Task 38610230

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
2026-04-15 09:51:51 (281): wrapper (8.1.26018): starting
2026-04-15 09:52:06 (281): wrapper: running bin/python (bin/conda-unpack)
2026-04-15 09:52:06 (281): wrapper: created child process 283
2026-04-15 09:52:07 (281): bin/python exited; CPU time 0.053752
2026-04-15 09:52:07 (281): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-04-15 09:52:07 (281): wrapper: created child process 284
2026-04-15 09:52:08 (281): bin/tar exited; CPU time 0.510503
2026-04-15 09:52:08 (281): wrapper: running bin/bash (run.sh)
2026-04-15 09:52:08 (281): wrapper: created child process 286
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/home/fornax/slots/0/bin
+++ dirname /home/fornax/slots/0/bin
++ local full_path_env=/home/fornax/slots/0
+++ basename /home/fornax/slots/0
++ local env_name=0
++ '[' -n '' ']'
++ export CONDA_PREFIX=/home/fornax/slots/0
++ CONDA_PREFIX=/home/fornax/slots/0
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(0) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/home/fornax/slots/0/etc/conda/activate.d
++ '[' -d /home/fornax/slots/0/etc/conda/activate.d ']'
+ export PATH=/home/fornax/slots/0:/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/home/fornax/slots/0:/home/fornax/slots/0/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ echo 'Create a temporary directory'
+ export TMP=/home/fornax/slots/0/tmp
+ TMP=/home/fornax/slots/0/tmp
+ mkdir -p /home/fornax/slots/0/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/home/fornax/slots/0/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
tar: r0/checkpoint.xml: time stamp 2026-04-15 09:55:10 is 180.418238788 s in the future
tar: r1/checkpoint.xml: time stamp 2026-04-15 09:55:10 is 180.218890821 s in the future
tar: r10/checkpoint.xml: time stamp 2026-04-15 09:55:16 is 186.01913148 s in the future
tar: r11/checkpoint.xml: time stamp 2026-04-15 09:55:17 is 186.819329017 s in the future
tar: r12/checkpoint.xml: time stamp 2026-04-15 09:55:18 is 187.619527497 s in the future
tar: r13/checkpoint.xml: time stamp 2026-04-15 09:55:18 is 187.419750643 s in the future
tar: r14/checkpoint.xml: time stamp 2026-04-15 09:55:19 is 188.219916691 s in the future
tar: r15/checkpoint.xml: time stamp 2026-04-15 09:55:20 is 189.030072321 s in the future
tar: r16/checkpoint.xml: time stamp 2026-04-15 09:55:20 is 188.830551689 s in the future
tar: r17/checkpoint.xml: time stamp 2026-04-15 09:55:21 is 189.630673835 s in the future
tar: r18/checkpoint.xml: time stamp 2026-04-15 09:55:22 is 190.430890268 s in the future
tar: r19/checkpoint.xml: time stamp 2026-04-15 09:55:22 is 190.231264719 s in the future
tar: r2/checkpoint.xml: time stamp 2026-04-15 09:55:11 is 179.029429393 s in the future
tar: r20/checkpoint.xml: time stamp 2026-04-15 09:55:23 is 190.828297039 s in the future
tar: r21/checkpoint.xml: time stamp 2026-04-15 09:55:24 is 191.627814918 s in the future
tar: r3/checkpoint.xml: time stamp 2026-04-15 09:55:12 is 179.438415886 s in the future
tar: r4/checkpoint.xml: time stamp 2026-04-15 09:55:12 is 179.238195568 s in the future
tar: r5/checkpoint.xml: time stamp 2026-04-15 09:55:13 is 180.037721872 s in the future
tar: r6/checkpoint.xml: time stamp 2026-04-15 09:55:14 is 180.837891909 s in the future
tar: r7/checkpoint.xml: time stamp 2026-04-15 09:55:14 is 180.638500119 s in the future
tar: r8/checkpoint.xml: time stamp 2026-04-15 09:55:15 is 181.438822281 s in the future
tar: r9/checkpoint.xml: time stamp 2026-04-15 09:55:16 is 182.247901496 s in the future
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A08_A11_input.yaml
+ python bin/rbfe_production QB_A08_A11_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_A08_A11.out r1/QB_A08_A11.out r10/QB_A08_A11.out r11/QB_A08_A11.out r12/QB_A08_A11.out r13/QB_A08_A11.out r14/QB_A08_A11.out r15/QB_A08_A11.out r16/QB_A08_A11.out r17/QB_A08_A11.out r18/QB_A08_A11.out r19/QB_A08_A11.out r2/QB_A08_A11.out r20/QB_A08_A11.out r21/QB_A08_A11.out r3/QB_A08_A11.out r4/QB_A08_A11.out r5/QB_A08_A11.out r6/QB_A08_A11.out r7/QB_A08_A11.out r8/QB_A08_A11.out r9/QB_A08_A11.out r0/QB_A08_A11.xtc r1/QB_A08_A11.xtc r10/QB_A08_A11.xtc r11/QB_A08_A11.xtc r12/QB_A08_A11.xtc r13/QB_A08_A11.xtc r14/QB_A08_A11.xtc r15/QB_A08_A11.xtc r16/QB_A08_A11.xtc r17/QB_A08_A11.xtc r18/QB_A08_A11.xtc r19/QB_A08_A11.xtc r2/QB_A08_A11.xtc r20/QB_A08_A11.xtc r21/QB_A08_A11.xtc r3/QB_A08_A11.xtc r4/QB_A08_A11.xtc r5/QB_A08_A11.xtc r6/QB_A08_A11.xtc r7/QB_A08_A11.xtc r8/QB_A08_A11.xtc r9/QB_A08_A11.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 12:01:16 (281): bin/bash exited; CPU time 7976.293893
2026-04-15 12:01:16 (281): called boinc_finish(0)

</stderr_txt>
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