Task 38600062

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-09 02:00:04 (92318): wrapper (8.1.26018): starting
2026-04-09 02:00:05 (3560): wrapper (8.1.26018): starting
2026-04-09 02:01:08 (3560): wrapper: running bin/python (bin/conda-unpack)
2026-04-09 02:01:08 (3560): wrapper: created child process 3609
2026-04-09 02:01:09 (3560): bin/python exited; CPU time 0.150185
2026-04-09 02:01:09 (3560): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-09 02:01:09 (3560): wrapper: created child process 3612
2026-04-09 02:01:10 (3560): bin/tar exited; CPU time 0.563567
2026-04-09 02:01:10 (3560): wrapper: running bin/bash (run.sh)
2026-04-09 02:01:10 (3560): wrapper: created child process 3614
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/35/bin
+++ dirname /var/lib/boinc-client/slots/35/bin
++ local full_path_env=/var/lib/boinc-client/slots/35
+++ basename /var/lib/boinc-client/slots/35
++ local env_name=35
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/35
++ CONDA_PREFIX=/var/lib/boinc-client/slots/35
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/35/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(35) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/35/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/35/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/35:/var/lib/boinc-client/slots/35/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/35:/var/lib/boinc-client/slots/35/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/35/tmp
+ TMP=/var/lib/boinc-client/slots/35/tmp
+ mkdir -p /var/lib/boinc-client/slots/35/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/35/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_A07_A26_input.yaml
+ python bin/rbfe_production QB_A07_A26_input.yaml
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
SIGSEGV: segmentation violation
Stack trace (15 frames):
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x42c050]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x45cb0) [0x7b4e96a45cb0]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x463138]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x45f5d5]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x45cb0) [0x7b4e96a45cb0]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0xacae2) [0x7b4e96aacae2]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0xa05ec) [0x7b4e96aa05ec]
/usr/lib/x86_64-linux-gnu/libc.so.6(clock_nanosleep+0x32) [0x7b4e96af5df2]
/usr/lib/x86_64-linux-gnu/libc.so.6(nanosleep+0x17) [0x7b4e96b03a07]
/usr/lib/x86_64-linux-gnu/libc.so.6(usleep+0x4a) [0x7b4e96b3731a]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x4398c2]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x40b2e5]
/usr/lib/x86_64-linux-gnu/libc.so.6(+0x2a601) [0x7b4e96a2a601]
/usr/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x88) [0x7b4e96a2a718]
../../projects/gpugrid.net_gpugrid/wrapper_dev_x86_64-pc-linux-gnu() [0x407cc5]

Exiting...
/var/lib/boinc-client/slots/35/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 '
2026-04-09 02:02:47 (4410): wrapper (8.1.26018): starting
2026-04-09 02:02:47 (4410): wrapper: running bin/bash (run.sh)
2026-04-09 02:02:47 (4410): wrapper: created child process 4413
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/35/bin
+++ dirname /var/lib/boinc-client/slots/35/bin
++ local full_path_env=/var/lib/boinc-client/slots/35
+++ basename /var/lib/boinc-client/slots/35
++ local env_name=35
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/35
++ CONDA_PREFIX=/var/lib/boinc-client/slots/35
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/35/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(35) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/35/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/35/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/35:/var/lib/boinc-client/slots/35/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/35:/var/lib/boinc-client/slots/35/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/35/tmp
+ TMP=/var/lib/boinc-client/slots/35/tmp
+ mkdir -p /var/lib/boinc-client/slots/35/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/slots/35/tmp
+ FILE=starting_sample
+ '[' -f starting_sample ']'
+ echo 'starting_sample exists, not extracting restart'
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A07_A26_input.yaml
+ python bin/rbfe_production QB_A07_A26_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_A07_A26.out r1/QB_A07_A26.out r10/QB_A07_A26.out r11/QB_A07_A26.out r12/QB_A07_A26.out r13/QB_A07_A26.out r14/QB_A07_A26.out r15/QB_A07_A26.out r16/QB_A07_A26.out r17/QB_A07_A26.out r18/QB_A07_A26.out r19/QB_A07_A26.out r2/QB_A07_A26.out r20/QB_A07_A26.out r21/QB_A07_A26.out r3/QB_A07_A26.out r4/QB_A07_A26.out r5/QB_A07_A26.out r6/QB_A07_A26.out r7/QB_A07_A26.out r8/QB_A07_A26.out r9/QB_A07_A26.out 'r*/*.dcd' r0/QB_A07_A26.xtc r1/QB_A07_A26.xtc r10/QB_A07_A26.xtc r11/QB_A07_A26.xtc r12/QB_A07_A26.xtc r13/QB_A07_A26.xtc r14/QB_A07_A26.xtc r15/QB_A07_A26.xtc r16/QB_A07_A26.xtc r17/QB_A07_A26.xtc r18/QB_A07_A26.xtc r19/QB_A07_A26.xtc r2/QB_A07_A26.xtc r20/QB_A07_A26.xtc r21/QB_A07_A26.xtc r3/QB_A07_A26.xtc r4/QB_A07_A26.xtc r5/QB_A07_A26.xtc r6/QB_A07_A26.xtc r7/QB_A07_A26.xtc r8/QB_A07_A26.xtc r9/QB_A07_A26.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
2026-04-09 05:54:38 (4410): bin/bash exited; CPU time 13925.864924
2026-04-09 05:54:38 (4410): called boinc_finish(0)

</stderr_txt>
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