Task 38609878
| Name | MCL1_A27_A40_r0_3-QUICO_ATM_OpenFF_MCL1-3-6-RND1630_0 |
| Workunit | 31562868 |
| Created | 15 Apr 2026, 3:52:38 UTC |
| Sent | 15 Apr 2026, 3:52:54 UTC |
| Report deadline | 20 Apr 2026, 3:52:54 UTC |
| Received | 15 Apr 2026, 7:05:01 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 652033 |
| Run time | 33 min 18 sec |
| CPU time | 32 min 49 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 91,617.08 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 432.81 MB |
| Peak swap size | 11.61 GB |
| Peak disk usage | 2.90 GB |
Stderr output
<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-15 05:42:17 (8346): wrapper (8.1.26018): starting
2026-04-15 05:42:32 (8346): wrapper: running bin/python (bin/conda-unpack)
2026-04-15 05:42:32 (8346): wrapper: created child process 8350
2026-04-15 05:42:33 (8346): bin/python exited; CPU time 0.103267
2026-04-15 05:42:33 (8346): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-15 05:42:33 (8346): wrapper: created child process 8351
2026-04-15 05:42:34 (8346): bin/tar exited; CPU time 0.250619
2026-04-15 05:42:34 (8346): wrapper: running bin/bash (run.sh)
2026-04-15 05:42:34 (8346): wrapper: created child process 8353
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/1/bin
+++ dirname /var/lib/boinc/slots/1/bin
++ local full_path_env=/var/lib/boinc/slots/1
+++ basename /var/lib/boinc/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/1
++ CONDA_PREFIX=/var/lib/boinc/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/1:/var/lib/boinc/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/1:/var/lib/boinc/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/slots/1/tmp
+ TMP=/var/lib/boinc/slots/1/tmp
+ mkdir -p /var/lib/boinc/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/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_A27_A40_input.yaml
+ python bin/rbfe_production QB_A27_A40_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (14 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x42c050]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x758232245330]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x460884]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x44251e]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x45f5f0]
/lib/x86_64-linux-gnu/libc.so.6(+0x45330)[0x758232245330]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xbf)[0x7582322ecadf]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17)[0x7582322f9a27]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4c)[0x75823232975c]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x40b2e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x2a1ca)[0x75823222a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x75823222a28b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]
Exiting...
/var/lib/boinc/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 '
2026-04-15 06:31:14 (15841): wrapper (8.1.26018): starting
2026-04-15 06:31:14 (15841): wrapper: running bin/bash (run.sh)
2026-04-15 06:31:14 (15841): wrapper: created child process 15844
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/1/bin
+++ dirname /var/lib/boinc/slots/1/bin
++ local full_path_env=/var/lib/boinc/slots/1
+++ basename /var/lib/boinc/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/1
++ CONDA_PREFIX=/var/lib/boinc/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/1:/var/lib/boinc/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/1:/var/lib/boinc/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/slots/1/tmp
+ TMP=/var/lib/boinc/slots/1/tmp
+ mkdir -p /var/lib/boinc/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A27_A40_input.yaml
+ python bin/rbfe_production QB_A27_A40_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
/var/lib/boinc/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 '
2026-04-15 06:31:32 (18117): wrapper (8.1.26018): starting
2026-04-15 06:31:32 (18117): wrapper: running bin/bash (run.sh)
2026-04-15 06:31:32 (18117): wrapper: created child process 18120
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/1/bin
+++ dirname /var/lib/boinc/slots/1/bin
++ local full_path_env=/var/lib/boinc/slots/1
+++ basename /var/lib/boinc/slots/1
++ local env_name=1
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/1
++ CONDA_PREFIX=/var/lib/boinc/slots/1
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(1) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/1/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/1/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/1:/var/lib/boinc/slots/1/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/1:/var/lib/boinc/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/slots/1/tmp
+ TMP=/var/lib/boinc/slots/1/tmp
+ mkdir -p /var/lib/boinc/slots/1/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/1/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A27_A40_input.yaml
+ python bin/rbfe_production QB_A27_A40_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_A27_A40.out r1/QB_A27_A40.out r10/QB_A27_A40.out r11/QB_A27_A40.out r12/QB_A27_A40.out r13/QB_A27_A40.out r14/QB_A27_A40.out r15/QB_A27_A40.out r16/QB_A27_A40.out r17/QB_A27_A40.out r18/QB_A27_A40.out r19/QB_A27_A40.out r2/QB_A27_A40.out r20/QB_A27_A40.out r21/QB_A27_A40.out r3/QB_A27_A40.out r4/QB_A27_A40.out r5/QB_A27_A40.out r6/QB_A27_A40.out r7/QB_A27_A40.out r8/QB_A27_A40.out r9/QB_A27_A40.out r0/QB_A27_A40.xtc r1/QB_A27_A40.xtc r10/QB_A27_A40.xtc r11/QB_A27_A40.xtc r12/QB_A27_A40.xtc r13/QB_A27_A40.xtc r14/QB_A27_A40.xtc r15/QB_A27_A40.xtc r16/QB_A27_A40.xtc r17/QB_A27_A40.xtc r18/QB_A27_A40.xtc r19/QB_A27_A40.xtc r2/QB_A27_A40.xtc r20/QB_A27_A40.xtc r21/QB_A27_A40.xtc r3/QB_A27_A40.xtc r4/QB_A27_A40.xtc r5/QB_A27_A40.xtc r6/QB_A27_A40.xtc r7/QB_A27_A40.xtc r8/QB_A27_A40.xtc r9/QB_A27_A40.xtc
tar: run.log: file changed as we read it
+ true
+ echo 'Save restart'
+ tar cjvf restart.tar.bz2 r0/checkpoint.xml r1/checkpoint.xml r10/checkpoint.xml r11/checkpoint.xml r12/checkpoint.xml r13/checkpoint.xml r14/checkpoint.xml r15/checkpoint.xml r16/checkpoint.xml r17/checkpoint.xml r18/checkpoint.xml r19/checkpoint.xml r2/checkpoint.xml r20/checkpoint.xml r21/checkpoint.xml r3/checkpoint.xml r4/checkpoint.xml r5/checkpoint.xml r6/checkpoint.xml r7/checkpoint.xml r8/checkpoint.xml r9/checkpoint.xml
2026-04-15 07:04:50 (18117): bin/bash exited; CPU time 1968.753696
2026-04-15 07:04:50 (18117): called boinc_finish(0)
</stderr_txt>
]]>
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