Task 38611324

Name tnks2_A09_A03_r0_5-QUICO_ATM_GAFF2_NAGL_TNKS2-5-6-RND7324_0
Workunit 31564085
Created 15 Apr 2026, 18:27:10 UTC
Sent 15 Apr 2026, 18:27:16 UTC
Report deadline 20 Apr 2026, 18:27:16 UTC
Received 16 Apr 2026, 5:53:32 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 652030
Run time 31 min 35 sec
CPU time 31 min 35 sec
Validate state Valid
Credit 750,000.00
Device peak FLOPS 29,499.88 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
x86_64-pc-linux-gnu
Peak working set size 505.70 MB
Peak swap size 12.49 GB
Peak disk usage 2.94 GB

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-16 05:40:18 (2217): wrapper (8.1.26018): starting
2026-04-16 05:40:33 (2217): wrapper: running bin/python (bin/conda-unpack)
2026-04-16 05:40:33 (2217): wrapper: created child process 2221
2026-04-16 05:40:34 (2217): bin/python exited; CPU time 0.069640
2026-04-16 05:40:34 (2217): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-16 05:40:34 (2217): wrapper: created child process 2222
2026-04-16 05:40:35 (2217): bin/tar exited; CPU time 0.343851
2026-04-16 05:40:35 (2217): wrapper: running bin/bash (run.sh)
2026-04-16 05:40:35 (2217): wrapper: created child process 2224
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/fornax/slots/0/bin
+++ dirname /home/fornax/slots/0/bin
++ local full_path_env=/home/fornax/slots/0
+++ basename /home/fornax/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/fornax/slots/0
++ CONDA_PREFIX=/home/fornax/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/fornax/slots/0/etc/conda/activate.d
++ '[' -d /home/fornax/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/fornax/slots/0:/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/fornax/slots/0:/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/fornax/slots/0/tmp
+ TMP=/home/fornax/slots/0/tmp
+ mkdir -p /home/fornax/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/fornax/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_A09_A03_input.yaml
+ python bin/rbfe_production QB_A09_A03_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (14 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x42c050]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x415c0) [0x7fc3306cd5c0]
/usr/lib/x86_64-linux-gnu/libc.so.6(__libc_free+0x25) [0x7fc330735425]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x44255a]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x45f5f0]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x415c0) [0x7fc3306cd5c0]
/usr/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0x63) [0x7fc3307711e3]
/usr/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17) [0x7fc33077d367]
/usr/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4a) [0x7fc3307a8a5a]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x40b2e5]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x2a3c8) [0x7fc3306b63c8]
/usr/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b) [0x7fc3306b648b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x407cc5]

Exiting...
/home/fornax/slots/0/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 3 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '
2026-04-16 07:21:51 (93): wrapper (8.1.26018): starting
2026-04-16 07:21:51 (93): wrapper: running bin/bash (run.sh)
2026-04-16 07:21:51 (93): wrapper: created child process 95
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/fornax/slots/0/bin
+++ dirname /home/fornax/slots/0/bin
++ local full_path_env=/home/fornax/slots/0
+++ basename /home/fornax/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/fornax/slots/0
++ CONDA_PREFIX=/home/fornax/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/fornax/slots/0/etc/conda/activate.d
++ '[' -d /home/fornax/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/fornax/slots/0:/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/fornax/slots/0:/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/fornax/slots/0/tmp
+ TMP=/home/fornax/slots/0/tmp
+ mkdir -p /home/fornax/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/fornax/slots/0/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A09_A03_input.yaml
+ python bin/rbfe_production QB_A09_A03_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_A09_A03.out r1/QB_A09_A03.out r10/QB_A09_A03.out r11/QB_A09_A03.out r12/QB_A09_A03.out r13/QB_A09_A03.out r14/QB_A09_A03.out r15/QB_A09_A03.out r16/QB_A09_A03.out r17/QB_A09_A03.out r18/QB_A09_A03.out r19/QB_A09_A03.out r2/QB_A09_A03.out r20/QB_A09_A03.out r21/QB_A09_A03.out r3/QB_A09_A03.out r4/QB_A09_A03.out r5/QB_A09_A03.out r6/QB_A09_A03.out r7/QB_A09_A03.out r8/QB_A09_A03.out r9/QB_A09_A03.out r0/QB_A09_A03.xtc r1/QB_A09_A03.xtc r10/QB_A09_A03.xtc r11/QB_A09_A03.xtc r12/QB_A09_A03.xtc r13/QB_A09_A03.xtc r14/QB_A09_A03.xtc r15/QB_A09_A03.xtc r16/QB_A09_A03.xtc r17/QB_A09_A03.xtc r18/QB_A09_A03.xtc r19/QB_A09_A03.xtc r2/QB_A09_A03.xtc r20/QB_A09_A03.xtc r21/QB_A09_A03.xtc r3/QB_A09_A03.xtc r4/QB_A09_A03.xtc r5/QB_A09_A03.xtc r6/QB_A09_A03.xtc r7/QB_A09_A03.xtc r8/QB_A09_A03.xtc r9/QB_A09_A03.xtc
tar: run.log: file changed as we read it
+ 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
2026-04-16 07:53:20 (93): bin/bash exited; CPU time 1856.463735
2026-04-16 07:53:20 (93): called boinc_finish(0)

</stderr_txt>
]]>


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