Task 38613429

Name p38_A19_A31_r0_2-QUICO_ATM_OpenFF_p38-5-6-RND0913_0
Workunit 31565913
Created 16 Apr 2026, 19:54:50 UTC
Sent 16 Apr 2026, 19:54:54 UTC
Report deadline 21 Apr 2026, 19:54:54 UTC
Received 17 Apr 2026, 14:22:22 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x00000000)
Computer ID 651954
Run time 4 hours 43 min 11 sec
CPU time 4 hours 43 min 11 sec
Validate state Valid
Credit 750,000.00
Device peak FLOPS 17,041.36 GFLOPS
Application version ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121)
x86_64-pc-linux-gnu
Peak working set size 652.18 MB
Peak swap size 40.81 GB
Peak disk usage 3.04 GB

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-17 09:11:32 (133098): wrapper (8.1.26018): starting
2026-04-17 09:11:54 (133098): wrapper: running bin/python (bin/conda-unpack)
2026-04-17 09:11:54 (133098): wrapper: created child process 133102
2026-04-17 09:11:55 (133098): bin/python exited; CPU time 0.086003
2026-04-17 09:11:55 (133098): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-17 09:11:55 (133098): wrapper: created child process 133103
2026-04-17 09:11:56 (133098): bin/tar exited; CPU time 0.721293
2026-04-17 09:11:56 (133098): wrapper: running bin/bash (run.sh)
2026-04-17 09:11:56 (133098): wrapper: created child process 133105
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/3/bin
+++ dirname /var/lib/boinc/slots/3/bin
++ local full_path_env=/var/lib/boinc/slots/3
+++ basename /var/lib/boinc/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/3
++ CONDA_PREFIX=/var/lib/boinc/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/3/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/3/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/3/tmp
+ TMP=/var/lib/boinc/slots/3/tmp
+ mkdir -p /var/lib/boinc/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/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
+ 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_A31_input.yaml
+ python bin/rbfe_production QB_A19_A31_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
SIGSEGV: segmentation violation
/var/lib/boinc/slots/3/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 '
Stack trace (13 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x42c050]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x72b0e1245330]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x463138]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x45f5d5]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x72b0e1245330]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xbf)[0x72b0e12ecadf]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17)[0x72b0e12f9a27]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4c)[0x72b0e132975c]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x40b2e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x72b0e122a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x72b0e122a28b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]

Exiting...
2026-04-17 10:31:36 (3016): wrapper (8.1.26018): starting
2026-04-17 10:31:36 (3016): wrapper: running bin/bash (run.sh)
2026-04-17 10:31:36 (3016): wrapper: created child process 3029
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/3/bin
+++ dirname /var/lib/boinc/slots/3/bin
++ local full_path_env=/var/lib/boinc/slots/3
+++ basename /var/lib/boinc/slots/3
++ local env_name=3
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/3
++ CONDA_PREFIX=/var/lib/boinc/slots/3
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(3) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/3/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/3/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/3:/var/lib/boinc/slots/3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/3/tmp
+ TMP=/var/lib/boinc/slots/3/tmp
+ mkdir -p /var/lib/boinc/slots/3/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/slots/3/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A19_A31_input.yaml
+ python bin/rbfe_production QB_A19_A31_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_A19_A31.out r1/QB_A19_A31.out r10/QB_A19_A31.out r11/QB_A19_A31.out r12/QB_A19_A31.out r13/QB_A19_A31.out r14/QB_A19_A31.out r15/QB_A19_A31.out r16/QB_A19_A31.out r17/QB_A19_A31.out r18/QB_A19_A31.out r19/QB_A19_A31.out r2/QB_A19_A31.out r20/QB_A19_A31.out r21/QB_A19_A31.out r3/QB_A19_A31.out r4/QB_A19_A31.out r5/QB_A19_A31.out r6/QB_A19_A31.out r7/QB_A19_A31.out r8/QB_A19_A31.out r9/QB_A19_A31.out r0/QB_A19_A31.xtc r1/QB_A19_A31.xtc r10/QB_A19_A31.xtc r11/QB_A19_A31.xtc r12/QB_A19_A31.xtc r13/QB_A19_A31.xtc r14/QB_A19_A31.xtc r15/QB_A19_A31.xtc r16/QB_A19_A31.xtc r17/QB_A19_A31.xtc r18/QB_A19_A31.xtc r19/QB_A19_A31.xtc r2/QB_A19_A31.xtc r20/QB_A19_A31.xtc r21/QB_A19_A31.xtc r3/QB_A19_A31.xtc r4/QB_A19_A31.xtc r5/QB_A19_A31.xtc r6/QB_A19_A31.xtc r7/QB_A19_A31.xtc r8/QB_A19_A31.xtc r9/QB_A19_A31.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
2026-04-17 15:06:05 (3016): bin/bash exited; CPU time 16736.081343
2026-04-17 15:06:05 (3016): called boinc_finish(0)

</stderr_txt>
]]>


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