Task 38601608
| Name | PTP1B_A07_A17_r0_3-QUICO_ATM_GAFF2_NAGL_PTP1B-1-6-RND8968_0 |
| Workunit | 31556137 |
| Created | 9 Apr 2026, 15:29:36 UTC |
| Sent | 9 Apr 2026, 15:29:54 UTC |
| Report deadline | 14 Apr 2026, 15:29:54 UTC |
| Received | 10 Apr 2026, 6:55:24 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 651702 |
| Run time | 3 hours 24 min 43 sec |
| CPU time | 3 hours 24 min 43 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 19,300.93 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 544.39 MB |
| Peak swap size | 32.64 GB |
| Peak disk usage | 2.99 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
t/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 22:53:24 (78557): wrapper (8.1.26018): starting
2026-04-09 22:53:24 (78557): wrapper: running bin/bash (run.sh)
2026-04-09 22:53:24 (78557): wrapper: created child process 78559
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 23:04:34 (79358): wrapper (8.1.26018): starting
2026-04-09 23:04:34 (79358): wrapper: running bin/bash (run.sh)
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
2026-04-09 23:04:34 (79358): wrapper: created child process 79360
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 23:15:18 (80163): wrapper (8.1.26018): starting
2026-04-09 23:15:18 (80163): wrapper: running bin/bash (run.sh)
2026-04-09 23:15:18 (80163): wrapper: created child process 80165
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 23:22:54 (80747): wrapper (8.1.26018): starting
2026-04-09 23:22:54 (80747): wrapper: running bin/bash (run.sh)
2026-04-09 23:22:54 (80747): wrapper: created child process 80749
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 23:31:25 (81399): wrapper (8.1.26018): starting
2026-04-09 23:31:25 (81399): wrapper: running bin/bash (run.sh)
2026-04-09 23:31:25 (81399): wrapper: created child process 81401
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 23:42:39 (82201): wrapper (8.1.26018): starting
2026-04-09 23:42:39 (82201): wrapper: running bin/bash (run.sh)
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
2026-04-09 23:42:39 (82201): wrapper: created child process 82203
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-09 23:58:17 (83217): wrapper (8.1.26018): starting
2026-04-09 23:58:17 (83217): wrapper: running bin/bash (run.sh)
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
2026-04-09 23:58:17 (83217): wrapper: created child process 83219
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 00:09:13 (84047): wrapper (8.1.26018): starting
2026-04-10 00:09:13 (84047): wrapper: running bin/bash (run.sh)
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
2026-04-10 00:09:13 (84047): wrapper: created child process 84049
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 00:23:31 (85000): wrapper (8.1.26018): starting
2026-04-10 00:23:31 (85000): wrapper: running bin/bash (run.sh)
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
2026-04-10 00:23:31 (85000): wrapper: created child process 85002
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 00:30:14 (85561): wrapper (8.1.26018): starting
2026-04-10 00:30:14 (85561): wrapper: running bin/bash (run.sh)
2026-04-10 00:30:14 (85561): wrapper: created child process 85563
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 00:37:28 (86140): wrapper (8.1.26018): starting
2026-04-10 00:37:28 (86140): wrapper: running bin/bash (run.sh)
2026-04-10 00:37:28 (86140): wrapper: created child process 86142
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 00:48:56 (86925): wrapper (8.1.26018): starting
2026-04-10 00:48:56 (86925): wrapper: running bin/bash (run.sh)
2026-04-10 00:48:56 (86925): wrapper: created child process 86927
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 00:58:04 (87664): wrapper (8.1.26018): starting
2026-04-10 00:58:04 (87664): wrapper: running bin/bash (run.sh)
2026-04-10 00:58:04 (87664): wrapper: created child process 87666
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 01:16:45 (88908): wrapper (8.1.26018): starting
2026-04-10 01:16:45 (88908): wrapper: running bin/bash (run.sh)
2026-04-10 01:16:45 (88908): wrapper: created child process 88910
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 01:25:32 (89559): wrapper (8.1.26018): starting
2026-04-10 01:25:32 (89559): wrapper: running bin/bash (run.sh)
2026-04-10 01:25:32 (89559): wrapper: created child process 89561
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 01:36:08 (90354): wrapper (8.1.26018): starting
2026-04-10 01:36:08 (90354): wrapper: running bin/bash (run.sh)
2026-04-10 01:36:08 (90354): wrapper: created child process 90356
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 01:52:21 (91403): wrapper (8.1.26018): starting
2026-04-10 01:52:21 (91403): wrapper: running bin/bash (run.sh)
2026-04-10 01:52:21 (91403): wrapper: created child process 91405
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 02:00:04 (92749): wrapper (8.1.26018): starting
2026-04-10 02:00:04 (92749): wrapper: running bin/bash (run.sh)
2026-04-10 02:00:04 (92749): wrapper: created child process 92752
