suma libGLU.so.1 issue

AFNI Message Board
1

I installed afni. The afni so far started with the plugin list seen (need to learn and play). However the sume had problem to start. It says no libGLU.so.1. But it is there, see attached “suma and libGLU.so.1” screenshot and the output of afni_system_check.py -check_all.

Hope it’s resolvable and thanks in advance for your help!

Apple

= = = = afni_system_check.py -check_all = = =
[root@localhost ~]# afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-862.9.1.el7.x86_64
version: #1 SMP Mon Jul 16 16:29:36 UTC 2018
distribution: CentOS Linux 7.5.1804 Core
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /root/abin/afni
afni version : Precompiled binary linux_openmp_64: Aug 11 2018
: AFNI_18.2.09
AFNI_version.txt : AFNI_18.2.09, linux_openmp_64, Aug 11 2018
which python : /usr/bin/python
python version : 2.7.5
which R : which: no R in (/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/root/abin)

which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/root/abin/afni)
R : 0
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 0

testing ability to start various programs…
afni : success
suma : FAILURE
suma: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
R: Command not found.

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

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/root/abin

PYTHONPATH =
R_LIBS = /root/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /root/abin

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3
========================= summary, please fix: =========================

  • failure under initial “AFNI and related program tests”
  • AFNI programs show FAILURE
  • missing R packages (see rPkgsInstall)
  • insufficient data for AFNI bootcamp
    [root@localhost ~]#
    = = = = = = = = = END = = = = = = = = =

suma_error.png
suma_error.png711×267 27.6 KB

2

Hi, Apple-

Just to be double-check, are you following the instructions here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_Fed_RH.html
for “CentOS/RHEL 7”?

–pt

3

And specifically, try using the CentOS7 package:

@update.afni.binaries -package linux_centos_7_64.tgz

  • rick
4

Also, it seems that you are installing AFNI as the
root user, which is generally not advised. Even if
binaries are installed as root for many users, it
is good to then put them under something more
standard, such as /usr/local/AFNI, say.

Admin rights are needed for the ‘yum’ commands
to install libraries (though sudo is usually the way
to go there). But for everything else, a standard
user should be sufficient.

  • rick
5

… and I see that part of the confusion might be due to the fact that we didn’t list the CentOS-specific binaries for the CentOS builds in the instructions. That has now been fixed and should be visible here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_Fed_RH.html
(basically just running @update.afni.binaries for the correct package specification, which Rick noted in a separate reply here).

–pt