Task 38583872

Name HIF2A_A29_A22_r0_3-QUICO_ATM_GAFF2_LOMAP_HIF2A-4-5-RND8300_0
Workunit 31547884
Created 14 Dec 2025, 20:51:55 UTC
Sent 14 Dec 2025, 20:52:02 UTC
Report deadline 19 Dec 2025, 20:52:02 UTC
Received 14 Dec 2025, 22:05:33 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 628374
Run time 1 hours 13 min 31 sec
CPU time 1 hours 13 min 51 sec
Validate state Valid
Credit 750,000.00
Device peak FLOPS 84,054.54 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
x86_64-pc-linux-gnu
Peak working set size 434.75 MB
Peak swap size 32.76 GB
Peak disk usage 2.94 GB

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
2025-12-14 21:52:35 (53171): wrapper (8.1.26018): starting
2025-12-14 21:52:49 (53171): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 21:52:49 (53171): wrapper: created child process 53201
2025-12-14 21:52:50 (53171): bin/python exited; CPU time 0.047088
2025-12-14 21:52:50 (53171): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 21:52:50 (53171): wrapper: created child process 53202
2025-12-14 21:52:51 (53171): bin/tar exited; CPU time 0.315325
2025-12-14 21:52:51 (53171): wrapper: running bin/bash (run.sh)
2025-12-14 21:52:51 (53171): wrapper: created child process 53208
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/maciek/BOINC/40000/slots/3/bin
+++ dirname /home/maciek/BOINC/40000/slots/3/bin
++ local full_path_env=/home/maciek/BOINC/40000/slots/3
+++ basename /home/maciek/BOINC/40000/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/maciek/BOINC/40000/slots/3
++ CONDA_PREFIX=/home/maciek/BOINC/40000/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/maciek/BOINC/40000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/maciek/BOINC/40000/slots/3/etc/conda/activate.d
++ '[' -d /home/maciek/BOINC/40000/slots/3/etc/conda/activate.d ']'
+ export PATH=/home/maciek/BOINC/40000/slots/3:/home/maciek/BOINC/40000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/maciek/BOINC/40000/slots/3:/home/maciek/BOINC/40000/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/maciek/BOINC/40000/slots/3/tmp
+ TMP=/home/maciek/BOINC/40000/slots/3/tmp
+ mkdir -p /home/maciek/BOINC/40000/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/maciek/BOINC/40000/slots/3/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
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ python -m pip install --no-dependencies atom-openmm -v
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))': /simple/atom-openmm/
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A29_A22_input.yaml
+ python bin/rbfe_production QB_A29_A22_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_A29_A22.out r1/QB_A29_A22.out r10/QB_A29_A22.out r11/QB_A29_A22.out r12/QB_A29_A22.out r13/QB_A29_A22.out r14/QB_A29_A22.out r15/QB_A29_A22.out r16/QB_A29_A22.out r17/QB_A29_A22.out r18/QB_A29_A22.out r19/QB_A29_A22.out r2/QB_A29_A22.out r20/QB_A29_A22.out r21/QB_A29_A22.out r3/QB_A29_A22.out r4/QB_A29_A22.out r5/QB_A29_A22.out r6/QB_A29_A22.out r7/QB_A29_A22.out r8/QB_A29_A22.out r9/QB_A29_A22.out 'r*/*.dcd' r0/QB_A29_A22.xtc r1/QB_A29_A22.xtc r10/QB_A29_A22.xtc r11/QB_A29_A22.xtc r12/QB_A29_A22.xtc r13/QB_A29_A22.xtc r14/QB_A29_A22.xtc r15/QB_A29_A22.xtc r16/QB_A29_A22.xtc r17/QB_A29_A22.xtc r18/QB_A29_A22.xtc r19/QB_A29_A22.xtc r2/QB_A29_A22.xtc r20/QB_A29_A22.xtc r21/QB_A29_A22.xtc r3/QB_A29_A22.xtc r4/QB_A29_A22.xtc r5/QB_A29_A22.xtc r6/QB_A29_A22.xtc r7/QB_A29_A22.xtc r8/QB_A29_A22.xtc r9/QB_A29_A22.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 23:04:49 (53171): bin/bash exited; CPU time 4320.341467
2025-12-14 23:04:49 (53171): called boinc_finish(0)

</stderr_txt>
]]>


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