Task 38648720
| Name | test_595-GPUGRID_TEST_ATM_4STEP_20261023-0-4-RND7234_1 |
| Workunit | 31592437 |
| Created | 23 Oct 2026, 20:49:38 UTC |
| Sent | 24 Oct 2026, 2:30:48 UTC |
| Report deadline | 29 Oct 2026, 2:30:48 UTC |
| Received | 24 Oct 2026, 3:48:26 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 463199 |
| Run time | 52 min 43 sec |
| CPU time | 52 min 12 sec |
| Validate state | Valid |
| Credit | 60,000.00 |
| Device peak FLOPS | 2,933.51 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 649.41 MB |
| Peak swap size | 17.00 GB |
| Peak disk usage | 2.96 GB |
Stderr output
<core_client_version>7.16.5</core_client_version>
<![CDATA[
<stderr_txt>
2026-10-24 04:55:27 (205281): wrapper (8.1.26018): starting
2026-10-24 04:55:48 (205281): wrapper: running bin/python (bin/conda-unpack)
2026-10-24 04:55:48 (205281): wrapper: created child process 205287
2026-10-24 04:55:49 (205281): bin/python exited; CPU time 0.112973
2026-10-24 04:55:49 (205281): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-10-24 04:55:49 (205281): wrapper: created child process 205288
2026-10-24 04:55:50 (205281): bin/tar exited; CPU time 0.782366
2026-10-24 04:55:50 (205281): wrapper: running bin/bash (run.sh)
2026-10-24 04:55:50 (205281): wrapper: created child process 205290
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/kle1boinc/BOINC/slots/13/bin
+++ dirname /home/kle1boinc/BOINC/slots/13/bin
++ local full_path_env=/home/kle1boinc/BOINC/slots/13
+++ basename /home/kle1boinc/BOINC/slots/13
++ local env_name=13
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/kle1boinc/BOINC/slots/13
++ CONDA_PREFIX=/home/kle1boinc/BOINC/slots/13
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/kle1boinc/BOINC/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(13) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/kle1boinc/BOINC/slots/13/etc/conda/activate.d
++ '[' -d /home/kle1boinc/BOINC/slots/13/etc/conda/activate.d ']'
+ export PATH=/home/kle1boinc/BOINC/slots/13:/home/kle1boinc/BOINC/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/kle1boinc/BOINC/slots/13:/home/kle1boinc/BOINC/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/kle1boinc/BOINC/slots/13/tmp
+ TMP=/home/kle1boinc/BOINC/slots/13/tmp
+ mkdir -p /home/kle1boinc/BOINC/slots/13/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/kle1boinc/BOINC/slots/13/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==26.2.1 -v
+ python -m pip install --no-dependencies atom-openmm==8.4.0 -v
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)")': /simple/atom-openmm/
+ 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' 'r*/*.xtc'
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: r*/*.xtc: 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
2026-10-24 05:48:09 (205281): bin/bash exited; CPU time 3131.264673
2026-10-24 05:48:09 (205281): called boinc_finish(0)
</stderr_txt>
]]>
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