Task 38635571
| Name | cdk8_A22_A12_r0_2-QUICO_ATM_OpenFF23_NAGL_cdk8-4-6-RND3201_1 |
| Workunit | 31579232 |
| Created | 28 Apr 2026, 14:18:53 UTC |
| Sent | 28 Apr 2026, 14:18:54 UTC |
| Report deadline | 3 May 2026, 14:18:54 UTC |
| Received | 30 Apr 2026, 2:42:53 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 652251 |
| Run time | 54 sec |
| CPU time | 43 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 15,398.30 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 743.05 MB |
| Peak swap size | 3.64 GB |
| Peak disk usage | 1.45 GB |
Stderr output
<core_client_version>8.2.5</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 06:47:38 (53625): wrapper (8.1.26018): starting
2026-04-29 06:47:38 (53625): wrapper: running bin/bash (run.sh)
2026-04-29 06:47:38 (53625): wrapper: created child process 53627
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 06:51:54 (53851): wrapper (8.1.26018): starting
2026-04-29 06:51:54 (53851): wrapper: running bin/bash (run.sh)
2026-04-29 06:51:54 (53851): wrapper: created child process 53853
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 07:00:31 (54217): wrapper (8.1.26018): starting
2026-04-29 07:00:31 (54217): wrapper: running bin/bash (run.sh)
2026-04-29 07:00:31 (54217): wrapper: created child process 54219
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 07:08:21 (54550): wrapper (8.1.26018): starting
2026-04-29 07:08:21 (54550): wrapper: running bin/bash (run.sh)
2026-04-29 07:08:21 (54550): wrapper: created child process 54552
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 07:17:22 (54926): wrapper (8.1.26018): starting
2026-04-29 07:17:22 (54926): wrapper: running bin/bash (run.sh)
2026-04-29 07:17:22 (54926): wrapper: created child process 54928
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 07:46:54 (56148): wrapper (8.1.26018): starting
2026-04-29 07:46:54 (56148): wrapper: running bin/bash (run.sh)
2026-04-29 07:46:54 (56148): wrapper: created child process 56150
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 09:53:11 (60572): wrapper (8.1.26018): starting
2026-04-29 09:53:11 (60572): wrapper: running bin/bash (run.sh)
2026-04-29 09:53:11 (60572): wrapper: created child process 60574
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 10:45:13 (62538): wrapper (8.1.26018): starting
2026-04-29 10:45:13 (62538): wrapper: running bin/bash (run.sh)
2026-04-29 10:45:13 (62538): wrapper: created child process 62540
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 11:11:56 (63557): wrapper (8.1.26018): starting
2026-04-29 11:11:56 (63557): wrapper: running bin/bash (run.sh)
2026-04-29 11:11:56 (63557): wrapper: created child process 63559
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/1/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 '
2026-04-29 12:31:52 (69228): wrapper (8.1.26018): starting
2026-04-29 12:31:52 (69228): wrapper: running bin/bash (run.sh)
2026-04-29 12:31:52 (69228): wrapper: created child process 69230
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 13:34:55 (73151): wrapper (8.1.26018): starting
2026-04-29 13:34:55 (73151): wrapper: running bin/bash (run.sh)
2026-04-29 13:34:55 (73151): wrapper: created child process 73153
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/1/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 '
2026-04-29 14:47:25 (77523): wrapper (8.1.26018): starting
2026-04-29 14:47:25 (77523): wrapper: running bin/bash (run.sh)
2026-04-29 14:47:25 (77523): wrapper: created child process 77525
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 16:10:40 (82558): wrapper (8.1.26018): starting
2026-04-29 16:10:40 (82558): wrapper: running bin/bash (run.sh)
2026-04-29 16:10:40 (82558): wrapper: created child process 82560
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 16:24:21 (86270): wrapper (8.1.26018): starting
2026-04-29 16:24:21 (86270): wrapper: running bin/bash (run.sh)
2026-04-29 16:24:21 (86270): wrapper: created child process 86272
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 16:41:19 (89445): wrapper (8.1.26018): starting
2026-04-29 16:41:19 (89445): wrapper: running bin/bash (run.sh)
2026-04-29 16:41:19 (89445): wrapper: created child process 89447
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 17:41:43 (97377): wrapper (8.1.26018): starting
2026-04-29 17:41:43 (97377): wrapper: running bin/bash (run.sh)
2026-04-29 17:41:43 (97377): wrapper: created child process 97379
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 18:26:56 (100179): wrapper (8.1.26018): starting
2026-04-29 18:26:56 (100179): wrapper: running bin/bash (run.sh)
2026-04-29 18:26:56 (100179): wrapper: created child process 100181
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 19:25:50 (112825): wrapper (8.1.26018): starting
2026-04-29 19:25:50 (112825): wrapper: running bin/bash (run.sh)
2026-04-29 19:25:50 (112825): wrapper: created child process 112827
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/1/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 '
2026-04-29 19:33:21 (113584): wrapper (8.1.26018): starting
2026-04-29 19:33:21 (113584): wrapper: running bin/bash (run.sh)
2026-04-29 19:33:21 (113584): wrapper: created child process 113586
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 19:39:28 (114111): wrapper (8.1.26018): starting
2026-04-29 19:39:28 (114111): wrapper: running bin/bash (run.sh)
2026-04-29 19:39:28 (114111): wrapper: created child process 114113
