Task 38602846
| Name | JNK1_A01_A08_r0_4-QUICO_ATM_GAFF2_NAGL_JNK1-4-6-RND7104_0 |
| Workunit | 31557192 |
| Created | 10 Apr 2026, 8:06:32 UTC |
| Sent | 10 Apr 2026, 8:06:37 UTC |
| Report deadline | 15 Apr 2026, 8:06:37 UTC |
| Received | 10 Apr 2026, 14:05:20 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 651909 |
| Run time | 3 hours 32 min 45 sec |
| CPU time | 3 hours 32 min 45 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 17,038.78 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 646.75 MB |
| Peak swap size | 40.81 GB |
| Peak disk usage | 3.06 GB |
Stderr output
<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-10 10:08:34 (5125): wrapper (8.1.26018): starting
2026-04-10 10:09:12 (5125): wrapper: running bin/python (bin/conda-unpack)
2026-04-10 10:09:12 (5125): wrapper: created child process 5141
2026-04-10 10:09:13 (5125): bin/python exited; CPU time 0.135339
2026-04-10 10:09:13 (5125): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-10 10:09:13 (5125): wrapper: created child process 5146
2026-04-10 10:09:15 (5125): bin/tar exited; CPU time 1.279345
2026-04-10 10:09:15 (5125): wrapper: running bin/bash (run.sh)
2026-04-10 10:09:15 (5125): wrapper: created child process 5148
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/2/bin
+++ dirname /var/lib/boinc/slots/2/bin
++ local full_path_env=/var/lib/boinc/slots/2
+++ basename /var/lib/boinc/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/2
++ CONDA_PREFIX=/var/lib/boinc/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/2/tmp
+ TMP=/var/lib/boinc/slots/2/tmp
+ mkdir -p /var/lib/boinc/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/slots/2/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_A01_A08_input.yaml
+ python bin/rbfe_production QB_A01_A08_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(+0x45330)[0x70cc73445330]
../../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(+0x45330)[0x70cc73445330]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xbf)[0x70cc734ecadf]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17)[0x70cc734f9a27]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4c)[0x70cc7352975c]
../../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)[0x70cc7342a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x70cc7342a28b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]
Exiting...
/var/lib/boinc/slots/2/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 '
2026-04-10 12:15:00 (3209): wrapper (8.1.26018): starting
2026-04-10 12:15:00 (3209): wrapper: running bin/bash (run.sh)
2026-04-10 12:15:00 (3209): wrapper: created child process 3214
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc/slots/2/bin
+++ dirname /var/lib/boinc/slots/2/bin
++ local full_path_env=/var/lib/boinc/slots/2
+++ basename /var/lib/boinc/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc/slots/2
++ CONDA_PREFIX=/var/lib/boinc/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc/slots/2:/var/lib/boinc/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc/slots/2/tmp
+ TMP=/var/lib/boinc/slots/2/tmp
+ mkdir -p /var/lib/boinc/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:1,1,CUDA,,/var/lib/boinc/slots/2/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A01_A08_input.yaml
+ python bin/rbfe_production QB_A01_A08_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_A01_A08.out r1/QB_A01_A08.out r10/QB_A01_A08.out r11/QB_A01_A08.out r12/QB_A01_A08.out r13/QB_A01_A08.out r14/QB_A01_A08.out r15/QB_A01_A08.out r16/QB_A01_A08.out r17/QB_A01_A08.out r18/QB_A01_A08.out r19/QB_A01_A08.out r2/QB_A01_A08.out r20/QB_A01_A08.out r21/QB_A01_A08.out r3/QB_A01_A08.out r4/QB_A01_A08.out r5/QB_A01_A08.out r6/QB_A01_A08.out r7/QB_A01_A08.out r8/QB_A01_A08.out r9/QB_A01_A08.out 'r*/*.dcd' r0/QB_A01_A08.xtc r1/QB_A01_A08.xtc r10/QB_A01_A08.xtc r11/QB_A01_A08.xtc r12/QB_A01_A08.xtc r13/QB_A01_A08.xtc r14/QB_A01_A08.xtc r15/QB_A01_A08.xtc r16/QB_A01_A08.xtc r17/QB_A01_A08.xtc r18/QB_A01_A08.xtc r19/QB_A01_A08.xtc r2/QB_A01_A08.xtc r20/QB_A01_A08.xtc r21/QB_A01_A08.xtc r3/QB_A01_A08.xtc r4/QB_A01_A08.xtc r5/QB_A01_A08.xtc r6/QB_A01_A08.xtc r7/QB_A01_A08.xtc r8/QB_A01_A08.xtc r9/QB_A01_A08.xtc
tar: run.log: file changed as we read it
tar: r*/*.dcd: 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
2026-04-10 15:39:48 (3209): bin/bash exited; CPU time 12592.801940
2026-04-10 15:39:48 (3209): called boinc_finish(0)
</stderr_txt>
]]>
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