Task 38644502
| Name | shp2_A01_A05_r0_4-QUICO_ATM_OpenFF23_NAGL_shp2-0-6-RND3583_5 |
| Workunit | 31589592 |
| Created | 8 May 2026, 19:34:32 UTC |
| Sent | 8 May 2026, 19:34:36 UTC |
| Report deadline | 13 May 2026, 19:34:36 UTC |
| Received | 10 May 2026, 11:33:21 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Aborted by user |
| Exit status | 203 (0x000000CB) EXIT_ABORTED_VIA_GUI |
| Computer ID | 652210 |
| Run time | 54 min 51 sec |
| CPU time | 54 min 33 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 1,134.32 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 832.91 MB |
| Peak swap size | 17.76 GB |
| Peak disk usage | 2.80 GB |
Stderr output
<core_client_version>8.2.13</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2026-05-08 21:35:24 (72825): wrapper (8.1.26018): starting
2026-05-08 21:35:41 (72825): wrapper: running bin/python (bin/conda-unpack)
2026-05-08 21:35:41 (72825): wrapper: created child process 72836
2026-05-08 21:35:42 (72825): bin/python exited; CPU time 0.073321
2026-05-08 21:35:42 (72825): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-05-08 21:35:42 (72825): wrapper: created child process 72837
2026-05-08 21:35:43 (72825): bin/tar exited; CPU time 0.872770
2026-05-08 21:35:43 (72825): wrapper: running bin/bash (run.sh)
2026-05-08 21:35:43 (72825): wrapper: created child process 72839
+ 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,0:0,1,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_A01_A05_input.yaml
+ python bin/rbfe_production QB_A01_A05_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
SIGSEGV: segmentation violation
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)[0x7244a8645330]
../../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)[0x7244a8645330]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xbf)[0x7244a86ecadf]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17)[0x7244a86f9a27]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4c)[0x7244a872975c]
../../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)[0x7244a862a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x7244a862a28b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]
Exiting...
/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 '
2026-05-10 12:37:50 (4609): wrapper (8.1.26018): starting
2026-05-10 12:37:50 (4609): wrapper: running bin/bash (run.sh)
2026-05-10 12:37:50 (4609): wrapper: created child process 4619
+ 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,0:0,1,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_A01_A05_input.yaml
+ python bin/rbfe_production QB_A01_A05_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
</stderr_txt>
]]>
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