Task 38641934
| Name | shp2_A21_A16_r0_3-QUICO_ATM_GAFF2_NAGL_shp2-5-6-RND4830_1 |
| Workunit | 31588837 |
| Created | 3 May 2026, 13:44:10 UTC |
| Sent | 3 May 2026, 13:44:12 UTC |
| Report deadline | 8 May 2026, 13:44:12 UTC |
| Received | 8 May 2026, 14:51:36 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 649995 |
| Run time | 1 min 13 sec |
| CPU time | 30 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 6,641.18 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 632.52 MB |
| Peak swap size | 3.43 GB |
| Peak disk usage | 1.44 GB |
Stderr output
<core_client_version>8.2.12</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
2026-05-03 15:50:48 (318): wrapper (8.1.26018): starting
2026-05-03 15:51:20 (318): wrapper: running bin/python (bin/conda-unpack)
2026-05-03 15:51:20 (318): wrapper: created child process 320
2026-05-03 15:51:21 (318): bin/python exited; CPU time 0.177253
2026-05-03 15:51:21 (318): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-05-03 15:51:21 (318): wrapper: created child process 321
2026-05-03 15:51:24 (318): bin/tar exited; CPU time 2.059682
2026-05-03 15:51:24 (318): wrapper: running bin/bash (run.sh)
2026-05-03 15:51:24 (318): wrapper: created child process 323
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample does not exist.'
+ echo 'Install ATM and deps'
+ python -m pip list
+ python -m pip install pyaml -v
+ python -m pip install --no-dependencies atom-openmm -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-04 00:04:37 (105): wrapper (8.1.26018): starting
2026-05-04 00:04:37 (105): wrapper: running bin/bash (run.sh)
2026-05-04 00:04:37 (105): wrapper: created child process 110
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-04 00:04:47 (105): BOINC client no longer exists - exiting
2026-05-04 00:04:47 (105): timer handler: client dead, exiting
/var/home/Migs/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 '
2026-05-04 06:15:31 (104): wrapper (8.1.26018): starting
2026-05-04 06:15:31 (104): wrapper: running bin/bash (run.sh)
2026-05-04 06:15:31 (104): wrapper: created child process 111
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-04 17:04:08 (104): wrapper (8.1.26018): starting
2026-05-04 17:04:08 (104): wrapper: running bin/bash (run.sh)
2026-05-04 17:04:08 (104): wrapper: created child process 112
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-04 21:38:29 (104): wrapper (8.1.26018): starting
2026-05-04 21:38:29 (104): wrapper: running bin/bash (run.sh)
2026-05-04 21:38:29 (104): wrapper: created child process 112
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-05 06:15:57 (104): wrapper (8.1.26018): starting
2026-05-05 06:15:57 (104): wrapper: running bin/bash (run.sh)
2026-05-05 06:15:57 (104): wrapper: created child process 110
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/home/Migs/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 '
2026-05-05 22:03:53 (104): wrapper (8.1.26018): starting
2026-05-05 22:03:53 (104): wrapper: running bin/bash (run.sh)
2026-05-05 22:03:53 (104): wrapper: created child process 110
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-06 17:22:00 (104): wrapper (8.1.26018): starting
2026-05-06 17:22:00 (104): wrapper: running bin/bash (run.sh)
2026-05-06 17:22:00 (104): wrapper: created child process 108
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-06 23:17:27 (104): wrapper (8.1.26018): starting
2026-05-06 23:17:27 (104): wrapper: running bin/bash (run.sh)
2026-05-06 23:17:27 (104): wrapper: created child process 109
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/home/Migs/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 '
2026-05-07 21:04:34 (104): wrapper (8.1.26018): starting
2026-05-07 21:04:34 (104): wrapper: running bin/bash (run.sh)
2026-05-07 21:04:34 (104): wrapper: created child process 109
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-05-07 23:16:06 (104): wrapper (8.1.26018): starting
2026-05-07 23:16:06 (104): wrapper: running bin/bash (run.sh)
2026-05-07 23:16:06 (104): wrapper: created child process 109
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/home/Migs/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 '
2026-05-08 16:49:36 (104): wrapper (8.1.26018): starting
2026-05-08 16:49:36 (104): wrapper: running bin/bash (run.sh)
2026-05-08 16:49:36 (104): wrapper: created child process 111
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/home/Migs/slots/1/bin
+++ dirname /var/home/Migs/slots/1/bin
++ local full_path_env=/var/home/Migs/slots/1
+++ basename /var/home/Migs/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/home/Migs/slots/1
++ CONDA_PREFIX=/var/home/Migs/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/home/Migs/slots/1/etc/conda/activate.d
++ '[' -d /var/home/Migs/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/home/Migs/slots/1:/var/home/Migs/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/home/Migs/slots/1/tmp
+ TMP=/var/home/Migs/slots/1/tmp
+ mkdir -p /var/home/Migs/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/home/Migs/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A21_A16_input.yaml
+ python bin/rbfe_production QB_A21_A16_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Traceback (most recent call last):
File "/var/home/Migs/slots/1/bin/rbfe_production", line 8, in <module>
sys.exit(rbfe_production())
^^^^^^^^^^^^^^^^^
File "/var/home/Migs/slots/1/lib/python3.11/site-packages/atom_openmm/rbfe_production.py", line 29, in rbfe_production
rx = openmm_job_RBFE(
^^^^^^^^^^^^^^^^
File "/var/home/Migs/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/home/Migs/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 53, in __init__
self.start_worker()
File "/var/home/Migs/slots/1/lib/python3.11/site-packages/atom_openmm/ommworker.py", line 444, in start_worker
self._openmm_worker_makecontext()
File "/var/home/Migs/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/home/Migs/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/home/Migs/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 loading CUDA module: CUDA_ERROR_JIT_COMPILER_NOT_FOUND (221)
2026-05-08 16:50:11 (104): bin/bash exited; CPU time 32.086490
2026-05-08 16:50:11 (104): app exit status: 0x1
2026-05-08 16:50:11 (104): called boinc_finish(195)
</stderr_txt>
]]>
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