Fix issues with regression suite after toss4 upgrade.

[brugger1]

Pascal was upgraded from toss3 to toss4 and while the regression suite it is passing, there are some skips we should fix.

• ffp.py - We need to build the libstripack for the ffp operator to work.
• movie.py - We need ffmpeg installed for some functions used in visit_utils to work.
• gdal.py - The GDAL plugin has a runtime link failure with xerces.
• Git commands are failing (e.g. git checkout, git pull, ...).

[brugger1]

@biagas Here is the output from the git commands failing on pascal when they are run from a cron job.

pascal83
git version 2.29.1
rm -f .git/index.lock
git checkout develop
Already on 'develop'
Your branch is ahead of 'origin/develop' by 3 commits.
  (use "git push" to publish your local commits)
git pull
warning: Pulling without specifying how to reconcile divergent branches is
discouraged. You can squelch this message by running one of the following
commands sometime before your next pull:

  git config pull.rebase false  # merge (the default strategy)
  git config pull.rebase true   # rebase
  git config pull.ff only       # fast-forward only

You can replace "git config" with "git config --global" to set a default
preference for all repositories. You can also pass --rebase, --no-rebase,
or --ff-only on the command line to override the configured default per
invocation.

git@github.com: Permission denied (publickey).^M
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
git lfs pull
Repository updated

[markcmiller86]

@brugger1...these same issues do not occur when running interactively from a shell?

https://askubuntu.com/questions/110565/why-is-git-not-using-my-pubkey-with-crontab

I think cron might somehow have a different notion of who you are

• where your home dir on pascal is
• what your username is

Do you set HOME or MAILTO in the cron job?

[brugger1]

The commands work fine when I am logged into pascal. I set SHELL and MAILTO in my cron file.

[brugger1]

Here is my crontab.

crontab -l
# use /bin/sh to run commands, no matter what /etc/passwd says
SHELL=/bin/sh
# mail any output to 'brugger1@llnl.gov', no matter whose crontab this is
MAILTO=brugger1@llnl.gov
#
# run at 10:00 PM, every day
0 22 * * * $HOME/visit_run_tests/pascal_cron_script >> $HOME/visit_run_tests/out 2>&1

I believe HOME must be set properly or the command would not run properly.

I just deleted the old one and submitted it again. Who knows, maybe that will help.

[markcmiller86]

I just deleted the old one and submitted it again. Who knows, maybe that will help.

That actually might have an effect. Maybe carrying an edited crontab across an OS upgrade leads to differences in how the cron job actually runs relative to what you get when you create the crontab anew for the new OS.

[markcmiller86]

@tgamblin if you have a quick moment...are you aware of any changes in behavior of git from cron jobs on LLNL systems after the upgard to TOSS4?

[markcmiller86]

@brugger1 if you need more ideas debugging

• disable redirects in scripts launched from the cron job
• see if which git is returning same client from cron (module command shows 3 diff versions of git available) you get interactively
• maybe remove redirect on command launched from crontab
• possibly strace the whole script launched from crontab. You wanna catch child processes too so command would be something like strace -f -s 256 prefacing whatever you launch as in...

  0 22 * * * /usr/bin/strace -f -s 256 $HOME/visit_run_tests/pascal_cron_script
  

[markcmiller86]

Some other ideas.

• https://docs.github.com/en/authentication/troubleshooting-ssh/error-permission-denied-publickey
• Oh, what about keys in ~/.ssh/known_hosts for github?
• Is your id_rsa.pub you uploaded to GitHub one you actually generated on a TOSS3 CZ system?

[markcmiller86]

I am also wondering about your git config for your email and/or name might somehow be off.