Task 38582838

Name	JNK1_A04_A12_r2_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-3-5-RND7806_0
Workunit	31547078
Created	13 Dec 2025, 12:48:29 UTC
Sent	13 Dec 2025, 12:48:36 UTC
Report deadline	18 Dec 2025, 12:48:36 UTC
Received	14 Dec 2025, 0:52:44 UTC
Server state	Over
Outcome	Success
Client state	Done
Exit status	0 (0x00000000)
Computer ID	644401
Run time	11 hours 46 min 54 sec
CPU time	10 hours 52 min 39 sec
Validate state	Valid
Credit	750,000.00
Device peak FLOPS	4,116.03 GFLOPS
Application version	ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu
Peak working set size	669.22 MB
Peak swap size	21.05 GB
Peak disk usage	3.96 GB

Stderr output

<core_client_version>8.0.4</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-13 21:04:49 (1727361): wrapper (8.1.26018): starting
2025-12-13 21:05:23 (1727361): wrapper: running bin/python (bin/conda-unpack)
2025-12-13 21:05:23 (1727361): wrapper: created child process 1727652
2025-12-13 21:05:24 (1727361): bin/python exited; CPU time 0.409695
2025-12-13 21:05:24 (1727361): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-13 21:05:24 (1727361): wrapper: created child process 1727653
2025-12-13 21:05:27 (1727361): bin/tar exited; CPU time 2.085859
2025-12-13 21:05:27 (1727361): wrapper: running bin/bash (run.sh)
2025-12-13 21:05:27 (1727361): wrapper: created child process 1727671
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/32/bin
+++ dirname /var/lib/boinc-client/slots/32/bin
++ local full_path_env=/var/lib/boinc-client/slots/32
+++ basename /var/lib/boinc-client/slots/32
++ local env_name=32
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/32
++ CONDA_PREFIX=/var/lib/boinc-client/slots/32
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/32/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(32) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/32/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/32/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/32:/var/lib/boinc-client/slots/32/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/32:/var/lib/boinc-client/slots/32/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/32/tmp
+ TMP=/var/lib/boinc-client/slots/32/tmp
+ mkdir -p /var/lib/boinc-client/slots/32/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/32/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_A04_A12_input.yaml
+ python bin/rbfe_production QB_A04_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_A04_A12.out r1/QB_A04_A12.out r10/QB_A04_A12.out r11/QB_A04_A12.out r12/QB_A04_A12.out r13/QB_A04_A12.out r14/QB_A04_A12.out r15/QB_A04_A12.out r16/QB_A04_A12.out r17/QB_A04_A12.out r18/QB_A04_A12.out r19/QB_A04_A12.out r2/QB_A04_A12.out r20/QB_A04_A12.out r21/QB_A04_A12.out r3/QB_A04_A12.out r4/QB_A04_A12.out r5/QB_A04_A12.out r6/QB_A04_A12.out r7/QB_A04_A12.out r8/QB_A04_A12.out r9/QB_A04_A12.out 'r*/*.dcd' r0/QB_A04_A12.xtc r1/QB_A04_A12.xtc r10/QB_A04_A12.xtc r11/QB_A04_A12.xtc r12/QB_A04_A12.xtc r13/QB_A04_A12.xtc r14/QB_A04_A12.xtc r15/QB_A04_A12.xtc r16/QB_A04_A12.xtc r17/QB_A04_A12.xtc r18/QB_A04_A12.xtc r19/QB_A04_A12.xtc r2/QB_A04_A12.xtc r20/QB_A04_A12.xtc r21/QB_A04_A12.xtc r3/QB_A04_A12.xtc r4/QB_A04_A12.xtc r5/QB_A04_A12.xtc r6/QB_A04_A12.xtc r7/QB_A04_A12.xtc r8/QB_A04_A12.xtc r9/QB_A04_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
2025-12-14 08:51:41 (1727361): bin/bash exited; CPU time 39077.134295
2025-12-14 08:51:41 (1727361): called boinc_finish(0)

</stderr_txt>
]]>