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 19:53:33 (116228): wrapper (8.1.26018): starting
2026-04-29 19:53:33 (116228): wrapper: running bin/bash (run.sh)
2026-04-29 19:53:33 (116228): wrapper: created child process 116230
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 20:16:15 (133382): wrapper (8.1.26018): starting
2026-04-29 20:16:15 (133382): wrapper: running bin/bash (run.sh)
2026-04-29 20:16:15 (133382): wrapper: created child process 133384
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 20:40:56 (306273): wrapper (8.1.26018): starting
2026-04-29 20:40:56 (306273): wrapper: running bin/bash (run.sh)
2026-04-29 20:40:56 (306273): wrapper: created child process 306280
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 21:00:48 (454408): wrapper (8.1.26018): starting
2026-04-29 21:00:48 (454408): wrapper: running bin/bash (run.sh)
2026-04-29 21:00:48 (454408): wrapper: created child process 454410
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 21:08:26 (455115): wrapper (8.1.26018): starting
2026-04-29 21:08:26 (455115): wrapper: running bin/bash (run.sh)
2026-04-29 21:08:26 (455115): wrapper: created child process 455117
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 21:19:49 (536923): wrapper (8.1.26018): starting
2026-04-29 21:19:49 (536923): wrapper: running bin/bash (run.sh)
2026-04-29 21:19:49 (536923): wrapper: created child process 536925
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 21:24:19 (583160): wrapper (8.1.26018): starting
2026-04-29 21:24:19 (583160): wrapper: running bin/bash (run.sh)
2026-04-29 21:24:19 (583160): wrapper: created child process 583167
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc-client/slots/1/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 '
2026-04-29 21:54:55 (52162): wrapper (8.1.26018): starting
2026-04-29 21:54:55 (52162): wrapper: running bin/bash (run.sh)
2026-04-29 21:54:55 (52162): wrapper: created child process 52164
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/lib/boinc-client/slots/1/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
rx = openmm_job_RBFE(
^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 443, in __init__
self.openmm_workers.append(ommworkercls(self.basename, ommsys, self.keywords, node_info = node, compute = True, logger = self.logger))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
self.start_worker()
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 444, in start_worker
self._openmm_worker_makecontext()
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 251, in _openmm_worker_makecontext
self.simulation = Simulation(self.topology, self.system, self.integrator, self.platform, self.platform_properties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/openmm/app/simulation.py", line 106, in __init__
self.context = mm.Context(self.system, self.integrator, platform, platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/openmm/openmm.py", line 15566, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_COMPAT_NOT_SUPPORTED_ON_DEVICE (804) at /home/conda/feedstock_root/build_artifacts/openmm_1731111931527/work/platforms/cuda/src/CudaContext.cpp:92
2026-04-29 21:56:58 (52162): bin/bash exited; CPU time 36.539890
2026-04-29 21:56:58 (52162): app exit status: 0x1
2026-04-29 21:56:58 (52162): called boinc_finish(195)
2026-04-29 22:14:41 (84569): wrapper (8.1.26018): starting
2026-04-29 22:14:41 (84569): wrapper: running bin/bash (run.sh)
2026-04-29 22:14:41 (84569): wrapper: created child process 84571
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/1/bin
+++ dirname /var/lib/boinc-client/slots/1/bin
++ local full_path_env=/var/lib/boinc-client/slots/1
+++ basename /var/lib/boinc-client/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ CONDA_PREFIX=/var/lib/boinc-client/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/1:/var/lib/boinc-client/slots/1/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/1/tmp
+ TMP=/var/lib/boinc-client/slots/1/tmp
+ mkdir -p /var/lib/boinc-client/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A22_A12_input.yaml
+ python bin/rbfe_production QB_A22_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/lib/boinc-client/slots/1/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
rx = openmm_job_RBFE(
^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/openmm_async_re.py", line 443, in __init__
self.openmm_workers.append(ommworkercls(self.basename, ommsys, self.keywords, node_info = node, compute = True, logger = self.logger))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
self.start_worker()
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 444, in start_worker
self._openmm_worker_makecontext()
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 251, in _openmm_worker_makecontext
self.simulation = Simulation(self.topology, self.system, self.integrator, self.platform, self.platform_properties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/openmm/app/simulation.py", line 106, in __init__
self.context = mm.Context(self.system, self.integrator, platform, platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/lib/boinc-client/slots/1/lib/python3.11/site-packages/openmm/openmm.py", line 15566, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_COMPAT_NOT_SUPPORTED_ON_DEVICE (804) at /home/conda/feedstock_root/build_artifacts/openmm_1731111931527/work/platforms/cuda/src/CudaContext.cpp:92
2026-04-29 22:15:22 (84569): b
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