Task 38684438

Stderr output

<core_client_version>8.2.13</core_client_version>
<![CDATA[
<stderr_txt>
2026-10-27 17:17:41 (17361): wrapper (8.1.26018): starting
2026-10-27 17:17:56 (17361): wrapper: running bin/python (bin/conda-unpack)
2026-10-27 17:17:56 (17361): wrapper: created child process 17366
2026-10-27 17:17:57 (17361): bin/python exited; CPU time 0.047054
2026-10-27 17:17:57 (17361): wrapper: running bin/tar (xjvf input.tar.bz2)
2026-10-27 17:17:57 (17361): wrapper: created child process 17369
2026-10-27 17:17:58 (17361): bin/tar exited; CPU time 0.463302
2026-10-27 17:17:58 (17361): wrapper: running bin/bash (run.sh)
2026-10-27 17:17:58 (17361): wrapper: created child process 17379
+ echo 'Setup environment'
+ source bin/activate
++ _conda_pack_activate
++ local _CONDA_SHELL_FLAVOR
++ '[' -n x ']'
++ _CONDA_SHELL_FLAVOR=bash
++ local script_dir
++ case "$_CONDA_SHELL_FLAVOR" in
+++ dirname bin/activate
++ script_dir=bin
+++ cd bin
+++ pwd
++ local full_path_script_dir=/var/lib/boinc-client/slots/2/bin
+++ dirname /var/lib/boinc-client/slots/2/bin
++ local full_path_env=/var/lib/boinc-client/slots/2
+++ basename /var/lib/boinc-client/slots/2
++ local env_name=2
++ '[' -n '' ']'
++ export CONDA_PREFIX=/var/lib/boinc-client/slots/2
++ CONDA_PREFIX=/var/lib/boinc-client/slots/2
++ export _CONDA_PACK_OLD_PS1=
++ _CONDA_PACK_OLD_PS1=
++ PATH=/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
++ PS1='(2) '
++ case "$_CONDA_SHELL_FLAVOR" in
++ hash -r
++ local _script_dir=/var/lib/boinc-client/slots/2/etc/conda/activate.d
++ '[' -d /var/lib/boinc-client/slots/2/etc/conda/activate.d ']'
+ export PATH=/var/lib/boinc-client/slots/2:/var/lib/boinc-client/slots/2/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:.
+ PATH=/var/lib/boinc-client/slots/2:/var/lib/boinc-client/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-client/slots/2/tmp
+ TMP=/var/lib/boinc-client/slots/2/tmp
+ mkdir -p /var/lib/boinc-client/slots/2/tmp
+ echo 'Configure AToM'
+ echo localhost,0:0,1,CUDA,,/var/lib/boinc-client/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==26.2.1 -v
+ python -m pip install --no-dependencies atom-openmm==8.4.0 -v
+ python -m pip list
+ echo 'Extract restart'
+ tar xjvf restart.tar.bz2
tar: r0/checkpoint.xml: time stamp 2026-10-27 17:18:59 is 58.755103017 s in the future
tar: r1/checkpoint.xml: time stamp 2026-10-27 17:19:00 is 59.559322666 s in the future
tar: r10/checkpoint.xml: time stamp 2026-10-27 17:19:14 is 73.363923455 s in the future
tar: r11/checkpoint.xml: time stamp 2026-10-27 17:19:16 is 75.167570164 s in the future
tar: r12/checkpoint.xml: time stamp 2026-10-27 17:19:18 is 76.972247703 s in the future
tar: r13/checkpoint.xml: time stamp 2026-10-27 17:19:19 is 77.775580932 s in the future
tar: r14/checkpoint.xml: time stamp 2026-10-27 17:19:20 is 78.579978971 s in the future
tar: r15/checkpoint.xml: time stamp 2026-10-27 17:19:22 is 80.38368076 s in the future
tar: r16/checkpoint.xml: time stamp 2026-10-27 17:19:23 is 81.18802596 s in the future
tar: r17/checkpoint.xml: time stamp 2026-10-27 17:19:25 is 82.991733979 s in the future
tar: r18/checkpoint.xml: time stamp 2026-10-27 17:19:26 is 83.795484598 s in the future
tar: r19/checkpoint.xml: time stamp 2026-10-27 17:19:28 is 85.599868307 s in the future
tar: r2/checkpoint.xml: time stamp 2026-10-27 17:19:02 is 59.402647946 s in the future
tar: r20/checkpoint.xml: time stamp 2026-10-27 17:19:29 is 86.195740313 s in the future
tar: r21/checkpoint.xml: time stamp 2026-10-27 17:19:31 is 87.998972872 s in the future
tar: r3/checkpoint.xml: time stamp 2026-10-27 17:19:04 is 60.802177251 s in the future
tar: r4/checkpoint.xml: time stamp 2026-10-27 17:19:05 is 61.60607342 s in the future
tar: r5/checkpoint.xml: time stamp 2026-10-27 17:19:07 is 63.409352479 s in the future
tar: r6/checkpoint.xml: time stamp 2026-10-27 17:19:08 is 64.213249498 s in the future
tar: r7/checkpoint.xml: time stamp 2026-10-27 17:19:10 is 66.016188197 s in the future
tar: r8/checkpoint.xml: time stamp 2026-10-27 17:19:11 is 66.808186513 s in the future
tar: r9/checkpoint.xml: time stamp 2026-10-27 17:19:13 is 68.609913422 s in the future
+ echo 'Run AToM'
+ CONFIG_FILE=QB_A34_A12_input.yaml
+ python bin/rbfe_production QB_A34_A12_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_A34_A12.out r1/QB_A34_A12.out r10/QB_A34_A12.out r11/QB_A34_A12.out r12/QB_A34_A12.out r13/QB_A34_A12.out r14/QB_A34_A12.out r15/QB_A34_A12.out r16/QB_A34_A12.out r17/QB_A34_A12.out r18/QB_A34_A12.out r19/QB_A34_A12.out r2/QB_A34_A12.out r20/QB_A34_A12.out r21/QB_A34_A12.out r3/QB_A34_A12.out r4/QB_A34_A12.out r5/QB_A34_A12.out r6/QB_A34_A12.out r7/QB_A34_A12.out r8/QB_A34_A12.out r9/QB_A34_A12.out 'r*/*.dcd' 'r*/*.xtc'
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: r*/*.xtc: 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
2026-10-27 17:35:55 (17361): bin/bash exited; CPU time 1105.816394
2026-10-27 17:35:55 (17361): called boinc_finish(0)

</stderr_txt>
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