Task 38609969
| Name | TYK2_A11_A08_r0_1-QUICO_ATM_OpenFF_TYK2-2-6-RND6218_0 |
| Workunit | 31562950 |
| Created | 15 Apr 2026, 5:06:48 UTC |
| Sent | 15 Apr 2026, 5:06:55 UTC |
| Report deadline | 20 Apr 2026, 5:06:55 UTC |
| Received | 20 Apr 2026, 8:32:10 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 648796 |
| Run time | 7 hours 6 min 41 sec |
| CPU time | 7 hours 6 min 41 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 1,709.79 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 649.98 MB |
| Peak swap size | 13.16 GB |
| Peak disk usage | 3.06 GB |
Stderr output
<core_client_version>8.2.5</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-16 09:15:02 (2534677): wrapper (8.1.26018): starting
2026-04-16 09:15:19 (2534677): wrapper: running bin/python (bin/conda-unpack)
2026-04-16 09:15:19 (2534677): wrapper: created child process 2535885
2026-04-16 09:15:20 (2534677): bin/python exited; CPU time 0.104600
2026-04-16 09:15:20 (2534677): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-16 09:15:20 (2534677): wrapper: created child process 2535938
2026-04-16 09:15:28 (2534677): bin/tar exited; CPU time 0.528302
2026-04-16 09:15:28 (2534677): wrapper: running bin/bash (run.sh)
2026-04-16 09:15:28 (2534677): wrapper: created child process 2536569
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/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_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/4/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 09:20:59 (2558485): wrapper (8.1.26018): starting
2026-04-16 09:20:59 (2558485): wrapper: running bin/bash (run.sh)
2026-04-16 09:20:59 (2558485): wrapper: created child process 2558487
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 10:21:46 (2841343): wrapper (8.1.26018): starting
2026-04-16 10:21:46 (2841343): wrapper: running bin/bash (run.sh)
2026-04-16 10:21:46 (2841343): wrapper: created child process 2841345
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 10:27:03 (2866090): wrapper (8.1.26018): starting
2026-04-16 10:27:03 (2866090): wrapper: running bin/bash (run.sh)
2026-04-16 10:27:03 (2866090): wrapper: created child process 2866092
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 11:22:27 (3123729): wrapper (8.1.26018): starting
2026-04-16 11:22:27 (3123729): wrapper: running bin/bash (run.sh)
2026-04-16 11:22:27 (3123729): wrapper: created child process 3123731
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 12:24:32 (3411584): wrapper (8.1.26018): starting
2026-04-16 12:24:32 (3411584): wrapper: running bin/bash (run.sh)
2026-04-16 12:24:32 (3411584): wrapper: created child process 3411586
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 12:31:34 (3444557): wrapper (8.1.26018): starting
2026-04-16 12:31:34 (3444557): wrapper: running bin/bash (run.sh)
2026-04-16 12:31:34 (3444557): wrapper: created child process 3444559
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 13:33:04 (3730629): wrapper (8.1.26018): starting
2026-04-16 13:33:04 (3730629): wrapper: running bin/bash (run.sh)
2026-04-16 13:33:04 (3730629): wrapper: created child process 3730631
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 14:31:28 (4001331): wrapper (8.1.26018): starting
2026-04-16 14:31:28 (4001331): wrapper: running bin/bash (run.sh)
2026-04-16 14:31:28 (4001331): wrapper: created child process 4001333
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 15:32:37 (91836): wrapper (8.1.26018): starting
2026-04-16 15:32:37 (91836): wrapper: running bin/bash (run.sh)
2026-04-16 15:32:37 (91836): wrapper: created child process 91838
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 15:40:35 (128904): wrapper (8.1.26018): starting
2026-04-16 15:40:35 (128904): wrapper: running bin/bash (run.sh)
2026-04-16 15:40:35 (128904): wrapper: created child process 128906
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 16:34:22 (378261): wrapper (8.1.26018): starting
2026-04-16 16:34:22 (378261): wrapper: running bin/bash (run.sh)
