:44:42 (16828): wrapper: running bin/bash (run.sh)
2026-04-10 11:44:42 (16828): wrapper: created child process 16834
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc-client/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
+ python -m pip install --no-dependencies atom-openmm -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
tar: r0/checkpoint.xml: time stamp 2026-04-10 15:32:51 is 13682.089910497 s in the future
tar: r1/checkpoint.xml: time stamp 2026-04-10 15:32:57 is 13687.711535594 s in the future
tar: r10/checkpoint.xml: time stamp 2026-04-10 15:33:49 is 13739.330757576 s in the future
tar: r11/checkpoint.xml: time stamp 2026-04-10 15:33:55 is 13744.993589048 s in the future
tar: r12/checkpoint.xml: time stamp 2026-04-10 15:34:00 is 13749.645693627 s in the future
tar: r13/checkpoint.xml: time stamp 2026-04-10 15:34:05 is 13754.287669962 s in the future
tar: r14/checkpoint.xml: time stamp 2026-04-10 15:34:10 is 13758.951953156 s in the future
tar: r15/checkpoint.xml: time stamp 2026-04-10 15:34:15 is 13763.616316691 s in the future
tar: r16/checkpoint.xml: time stamp 2026-04-10 15:34:20 is 13768.258100002 s in the future
tar: r17/checkpoint.xml: time stamp 2026-04-10 15:34:24 is 13771.923381197 s in the future
tar: r18/checkpoint.xml: time stamp 2026-04-10 15:34:30 is 13777.587641651 s in the future
tar: r19/checkpoint.xml: time stamp 2026-04-10 15:34:35 is 13782.214148218 s in the future
tar: r2/checkpoint.xml: time stamp 2026-04-10 15:33:03 is 13689.880218037 s in the future
tar: r20/checkpoint.xml: time stamp 2026-04-10 15:34:39 is 13785.544625701 s in the future
tar: r21/checkpoint.xml: time stamp 2026-04-10 15:34:44 is 13790.186792245 s in the future
tar: r3/checkpoint.xml: time stamp 2026-04-10 15:33:10 is 13695.851982746 s in the future
tar: r4/checkpoint.xml: time stamp 2026-04-10 15:33:16 is 13701.516978806 s in the future
tar: r5/checkpoint.xml: time stamp 2026-04-10 15:33:22 is 13707.159492619 s in the future
tar: r6/checkpoint.xml: time stamp 2026-04-10 15:33:27 is 13711.824883101 s in the future
tar: r7/checkpoint.xml: time stamp 2026-04-10 15:33:33 is 13717.488484988 s in the future
tar: r8/checkpoint.xml: time stamp 2026-04-10 15:33:38 is 13722.130641689 s in the future
tar: r9/checkpoint.xml: time stamp 2026-04-10 15:33:44 is 13727.807076869 s in the future
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A18_A07_input.yaml
+ python bin/rbfe_production QB_A18_A07_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_A18_A07.out r1/QB_A18_A07.out r10/QB_A18_A07.out r11/QB_A18_A07.out r12/QB_A18_A07.out r13/QB_A18_A07.out r14/QB_A18_A07.out r15/QB_A18_A07.out r16/QB_A18_A07.out r17/QB_A18_A07.out r18/QB_A18_A07.out r19/QB_A18_A07.out r2/QB_A18_A07.out r20/QB_A18_A07.out r21/QB_A18_A07.out r3/QB_A18_A07.out r4/QB_A18_A07.out r5/QB_A18_A07.out r6/QB_A18_A07.out r7/QB_A18_A07.out r8/QB_A18_A07.out r9/QB_A18_A07.out 'r*/*.dcd' r0/QB_A18_A07.xtc r1/QB_A18_A07.xtc r10/QB_A18_A07.xtc r11/QB_A18_A07.xtc r12/QB_A18_A07.xtc r13/QB_A18_A07.xtc r14/QB_A18_A07.xtc r15/QB_A18_A07.xtc r16/QB_A18_A07.xtc r17/QB_A18_A07.xtc r18/QB_A18_A07.xtc r19/QB_A18_A07.xtc r2/QB_A18_A07.xtc r20/QB_A18_A07.xtc r21/QB_A18_A07.xtc r3/QB_A18_A07.xtc r4/QB_A18_A07.xtc r5/QB_A18_A07.xtc r6/QB_A18_A07.xtc r7/QB_A18_A07.xtc r8/QB_A18_A07.xtc r9/QB_A18_A07.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
2026-04-10 16:39:11 (16828): bin/bash exited; CPU time 18540.222110
2026-04-10 16:39:11 (16828): called boinc_finish(0)

</stderr_txt>
]]>