Task 38676999
| Name | test_275-GPUGRID_TEST_ATM_40STEP_20261023-15-40-RND3284_0 |
| Workunit | 31618886 |
| Created | 26 Oct 2026, 12:56:55 UTC |
| Sent | 26 Oct 2026, 12:56:59 UTC |
| Report deadline | 31 Oct 2026, 12:56:59 UTC |
| Received | 26 Oct 2026, 13:32:35 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 652821 |
| Run time | 16 min 21 sec |
| CPU time | 16 min 21 sec |
| Validate state | Valid |
| Credit | 60,000.00 |
| Device peak FLOPS | 41,936.43 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 628.45 MB |
| Peak swap size | 36.47 GB |
| Peak disk usage | 3.01 GB |
Stderr output
<core_client_version>8.2.15</core_client_version>
<![CDATA[
<stderr_txt>
2026-10-26 09:02:28 (632405): wrapper (8.1.26018): starting
2026-10-26 09:02:47 (632405): wrapper: running bin/python (bin/conda-unpack)
2026-10-26 09:02:47 (632405): wrapper: created child process 632767
2026-10-26 09:02:48 (632405): bin/python exited; CPU time 0.167375
2026-10-26 09:02:48 (632405): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-10-26 09:02:48 (632405): wrapper: created child process 632768
2026-10-26 09:02:49 (632405): bin/tar exited; CPU time 0.593092
2026-10-26 09:02:49 (632405): wrapper: running bin/bash (run.sh)
2026-10-26 09:02:49 (632405): wrapper: created child process 632770
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/13/bin
+++ dirname /var/lib/boinc/slots/13/bin
++ local full_path_env=/var/lib/boinc/slots/13
+++ basename /var/lib/boinc/slots/13
++ local env_name=13
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/13
++ CONDA_PREFIX=/var/lib/boinc/slots/13
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(13) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/13/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/13/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/13/tmp
+ TMP=/var/lib/boinc/slots/13/tmp
+ mkdir -p /var/lib/boinc/slots/13/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/slots/13/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample does not exist.'
+ echo 'Install ATM and deps'
+ python -m pip list
+ python -m pip install pyaml==26.2.1 -v
+ python -m pip install --no-dependencies atom-openmm==8.4.0 -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-10-26 09:03:19 (634146): wrapper (8.1.26018): starting
2026-10-26 09:03:19 (634146): wrapper: running bin/bash (run.sh)
2026-10-26 09:03:19 (634146): wrapper: created child process 634148
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/13/bin
+++ dirname /var/lib/boinc/slots/13/bin
++ local full_path_env=/var/lib/boinc/slots/13
+++ basename /var/lib/boinc/slots/13
++ local env_name=13
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/13
++ CONDA_PREFIX=/var/lib/boinc/slots/13
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(13) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/13/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/13/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/13/tmp
+ TMP=/var/lib/boinc/slots/13/tmp
+ mkdir -p /var/lib/boinc/slots/13/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/slots/13/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_A12_input.yaml
/var/lib/boinc/slots/13/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 '
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-10-26 09:03:41 (634852): wrapper (8.1.26018): starting
2026-10-26 09:03:41 (634852): wrapper: running bin/bash (run.sh)
2026-10-26 09:03:41 (634852): wrapper: created child process 634857
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/13/bin
+++ dirname /var/lib/boinc/slots/13/bin
++ local full_path_env=/var/lib/boinc/slots/13
+++ basename /var/lib/boinc/slots/13
++ local env_name=13
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/13
++ CONDA_PREFIX=/var/lib/boinc/slots/13
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(13) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/13/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/13/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/13/tmp
+ TMP=/var/lib/boinc/slots/13/tmp
+ mkdir -p /var/lib/boinc/slots/13/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/slots/13/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_A12_input.yaml
/var/lib/boinc/slots/13/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 '
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-10-26 09:16:32 (646726): wrapper (8.1.26018): starting
2026-10-26 09:16:32 (646726): wrapper: running bin/bash (run.sh)
2026-10-26 09:16:32 (646726): wrapper: created child process 646728
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/13/bin
+++ dirname /var/lib/boinc/slots/13/bin
++ local full_path_env=/var/lib/boinc/slots/13
+++ basename /var/lib/boinc/slots/13
++ local env_name=13
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/13
++ CONDA_PREFIX=/var/lib/boinc/slots/13
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(13) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/13/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/13/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/13:/var/lib/boinc/slots/13/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/13/tmp
+ TMP=/var/lib/boinc/slots/13/tmp
+ mkdir -p /var/lib/boinc/slots/13/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/13/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_A12_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
+ echo 'Save output'
+ tar cjvf output.tar.bz2 run.log stderr.txt r0/QB_A34_A12.out r1/QB_A34_A12.out r10/QB_A34_A12.out r11/QB_A34_A12.out r12/QB_A34_A12.out r13/QB_A34_A12.out r14/QB_A34_A12.out r15/QB_A34_A12.out r16/QB_A34_A12.out r17/QB_A34_A12.out r18/QB_A34_A12.out r19/QB_A34_A12.out r2/QB_A34_A12.out r20/QB_A34_A12.out r21/QB_A34_A12.out r3/QB_A34_A12.out r4/QB_A34_A12.out r5/QB_A34_A12.out r6/QB_A34_A12.out r7/QB_A34_A12.out r8/QB_A34_A12.out r9/QB_A34_A12.out 'r*/*.dcd' 'r*/*.xtc'
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: r*/*.xtc: 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/checkpoint.xml
2026-10-26 09:32:02 (646726): bin/bash exited; CPU time 968.801396
2026-10-26 09:32:02 (646726): called boinc_finish(0)
</stderr_txt>
]]>
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