Task 38580942

Name JNK1_A19_A12_r0_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-0-5-RND7584_4
Workunit 31545156
Created 12 Dec 2025, 7:25:56 UTC
Sent 12 Dec 2025, 7:26:01 UTC
Report deadline 17 Dec 2025, 7:26:01 UTC
Received 13 Dec 2025, 14:18:08 UTC
Server state Over
Outcome Computation error
Client state Aborted by user
Exit status 203 (0x000000CB) EXIT_ABORTED_VIA_GUI
Computer ID 621860
Run time 25 min 54 sec
CPU time 11 min 37 sec
Validate state Invalid
Credit 0.00
Device peak FLOPS 14,236.29 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
x86_64-pc-linux-gnu
Peak working set size 648.33 MB
Peak swap size 12.72 GB
Peak disk usage 3.29 GB

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2025-12-12 02:32:47 (152868): wrapper (8.1.26018): starting
2025-12-12 02:33:10 (152868): wrapper: running bin/python (bin/conda-unpack)
2025-12-12 02:33:10 (152868): wrapper: created child process 152876
2025-12-12 02:33:11 (152868): bin/python exited; CPU time 0.202648
2025-12-12 02:33:11 (152868): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-12 02:33:11 (152868): wrapper: created child process 152877
2025-12-12 02:33:13 (152868): bin/tar exited; CPU time 1.413576
2025-12-12 02:33:13 (152868): wrapper: running bin/bash (run.sh)
2025-12-12 02:33:13 (152868): wrapper: created child process 152879
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/0/bin
+++ dirname /var/lib/boinc-client/slots/0/bin
++ local full_path_env=/var/lib/boinc-client/slots/0
+++ basename /var/lib/boinc-client/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/0
++ CONDA_PREFIX=/var/lib/boinc-client/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/0/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/0/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/0:/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/0:/var/lib/boinc-client/slots/0/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/0/tmp
+ TMP=/var/lib/boinc-client/slots/0/tmp
+ mkdir -p /var/lib/boinc-client/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/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_A19_A12_input.yaml
+ python bin/rbfe_production QB_A19_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
2025-12-13 08:52:18 (190500): wrapper (8.1.26018): starting
2025-12-13 08:52:18 (190500): wrapper: running bin/bash (run.sh)
2025-12-13 08:52:18 (190500): wrapper: created child process 190502
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/0/bin
+++ dirname /var/lib/boinc-client/slots/0/bin
++ local full_path_env=/var/lib/boinc-client/slots/0
+++ basename /var/lib/boinc-client/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/0
++ CONDA_PREFIX=/var/lib/boinc-client/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/0/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/0/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/0:/var/lib/boinc-client/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/0:/var/lib/boinc-client/slots/0/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/0/tmp
+ TMP=/var/lib/boinc-client/slots/0/tmp
+ mkdir -p /var/lib/boinc-client/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/0/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A19_A12_input.yaml
+ python bin/rbfe_production QB_A19_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.

</stderr_txt>
]]>


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