AFNI Install No GUI, HPC

AFNI Message Board
1

Dear AFNI,

I’m representing several AFNI users at our institution in an attempt to install it on our HPC for command line, batch processing only. Our idiosyncrasy is that we’d can’t use the gui functionality and our security guys would really like to avoid online checks/updates. I suspect I might not be the only one with this issue, so this is one for the message board!

The workflow would be to do image checks and viewing on local machines. In addition, we are hoping to do an offline install and remain offline. So, is this reasonably workable?

Next, would you please comment on my installation process?
Each user installs into their own home directory.

Dependencies:
All dependencies installed except:
Skipping the GUI:
No package xorg-x11-fonts-misc available.
No package PyQt4 available.
No package gnome-tweak-tool available.
No package xorg-x11-server-Xvfb available.
Our HPC:
No package netpbm-progs available.

Installation:
Download:
https://afni.nimh.nih.gov/pub/dist/bin/linux_ubuntu_16_64/@update.afni.binaries
https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz
And then:
tcsh @update.afni.binaries -local_package linux_openmp_64.tgz -do_extras

Follow RedHat linux essentials, skipping the sections called “Install prerequisite packages” and “Make tcsh default shell” and “Reboot” and “Prepare for Bootcamp”

Thank you!

Joel

2

Should work, but I think you will probably want the Xvfb and netpbm packages installed. They’re useful for driving afni scripts for images and montages, especially when you don’t have remote display capabilities. @chauffeur_afni can be used to make this simpler.

3

Hi Joel,

I don’t think the -do_extras option is necessary there,
assuming it is an administrator running the command.
That would update the PATH and setup the -help output
for tab completion, which an admin probably does not
need.

  • rick
4

Thank you very much!