Task 38635426
| Name | shp2_A20_A10_r0_5-QUICO_ATM_GAFF2_NAGL_shp2-0-6-RND9557_0 |
| Workunit | 31583882 |
| Created | 28 Apr 2026, 13:12:37 UTC |
| Sent | 28 Apr 2026, 13:19:02 UTC |
| Report deadline | 3 May 2026, 13:19:02 UTC |
| Received | 29 Apr 2026, 13:25:28 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 638919 |
| Run time | 4 hours 18 min 18 sec |
| CPU time | 4 hours 18 min 18 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 35,583.79 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 829.18 MB |
| Peak swap size | 67.27 GB |
| Peak disk usage | 3.13 GB |
Stderr output
<core_client_version>8.2.5</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-28 15:21:13 (165942): wrapper (8.1.26018): starting
2026-04-28 15:21:41 (165942): wrapper: running bin/python (bin/conda-unpack)
2026-04-28 15:21:41 (165942): wrapper: created child process 166352
2026-04-28 15:21:42 (165942): bin/python exited; CPU time 0.227365
2026-04-28 15:21:42 (165942): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-28 15:21:42 (165942): wrapper: created child process 166367
2026-04-28 15:21:46 (165942): bin/tar exited; CPU time 2.949625
2026-04-28 15:21:46 (165942): wrapper: running bin/bash (run.sh)
2026-04-28 15:21:46 (165942): wrapper: created child process 166426
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/7/bin
+++ dirname /var/lib/boinc/slots/7/bin
++ local full_path_env=/var/lib/boinc/slots/7
+++ basename /var/lib/boinc/slots/7
++ local env_name=7
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/7
++ CONDA_PREFIX=/var/lib/boinc/slots/7
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(7) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/7/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/7/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/7:/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/7:/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/7/tmp
+ TMP=/var/lib/boinc/slots/7/tmp
+ mkdir -p /var/lib/boinc/slots/7/tmp
+ echo 'Configure AToM'
+ echo localhost,0:4,1,CUDA,,/var/lib/boinc/slots/7/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_A20_A10_input.yaml
+ python bin/rbfe_production QB_A20_A10_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (13 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x42c050]
/lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x759a3e842520]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x463138]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x45f5d5]
/lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x759a3e842520]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xc8)[0x759a3e8e57f8]
/lib/x86_64-linux-gnu/libc.so.6(__nanosleep+0x17)[0x759a3e8ea677]
/lib/x86_64-linux-gnu/libc.so.6(sleep+0x3e)[0x759a3e8ea5ae]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x43987a]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x40b2e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x759a3e829d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x759a3e829e40]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]
Exiting...
/var/lib/boinc/slots/7/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 11:12:18 (3919): wrapper (8.1.26018): starting
2026-04-29 11:12:18 (3919): wrapper: running bin/bash (run.sh)
2026-04-29 11:12:18 (3919): wrapper: created child process 3941
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/7/bin
+++ dirname /var/lib/boinc/slots/7/bin
++ local full_path_env=/var/lib/boinc/slots/7
+++ basename /var/lib/boinc/slots/7
++ local env_name=7
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/7
++ CONDA_PREFIX=/var/lib/boinc/slots/7
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(7) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/7/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/7/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/7:/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/7:/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/7/tmp
+ TMP=/var/lib/boinc/slots/7/tmp
+ mkdir -p /var/lib/boinc/slots/7/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc/slots/7/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A10_input.yaml
+ python bin/rbfe_production QB_A20_A10_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
2026-04-29 11:16:20 (8125): wrapper (8.1.26018): starting
2026-04-29 11:16:20 (8125): wrapper: running bin/bash (run.sh)
2026-04-29 11:16:20 (8125): wrapper: created child process 8127
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/7/bin
+++ dirname /var/lib/boinc/slots/7/bin
++ local full_path_env=/var/lib/boinc/slots/7
+++ basename /var/lib/boinc/slots/7
++ local env_name=7
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/7
++ CONDA_PREFIX=/var/lib/boinc/slots/7
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(7) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/7/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/7/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/7:/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/7:/var/lib/boinc/slots/7/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/7/tmp
+ TMP=/var/lib/boinc/slots/7/tmp
+ mkdir -p /var/lib/boinc/slots/7/tmp
+ echo 'Configure AToM'
+ echo localhost,0:3,1,CUDA,,/var/lib/boinc/slots/7/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A20_A10_input.yaml
+ python bin/rbfe_production QB_A20_A10_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_A20_A10.out r1/QB_A20_A10.out r10/QB_A20_A10.out r11/QB_A20_A10.out r12/QB_A20_A10.out r13/QB_A20_A10.out r14/QB_A20_A10.out r15/QB_A20_A10.out r16/QB_A20_A10.out r17/QB_A20_A10.out r18/QB_A20_A10.out r19/QB_A20_A10.out r2/QB_A20_A10.out r20/QB_A20_A10.out r21/QB_A20_A10.out r3/QB_A20_A10.out r4/QB_A20_A10.out r5/QB_A20_A10.out r6/QB_A20_A10.out r7/QB_A20_A10.out r8/QB_A20_A10.out r9/QB_A20_A10.out r0/QB_A20_A10.xtc r1/QB_A20_A10.xtc r10/QB_A20_A10.xtc r11/QB_A20_A10.xtc r12/QB_A20_A10.xtc r13/QB_A20_A10.xtc r14/QB_A20_A10.xtc r15/QB_A20_A10.xtc r16/QB_A20_A10.xtc r17/QB_A20_A10.xtc r18/QB_A20_A10.xtc r19/QB_A20_A10.xtc r2/QB_A20_A10.xtc r20/QB_A20_A10.xtc r21/QB_A20_A10.xtc r3/QB_A20_A10.xtc r4/QB_A20_A10.xtc r5/QB_A20_A10.xtc r6/QB_A20_A10.xtc r7/QB_A20_A10.xtc r8/QB_A20_A10.xtc r9/QB_A20_A10.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
2026-04-29 15:25:14 (8125): bin/bash exited; CPU time 15279.281514
2026-04-29 15:25:14 (8125): called boinc_finish(0)
</stderr_txt>
]]>
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