Task 38611277
| Name | CDK2_A14_A11_r0_4-QUICO_ATM_GAFF2_NAGL_CDK2-2-6-RND1792_0 |
| Workunit | 31564044 |
| Created | 15 Apr 2026, 17:59:48 UTC |
| Sent | 15 Apr 2026, 17:59:59 UTC |
| Report deadline | 20 Apr 2026, 17:59:59 UTC |
| Received | 15 Apr 2026, 23:16:40 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 651860 |
| Run time | 5 hours 0 min 27 sec |
| CPU time | 5 hours 0 min 27 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 20,850.86 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 728.65 MB |
| Peak swap size | 17.02 GB |
| Peak disk usage | 3.12 GB |
Stderr output
<core_client_version>7.24.1</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-15 13:29:44 (158983): wrapper (8.1.26018): starting
2026-04-15 13:30:02 (158983): wrapper: running bin/python (bin/conda-unpack)
2026-04-15 13:30:02 (158983): wrapper: created child process 158989
2026-04-15 13:30:03 (158983): bin/python exited; CPU time 0.138339
2026-04-15 13:30:03 (158983): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-15 13:30:03 (158983): wrapper: created child process 158990
2026-04-15 13:30:04 (158983): bin/tar exited; CPU time 0.904644
2026-04-15 13:30:04 (158983): wrapper: running bin/bash (run.sh)
2026-04-15 13:30:04 (158983): wrapper: created child process 158992
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/orangekid/40000/slots/1/bin
+++ dirname /home/orangekid/40000/slots/1/bin
++ local full_path_env=/home/orangekid/40000/slots/1
+++ basename /home/orangekid/40000/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/orangekid/40000/slots/1
++ CONDA_PREFIX=/home/orangekid/40000/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/orangekid/40000/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/orangekid/40000/slots/1/etc/conda/activate.d
++ '[' -d /home/orangekid/40000/slots/1/etc/conda/activate.d ']'
+ export PATH=/home/orangekid/40000/slots/1:/home/orangekid/40000/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/orangekid/40000/slots/1:/home/orangekid/40000/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/orangekid/40000/slots/1/tmp
+ TMP=/home/orangekid/40000/slots/1/tmp
+ mkdir -p /home/orangekid/40000/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/orangekid/40000/slots/1/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: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f2314903990>: Failed to establish a new connection: [Errno -2] Name or service not known')': /simple/pyaml/
+ 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_A14_A11_input.yaml
+ python bin/rbfe_production QB_A14_A11_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_A14_A11.out r1/QB_A14_A11.out r10/QB_A14_A11.out r11/QB_A14_A11.out r12/QB_A14_A11.out r13/QB_A14_A11.out r14/QB_A14_A11.out r15/QB_A14_A11.out r16/QB_A14_A11.out r17/QB_A14_A11.out r18/QB_A14_A11.out r19/QB_A14_A11.out r2/QB_A14_A11.out r20/QB_A14_A11.out r21/QB_A14_A11.out r3/QB_A14_A11.out r4/QB_A14_A11.out r5/QB_A14_A11.out r6/QB_A14_A11.out r7/QB_A14_A11.out r8/QB_A14_A11.out r9/QB_A14_A11.out 'r*/*.dcd' r0/QB_A14_A11.xtc r1/QB_A14_A11.xtc r10/QB_A14_A11.xtc r11/QB_A14_A11.xtc r12/QB_A14_A11.xtc r13/QB_A14_A11.xtc r14/QB_A14_A11.xtc r15/QB_A14_A11.xtc r16/QB_A14_A11.xtc r17/QB_A14_A11.xtc r18/QB_A14_A11.xtc r19/QB_A14_A11.xtc r2/QB_A14_A11.xtc r20/QB_A14_A11.xtc r21/QB_A14_A11.xtc r3/QB_A14_A11.xtc r4/QB_A14_A11.xtc r5/QB_A14_A11.xtc r6/QB_A14_A11.xtc r7/QB_A14_A11.xtc r8/QB_A14_A11.xtc r9/QB_A14_A11.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
2026-04-15 18:13:07 (158983): bin/bash exited; CPU time 17762.407268
2026-04-15 18:13:07 (158983): called boinc_finish(0)
</stderr_txt>
]]>
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