Update AFNI to work with R 4.2.0 [IN05781228]

[balston]

The current AFNI (module afni/22.2.05) was built using GSL 2.4 which depends on GNU 4.9.2. We need to update it to use gsl/2.7/gnu-10.2.0.

Required on Myriad first.

[balston]

Might as well use the latest version - AFNI_23.0.02

[balston]

Downloaded the source code which has no obvious version number so checking to make sure it is 23.0.02 😢

[balston]

I had to do a test build from the downloaded source to get at the version number. Confirmed that it is 23.0.02:

afni version         : Precompiled binary linux_openmp_64: Jan 27 2023
                     : AFNI_23.0.02 'Commodus'
AFNI_version.txt     : AFNI_23.0.02, linux_openmp_64, Jan 27 2023

I will now update the build script and do an install into /shared/ucl/apps.

[balston]

Downloaded source archive is now in:

/shared/ucl/apps/pkg-store/afni-23.0.02.tgz

on both Myriad and Kathleen.

[balston]

I've now got an updated build script ready to go. Will pull down to Myriad and run on Monday.

[balston]

Build script run as follows on Myriad:

cd /shared./ucl/apps/build_scripts
./afni-23.0.02_install 2>&1 | tee ~/Software/AFNI/afni-23.0.02_install.log-30012023

has completed without errors.

[balston]

Module file updated for new version.

[balston]

Using the following modules:

module -f unload compilers mpi gcc-libs
module load r/recommended
module load afni/23.0.02

quick test running:

afni_system_check.py -check_all | less

shows:

-------------------------------- general ---------------------------------
architecture:         64bit ELF
cpu type:             x86_64
system:               Linux
release:              3.10.0-1127.el7.x86_64
version:              #1 SMP Tue Feb 18 16:39:12 EST 2020
distribution:         rhel 7.8 Maipo
number of CPUs:       36
apparent login shell: bash
shell RC file:        .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni           : /shared/ucl/apps/afni/23.0.02/gnu-10.2.0/afni
afni version         : Precompiled binary linux_openmp_64: Jan 30 2023
                     : AFNI_23.0.02 'Commodus'
AFNI_version.txt     : AFNI_23.0.02, linux_openmp_64, Jan 30 2023
which python         : /shared/ucl/apps/python/bundles/gnu-10.2.0/python39-6.0.0/venv/bin/python
python version       : 3.9.6
which R              : /shared/ucl/apps/R/R-4.2.0-OpenBLAS/bin/R
R version            : R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
which tcsh           : /usr/bin/tcsh

instances of various programs found in PATH:
    afni    : 1   (/lustre/shared/ucl/apps/afni/23.0.02/gnu-10.2.0/afni)
    R       : 2
      /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/bin/R
      /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/snow/R
    python  : 2
      /lustre/shared/ucl/apps/python/3.9.6/gnu-10.2.0/bin/python3.9
      /usr/bin/python2.7
    python2 : 1   (/usr/bin/python2.7)
    python3 : 1   (/lustre/shared/ucl/apps/python/3.9.6/gnu-10.2.0/bin/python3.9)

testing ability to start various programs...
    afni                 : success
    suma                 : success
    3dSkullStrip         : success
    uber_subject.py      : success
    3dAllineate          : success
    3dRSFC               : success
    SurfMesh             : success
    3dClustSim           : success
    3dMVM                : success

checking for R packages...
    rPkgsInstall -pkgs ALL -check : FAILURE

        oo Warning:
           These packages are not installed on the computer: afex!
        These packages are not installed on the computer: phia!
        These packages are not installed on the computer: lmerTest!
        These packages are not installed on the computer: paran!
        These packages are not installed on the computer: brms!
        These packages are not installed on the computer: corrplot!

R RHOME : /shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R

checking for $HOME files...
    .afnirc                   : missing
    .sumarc                   : missing
    .afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp

++ module loaded: matplotlib.pyplot
   module file : /shared/ucl/apps/python/bundles/gnu-10.2.0/python39-6.0.0/venv/lib/python3.9/site-packages/matplotlib/pyplot.py
   matplotlib version : 3.4.3

[balston]

Replied to requester who has tested and says it is working.

Will now install on Kathleen.

[balston]

Installed on Kathleen.

Done on Myriad and Kathleen.

[balston]

AFNI is not in Spack so will need to create a package file for it.

[balston]

There may be a problem with the installation and interaction with R. Need to investigate next week.

[balston]

The AFNI installation is missing some R packages which is why the integration of the two applications is not working. At least I think this may be the problem.

I'm updating the build script.

[balston]

Build script updated to install the ANFI R packages by adding:

  # Install ANFI R packages
  export PATH=${INSTALL_PREFIX}:$PATH
  export AFNI_PLUGINPATH=${INSTALL_PREFIX}
  rPkgsInstall -pkgs ALL

Run again on Myriad and back to the user for testing.

[balston]

User reports that this has worked.

Updating on Kathleen.

[balston]

Now also updated on Kathleen.