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 02:00:05 (3484): wrapper (8.1.26018): starting
2026-04-10 02:00:05 (3484): wrapper: running bin/bash (run.sh)
2026-04-10 02:00:05 (3484): wrapper: created child process 3499
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 02:03:41 (4472): wrapper (8.1.26018): starting
2026-04-10 02:03:41 (4472): wrapper: running bin/bash (run.sh)
2026-04-10 02:03:41 (4472): wrapper: created child process 4474
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 02:13:29 (5198): wrapper (8.1.26018): starting
2026-04-10 02:13:29 (5198): wrapper: running bin/bash (run.sh)
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
2026-04-10 02:13:29 (5198): wrapper: created child process 5200
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 02:33:24 (6508): wrapper (8.1.26018): starting
2026-04-10 02:33:24 (6508): wrapper: running bin/bash (run.sh)
2026-04-10 02:33:24 (6508): wrapper: created child process 6510
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 02:40:39 (7057): wrapper (8.1.26018): starting
2026-04-10 02:40:39 (7057): wrapper: running bin/bash (run.sh)
2026-04-10 02:40:39 (7057): wrapper: created child process 7059
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/12/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 '
2026-04-10 02:52:01 (7902): wrapper (8.1.26018): starting
2026-04-10 02:52:01 (7902): wrapper: running bin/bash (run.sh)
2026-04-10 02:52:01 (7902): wrapper: created child process 7904
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 03:03:40 (8756): wrapper (8.1.26018): starting
2026-04-10 03:03:40 (8756): wrapper: running bin/bash (run.sh)
2026-04-10 03:03:40 (8756): wrapper: created child process 8758
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 03:20:16 (9915): wrapper (8.1.26018): starting
2026-04-10 03:20:16 (9915): wrapper: running bin/bash (run.sh)
2026-04-10 03:20:16 (9915): wrapper: created child process 9917
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 03:30:08 (10671): wrapper (8.1.26018): starting
2026-04-10 03:30:08 (10671): wrapper: running bin/bash (run.sh)
2026-04-10 03:30:08 (10671): wrapper: created child process 10673
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 03:56:47 (12307): wrapper (8.1.26018): starting
2026-04-10 03:56:47 (12307): wrapper: running bin/bash (run.sh)
2026-04-10 03:56:47 (12307): wrapper: created child process 12309
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 04:08:09 (13123): wrapper (8.1.26018): starting
2026-04-10 04:08:09 (13123): wrapper: running bin/bash (run.sh)
2026-04-10 04:08:09 (13123): wrapper: created child process 13125
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/12/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 '
2026-04-10 04:20:17 (13937): wrapper (8.1.26018): starting
2026-04-10 04:20:17 (13937): wrapper: running bin/bash (run.sh)
2026-04-10 04:20:17 (13937): wrapper: created child process 13939
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-10 04:27:37 (14524): wrapper (8.1.26018): starting
2026-04-10 04:27:37 (14524): wrapper: running bin/bash (run.sh)
2026-04-10 04:27:37 (14524): wrapper: created child process 14526
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/12/bin
+++ dirname /var/lib/boinc-client/slots/12/bin
++ local full_path_env=/var/lib/boinc-client/slots/12
+++ basename /var/lib/boinc-client/slots/12
++ local env_name=12
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ CONDA_PREFIX=/var/lib/boinc-client/slots/12
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(12) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/12/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/12/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/12:/var/lib/boinc-client/slots/12/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/12/tmp
+ TMP=/var/lib/boinc-client/slots/12/tmp
+ mkdir -p /var/lib/boinc-client/slots/12/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/12/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A17_input.yaml
+ python bin/rbfe_production QB_A07_A17_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_A07_A17.out r1/QB_A07_A17.out r10/QB_A07_A17.out r11/QB_A07_A17.out r12/QB_A07_A17.out r13/QB_A07_A17.out r14/QB_A07_A17.out r15/QB_A07_A17.out r16/QB_A07_A17.out r17/QB_A07_A17.out r18/QB_A07_A17.out r19/QB_A07_A17.out r2/QB_A07_A17.out r20/QB_A07_A17.out r21/QB_A07_A17.out r3/QB_A07_A17.out r4/QB_A07_A17.out r5/QB_A07_A17.out r6/QB_A07_A17.out r7/QB_A07_A17.out r8/QB_A07_A17.out r9/QB_A07_A17.out 'r*/*.dcd' r0/QB_A07_A17.xtc r1/QB_A07_A17.xtc r10/QB_A07_A17.xtc r11/QB_A07_A17.xtc r12/QB_A07_A17.xtc r13/QB_A07_A17.xtc r14/QB_A07_A17.xtc r15/QB_A07_A17.xtc r16/QB_A07_A17.xtc r17/QB_A07_A17.xtc r18/QB_A07_A17.xtc r19/QB_A07_A17.xtc r2/QB_A07_A17.xtc r20/QB_A07_A17.xtc r21/QB_A07_A17.xtc r3/QB_A07_A17.xtc r4/QB_A07_A17.xtc r5/QB_A07_A17.xtc r6/QB_A07_A17.xtc r7/QB_A07_A17.xtc r8/QB_A07_A17.xtc r9/QB_A07_A17.xtc
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
+ 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/che
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