Task 38581629

Name	JNK1_A34_A12_r2_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-1-5-RND1917_0
Workunit	31546107
Created	12 Dec 2025, 11:30:21 UTC
Sent	12 Dec 2025, 11:30:23 UTC
Report deadline	17 Dec 2025, 11:30:23 UTC
Received	12 Dec 2025, 19:49:29 UTC
Server state	Over
Outcome	Success
Client state	Done
Exit status	0 (0x00000000)
Computer ID	637038
Run time	8 hours 19 min 6 sec
CPU time	8 hours 25 min 13 sec
Validate state	Valid
Credit	750,000.00
Device peak FLOPS	3,627.24 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	633.67 MB
Peak swap size	25.09 GB
Peak disk usage	3.98 GB

Stderr output

<core_client_version>8.3.0</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-12 06:33:45 (194994): wrapper (8.1.26018): starting
2025-12-12 06:34:13 (194994): wrapper: running bin/python (bin/conda-unpack)
2025-12-12 06:34:13 (194994): wrapper: created child process 195009
2025-12-12 06:34:14 (194994): bin/python exited; CPU time 0.238111
2025-12-12 06:34:14 (194994): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-12 06:34:14 (194994): wrapper: created child process 195010
2025-12-12 06:34:16 (194994): bin/tar exited; CPU time 1.662444
2025-12-12 06:34:16 (194994): wrapper: running bin/bash (run.sh)
2025-12-12 06:34:16 (194994): wrapper: created child process 195012
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/whitlerd/Desktop/BOINC/slots/0/bin
+++ dirname /home/whitlerd/Desktop/BOINC/slots/0/bin
++ local full_path_env=/home/whitlerd/Desktop/BOINC/slots/0
+++ basename /home/whitlerd/Desktop/BOINC/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/whitlerd/Desktop/BOINC/slots/0
++ CONDA_PREFIX=/home/whitlerd/Desktop/BOINC/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/whitlerd/Desktop/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/whitlerd/Desktop/BOINC/slots/0/etc/conda/activate.d
++ '[' -d /home/whitlerd/Desktop/BOINC/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/whitlerd/Desktop/BOINC/slots/0:/home/whitlerd/Desktop/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/whitlerd/Desktop/BOINC/slots/0:/home/whitlerd/Desktop/BOINC/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/whitlerd/Desktop/BOINC/slots/0/tmp
+ TMP=/home/whitlerd/Desktop/BOINC/slots/0/tmp
+ mkdir -p /home/whitlerd/Desktop/BOINC/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/whitlerd/Desktop/BOINC/slots/0/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
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_A12_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_A34_A12.out r1/QB_A34_A12.out r10/QB_A34_A12.out r11/QB_A34_A12.out r12/QB_A34_A12.out r13/QB_A34_A12.out r14/QB_A34_A12.out r15/QB_A34_A12.out r16/QB_A34_A12.out r17/QB_A34_A12.out r18/QB_A34_A12.out r19/QB_A34_A12.out r2/QB_A34_A12.out r20/QB_A34_A12.out r21/QB_A34_A12.out r3/QB_A34_A12.out r4/QB_A34_A12.out r5/QB_A34_A12.out r6/QB_A34_A12.out r7/QB_A34_A12.out r8/QB_A34_A12.out r9/QB_A34_A12.out 'r*/*.dcd' r0/QB_A34_A12.xtc r1/QB_A34_A12.xtc r10/QB_A34_A12.xtc r11/QB_A34_A12.xtc r12/QB_A34_A12.xtc r13/QB_A34_A12.xtc r14/QB_A34_A12.xtc r15/QB_A34_A12.xtc r16/QB_A34_A12.xtc r17/QB_A34_A12.xtc r18/QB_A34_A12.xtc r19/QB_A34_A12.xtc r2/QB_A34_A12.xtc r20/QB_A34_A12.xtc r21/QB_A34_A12.xtc r3/QB_A34_A12.xtc r4/QB_A34_A12.xtc r5/QB_A34_A12.xtc r6/QB_A34_A12.xtc r7/QB_A34_A12.xtc r8/QB_A34_A12.xtc r9/QB_A34_A12.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
2025-12-12 14:33:25 (194994): bin/bash exited; CPU time 29935.961883
2025-12-12 14:33:25 (194994): called boinc_finish(0)

</stderr_txt>
]]>