Task 38582933

Name PFKFB3_A13_A36_r0_2-QUICO_ATM_GAFF2_LOMAP_PFKFB3-2-5-RND0030_0
Workunit 31547161
Created 13 Dec 2025, 15:13:24 UTC
Sent 13 Dec 2025, 15:13:25 UTC
Report deadline 18 Dec 2025, 15:13:25 UTC
Received 14 Dec 2025, 6:08:13 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 628564
Run time 5 hours 2 min 53 sec
CPU time 5 hours 2 min 53 sec
Validate state Valid
Credit 750,000.00
Device peak FLOPS 13,177.75 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
x86_64-pc-linux-gnu
Peak working set size 734.41 MB
Peak swap size 12.56 GB
Peak disk usage 3.68 GB

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-13 16:16:39 (1252812): wrapper (8.1.26018): starting
2025-12-13 16:17:46 (1252812): wrapper: running bin/python (bin/conda-unpack)
2025-12-13 16:17:46 (1252812): wrapper: created child process 1254100
2025-12-13 16:17:49 (1252812): bin/python exited; CPU time 0.082177
2025-12-13 16:17:49 (1252812): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-13 16:17:49 (1252812): wrapper: created child process 1254156
2025-12-13 16:17:51 (1252812): bin/tar exited; CPU time 0.913236
2025-12-13 16:17:51 (1252812): wrapper: running bin/bash (run.sh)
2025-12-13 16:17:51 (1252812): wrapper: created child process 1254192
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/run/media/shared/boinc/GAMY/slots/0/bin
+++ dirname /run/media/shared/boinc/GAMY/slots/0/bin
++ local full_path_env=/run/media/shared/boinc/GAMY/slots/0
+++ basename /run/media/shared/boinc/GAMY/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/run/media/shared/boinc/GAMY/slots/0
++ CONDA_PREFIX=/run/media/shared/boinc/GAMY/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/run/media/shared/boinc/GAMY/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/run/media/shared/boinc/GAMY/slots/0/etc/conda/activate.d
++ '[' -d /run/media/shared/boinc/GAMY/slots/0/etc/conda/activate.d ']'
+ export PATH=/run/media/shared/boinc/GAMY/slots/0:/run/media/shared/boinc/GAMY/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/run/media/shared/boinc/GAMY/slots/0:/run/media/shared/boinc/GAMY/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/run/media/shared/boinc/GAMY/slots/0/tmp
+ TMP=/run/media/shared/boinc/GAMY/slots/0/tmp
+ mkdir -p /run/media/shared/boinc/GAMY/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/run/media/shared/boinc/GAMY/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_A13_A36_input.yaml
+ python bin/rbfe_production QB_A13_A36_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
2025-12-14 02:00:00 (1929620): wrapper (8.1.26018): starting
2025-12-14 02:00:00 (1929620): wrapper: running bin/bash (run.sh)
2025-12-14 02:00:00 (1929620): wrapper: created child process 1929622
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/run/media/shared/boinc/GAMY/slots/0/bin
+++ dirname /run/media/shared/boinc/GAMY/slots/0/bin
++ local full_path_env=/run/media/shared/boinc/GAMY/slots/0
+++ basename /run/media/shared/boinc/GAMY/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/run/media/shared/boinc/GAMY/slots/0
++ CONDA_PREFIX=/run/media/shared/boinc/GAMY/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/run/media/shared/boinc/GAMY/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/run/media/shared/boinc/GAMY/slots/0/etc/conda/activate.d
++ '[' -d /run/media/shared/boinc/GAMY/slots/0/etc/conda/activate.d ']'
+ export PATH=/run/media/shared/boinc/GAMY/slots/0:/run/media/shared/boinc/GAMY/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/run/media/shared/boinc/GAMY/slots/0:/run/media/shared/boinc/GAMY/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/run/media/shared/boinc/GAMY/slots/0/tmp
+ TMP=/run/media/shared/boinc/GAMY/slots/0/tmp
+ mkdir -p /run/media/shared/boinc/GAMY/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/run/media/shared/boinc/GAMY/slots/0/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A13_A36_input.yaml
+ python bin/rbfe_production QB_A13_A36_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_A13_A36.out r1/QB_A13_A36.out r10/QB_A13_A36.out r11/QB_A13_A36.out r12/QB_A13_A36.out r13/QB_A13_A36.out r14/QB_A13_A36.out r15/QB_A13_A36.out r16/QB_A13_A36.out r17/QB_A13_A36.out r18/QB_A13_A36.out r19/QB_A13_A36.out r2/QB_A13_A36.out r20/QB_A13_A36.out r21/QB_A13_A36.out r3/QB_A13_A36.out r4/QB_A13_A36.out r5/QB_A13_A36.out r6/QB_A13_A36.out r7/QB_A13_A36.out r8/QB_A13_A36.out r9/QB_A13_A36.out 'r*/*.dcd' r0/QB_A13_A36.xtc r1/QB_A13_A36.xtc r10/QB_A13_A36.xtc r11/QB_A13_A36.xtc r12/QB_A13_A36.xtc r13/QB_A13_A36.xtc r14/QB_A13_A36.xtc r15/QB_A13_A36.xtc r16/QB_A13_A36.xtc r17/QB_A13_A36.xtc r18/QB_A13_A36.xtc r19/QB_A13_A36.xtc r2/QB_A13_A36.xtc r20/QB_A13_A36.xtc r21/QB_A13_A36.xtc r3/QB_A13_A36.xtc r4/QB_A13_A36.xtc r5/QB_A13_A36.xtc r6/QB_A13_A36.xtc r7/QB_A13_A36.xtc r8/QB_A13_A36.xtc r9/QB_A13_A36.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 07:07:05 (1929620): bin/bash exited; CPU time 18172.306661
2025-12-14 07:07:05 (1929620): called boinc_finish(0)

</stderr_txt>
]]>


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