Task 38583484
| Name | JNK1_A16_A10_r0_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-1-5-RND0529_0 |
| Workunit | 31547609 |
| Created | 14 Dec 2025, 6:42:10 UTC |
| Sent | 14 Dec 2025, 6:42:12 UTC |
| Report deadline | 19 Dec 2025, 6:42:12 UTC |
| Received | 14 Dec 2025, 15:06:54 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Aborted by user |
| Exit status | 203 (0x000000CB) EXIT_ABORTED_VIA_GUI |
| Computer ID | 611154 |
| Run time | 25 min 12 sec |
| CPU time | 6 min 58 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 49,330.41 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) x86_64-pc-linux-gnu |
| Peak working set size | 646.86 MB |
| Peak swap size | 25.06 GB |
| Peak disk usage | 3.07 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
aborted by user</message>
<stderr_txt>
2025-12-14 14:06:19 (107576): wrapper (8.1.26018): starting
2025-12-14 14:06:38 (107576): wrapper: running bin/python (bin/conda-unpack)
2025-12-14 14:06:38 (107576): wrapper: created child process 107589
2025-12-14 14:06:39 (107576): bin/python exited; CPU time 0.081971
2025-12-14 14:06:39 (107576): wrapper: running bin/tar (xjvf input.tar.bz2)
2025-12-14 14:06:39 (107576): wrapper: created child process 107590
2025-12-14 14:06:41 (107576): bin/tar exited; CPU time 1.017101
2025-12-14 14:06:41 (107576): wrapper: running bin/bash (run.sh)
2025-12-14 14:06:41 (107576): wrapper: created child process 107594
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/34/bin
+++ dirname /var/lib/boinc-client/slots/34/bin
++ local full_path_env=/var/lib/boinc-client/slots/34
+++ basename /var/lib/boinc-client/slots/34
++ local env_name=34
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/34
++ CONDA_PREFIX=/var/lib/boinc-client/slots/34
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/34/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(34) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/34/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/34/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/34:/var/lib/boinc-client/slots/34/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/34:/var/lib/boinc-client/slots/34/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/34/tmp
+ TMP=/var/lib/boinc-client/slots/34/tmp
+ mkdir -p /var/lib/boinc-client/slots/34/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/34/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_A16_A10_input.yaml
+ python bin/rbfe_production QB_A16_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(+0x45330)[0x774b2ec45330]
../../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)[0x774b2ec45330]
/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0xbf)[0x774b2ececadf]
/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17)[0x774b2ecf9a27]
/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4c)[0x774b2ed2975c]
../../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)[0x774b2ec2a1ca]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x8b)[0x774b2ec2a28b]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu[0x407cc5]
Exiting...
/var/lib/boinc-client/slots/34/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 '
2025-12-14 15:41:52 (3115): wrapper (8.1.26018): starting
2025-12-14 15:41:52 (3115): wrapper: running bin/bash (run.sh)
2025-12-14 15:41:52 (3115): wrapper: created child process 3128
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/34/bin
+++ dirname /var/lib/boinc-client/slots/34/bin
++ local full_path_env=/var/lib/boinc-client/slots/34
+++ basename /var/lib/boinc-client/slots/34
++ local env_name=34
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/34
++ CONDA_PREFIX=/var/lib/boinc-client/slots/34
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/34/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(34) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/34/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/34/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/34:/var/lib/boinc-client/slots/34/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/34:/var/lib/boinc-client/slots/34/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/var/lib/boinc-client/slots/34/tmp
+ TMP=/var/lib/boinc-client/slots/34/tmp
+ mkdir -p /var/lib/boinc-client/slots/34/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/34/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A16_A10_input.yaml
+ python bin/rbfe_production QB_A16_A10_input.yaml
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
</stderr_txt>
]]>
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