Task 38667005
| Name | test_89-GPUGRID_TEST_ATM_100SAMPLES_20261025-0-1-RND1569_1 |
| Workunit | 31607437 |
| Created | 25 Oct 2026, 5:52:39 UTC |
| Sent | 25 Oct 2026, 5:53:03 UTC |
| Report deadline | 30 Oct 2026, 5:53:03 UTC |
| Received | 25 Oct 2026, 10:57:11 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 197 (0x000000C5) EXIT_TIME_LIMIT_EXCEEDED |
| Computer ID | 652821 |
| Run time | 4 hours 48 min 3 sec |
| CPU time | 4 hours 48 min 3 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 41,936.43 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 623.89 MB |
| Peak swap size | 36.19 GB |
| Peak disk usage | 2.96 GB |
Stderr output
<core_client_version>8.2.15</core_client_version>
<![CDATA[
<message>
exceeded elapsed time limit 16562.37 (10000000000.00G/604948.59G)</message>
<stderr_txt>
2026-10-25 01:59:22 (2997551): wrapper (8.1.26018): starting
2026-10-25 01:59:39 (2997551): wrapper: running bin/python (bin/conda-unpack)
2026-10-25 01:59:39 (2997551): wrapper: created child process 2997888
2026-10-25 01:59:40 (2997551): bin/python exited; CPU time 0.120833
2026-10-25 01:59:40 (2997551): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-10-25 01:59:40 (2997551): wrapper: created child process 2997933
2026-10-25 01:59:41 (2997551): bin/tar exited; CPU time 0.603858
2026-10-25 01:59:41 (2997551): wrapper: running bin/bash (run.sh)
2026-10-25 01:59:41 (2997551): wrapper: created child process 2997948
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/2/bin
+++ dirname /var/lib/boinc/slots/2/bin
++ local full_path_env=/var/lib/boinc/slots/2
+++ basename /var/lib/boinc/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/2
++ CONDA_PREFIX=/var/lib/boinc/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/2/tmp
+ TMP=/var/lib/boinc/slots/2/tmp
+ mkdir -p /var/lib/boinc/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:2,1,CUDA,,/var/lib/boinc/slots/2/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
+ 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.
/var/lib/boinc/slots/2/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 '
2026-10-25 02:19:54 (3009997): wrapper (8.1.26018): starting
2026-10-25 02:19:54 (3009997): wrapper: running bin/bash (run.sh)
2026-10-25 02:19:54 (3009997): wrapper: created child process 3009999
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/2/bin
+++ dirname /var/lib/boinc/slots/2/bin
++ local full_path_env=/var/lib/boinc/slots/2
+++ basename /var/lib/boinc/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/2
++ CONDA_PREFIX=/var/lib/boinc/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/2/tmp
+ TMP=/var/lib/boinc/slots/2/tmp
+ mkdir -p /var/lib/boinc/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:2,1,CUDA,,/var/lib/boinc/slots/2/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ 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.
</stderr_txt>
]]>
©2026 Universitat Pompeu Fabra