2026-04-16 16:34:22 (378261): wrapper: created child process 378263
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/4/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 16:42:16 (415079): wrapper (8.1.26018): starting
2026-04-16 16:42:16 (415079): wrapper: running bin/bash (run.sh)
2026-04-16 16:42:16 (415079): wrapper: created child process 415081
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 17:37:57 (673434): wrapper (8.1.26018): starting
2026-04-16 17:37:57 (673434): wrapper: running bin/bash (run.sh)
2026-04-16 17:37:57 (673434): wrapper: created child process 673436
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 17:42:32 (694878): wrapper (8.1.26018): starting
2026-04-16 17:42:32 (694878): wrapper: running bin/bash (run.sh)
2026-04-16 17:42:32 (694878): wrapper: created child process 694880
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 18:42:13 (972347): wrapper (8.1.26018): starting
2026-04-16 18:42:13 (972347): wrapper: running bin/bash (run.sh)
2026-04-16 18:42:13 (972347): wrapper: created child process 972349
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 18:49:14 (1005316): wrapper (8.1.26018): starting
2026-04-16 18:49:14 (1005316): wrapper: running bin/bash (run.sh)
2026-04-16 18:49:14 (1005316): wrapper: created child process 1005318
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 18:55:32 (1034779): wrapper (8.1.26018): starting
2026-04-16 18:55:32 (1034779): wrapper: running bin/bash (run.sh)
2026-04-16 18:55:32 (1034779): wrapper: created child process 1034781
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-16 23:45:41 (2379516): wrapper (8.1.26018): starting
2026-04-16 23:45:41 (2379516): wrapper: running bin/bash (run.sh)
2026-04-16 23:45:41 (2379516): wrapper: created child process 2379518
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-19 10:29:46 (69028): wrapper (8.1.26018): starting
2026-04-19 10:29:46 (69028): wrapper: running bin/bash (run.sh)
2026-04-19 10:29:46 (69028): wrapper: created child process 69033
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/4/bin
+++ dirname /var/lib/boinc-client/slots/4/bin
++ local full_path_env=/var/lib/boinc-client/slots/4
+++ basename /var/lib/boinc-client/slots/4
++ local env_name=4
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ CONDA_PREFIX=/var/lib/boinc-client/slots/4
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(4) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/4/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/4/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/4:/var/lib/boinc-client/slots/4/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/4/tmp
+ TMP=/var/lib/boinc-client/slots/4/tmp
+ mkdir -p /var/lib/boinc-client/slots/4/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/4/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A11_A08_input.yaml
+ python bin/rbfe_production QB_A11_A08_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_A11_A08.out r1/QB_A11_A08.out r10/QB_A11_A08.out r11/QB_A11_A08.out r12/QB_A11_A08.out r13/QB_A11_A08.out r14/QB_A11_A08.out r15/QB_A11_A08.out r16/QB_A11_A08.out r17/QB_A11_A08.out r18/QB_A11_A08.out r19/QB_A11_A08.out r2/QB_A11_A08.out r20/QB_A11_A08.out r21/QB_A11_A08.out r3/QB_A11_A08.out r4/QB_A11_A08.out r5/QB_A11_A08.out r6/QB_A11_A08.out r7/QB_A11_A08.out r8/QB_A11_A08.out r9/QB_A11_A08.out r0/QB_A11_A08.xtc r1/QB_A11_A08.xtc r10/QB_A11_A08.xtc r11/QB_A11_A08.xtc r12/QB_A11_A08.xtc r13/QB_A11_A08.xtc r14/QB_A11_A08.xtc r15/QB_A11_A08.xtc r16/QB_A11_A08.xtc r17/QB_A11_A08.xtc r18/QB_A11_A08.xtc r19/QB_A11_A08.xtc r2/QB_A11_A08.xtc r20/QB_A11_A08.xtc r21/QB_A11_A08.xtc r3/QB_A11_A08.xtc r4/QB_A11_A08.xtc r5/QB_A11_A08.xtc r6/QB_A11_A08.xtc r7/QB_A11_A08.xtc r8/QB_A11_A08.xtc r9/QB_A11_A08.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
2026-04-19 17:35:18 (69028): bin/bash exited; CPU time 25560.156985
2026-04-19 17:35:18 (69028): called boinc_finish(0)
</stderr_txt>
]]>
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