Hi,
The output from afni_system_check.py is:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-862.11.6.el7.x86_64
version: #1 SMP Fri Aug 10 16:55:11 UTC 2018
distribution: Red Hat Enterprise Linux Server 7.5 Maipo
number of CPUs: 24
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /N/soft/rhel7/afni/18.0.13/afni
afni version : Precompiled binary linux_openmp_64: Feb 5 2018
: AFNI_18.0.12
AFNI_version.txt : AFNI_18.0.12, linux_openmp_64, Feb 05 2018
which python : /N/soft/rhel7/python/2.7.13a/bin/python
python version : 2.7.13
which R : /N/soft/rhel7/r/3.3.1/bin/R
R version : R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/gpfs/hps/soft/rhel7/afni/18.0.13/afni)
R : 1 (/gpfs/hps/soft/rhel7/r/3.3.1/bin/R)
python : 2
/gpfs/hps/soft/rhel7/python/2.7.13a/bin/python2.7
/usr/bin/python2.7
python2 : 2
/gpfs/hps/soft/rhel7/python/2.7.13a/bin/python2.7
/usr/bin/python2.7
python3 : 0
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : 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!
checking for $HOME files...
.afnirc : missing
.sumarc : found
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
** python module not found: PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
-------------------------------- env vars --------------------------------
PATH = /N/u/dlevitas/Carbonate/bin/ants/bin/:/N/u/dlevitas/Carbonate/.local/bin/:/N/u/dlevitas/Carbonate/dbus/:/N/u/dlevitas/Carbonate/jq/:/N/u/dlevitas/Carbonate/inkscape-0.92.3/:/N/u/dlevitas/Carbonate/mricrogl_lx/pigz/:/N/u/dlevitas/Carbonate/mricrogl_lx/build/dcm2niix/bin/:/N/u/dlevitas/Carbonate/BrainSuite15c/bin/:/N/u/dlevitas/Carbonate/c3d-1.0.0-Linux-x86_64/bin/:/N/u/dlevitas/Carbonate/sublime_text_3/:/opt/moab/bin:/opt/moab/bin:/N/u/dlevitas/Carbonate/bin/ants/bin/:/N/u/dlevitas/Carbonate/.local/bin/:/N/u/dlevitas/Carbonate/dbus/:/N/u/dlevitas/Carbonate/jq/:/N/u/dlevitas/Carbonate/inkscape-0.92.3/:/N/u/dlevitas/Carbonate/mricrogl_lx/pigz/:/N/u/dlevitas/Carbonate/mricrogl_lx/build/dcm2niix/bin/:/N/u/dlevitas/Carbonate/BrainSuite15c/bin/:/N/u/dlevitas/Carbonate/c3d-1.0.0-Linux-x86_64/bin/:/N/u/dlevitas/Carbonate/sublime_text_3/:/N/soft/rhel7/singularity/2.5.2/bin:/N/soft/rhel7/cmake/gnu/3.11.4/bin:/N/soft/rhel7/freesurfer/6.0.0/freesurfer/bin:/N/soft/rhel7/fsl/5.0.11b/bin:/N/soft/rhel7/fsl/5.0.11b/extras/bin:/N/soft/rhel7/fsl/autoPtx/0.1.1:/N/soft/rhel7/libmng/2.0.3/bin:/N/soft/rhel7/lcms/2.8/bin:/N/soft/rhel7/matlab/2017a/bin/:/N/soft/rhel7/afni/18.0.13:/N/soft/rhel7/libpng/1.6.29/bin:/N/soft/rhel7/r/3.3.1/bin:/N/soft/rhel7/java/1.8.0_131/bin:/N/soft/rhel7/curl/intel/7.54.0/bin:/N/soft/rhel7/gsl/gnu/2.3/bin:/N/soft/rhel7/git/gnu/2.13.0/bin:/N/soft/rhel7/quotas:/N/soft/rhel7/perl/gnu/5.24.1/bin:/N/soft/rhel7/python/2.7.13a/bin:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/bin/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin:/N/soft/rhel7/gcc/6.3.0/bin:/opt/moab/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/N/u/dlevitas/Carbonate/bin
PYTHONPATH = /N/soft/rhel7/python/2.7.13a/lib/python2.7/site-packages
R_LIBS =
LD_LIBRARY_PATH = /N/soft/rhel7/singularity/2.5.2/lib:/N/soft/rhel7/freesurfer/6.0.0/freesurfer/lib:/N/soft/rhel7/fsl/5.0.11b/lib:/N/soft/rhel7/fsl/5.0.11b/extras/lib:/N/soft/rhel7/libmng/2.0.3/lib:/N/soft/rhel7/lcms/2.8/lib:/N/soft/rhel7/libpng/1.6.29/lib:/N/soft/rhel7/zlib/gnu/1.2.11/lib/:/N/soft/rhel7/bzip2/1.0.6/lib/:/N/soft/rhel7/xz/5.2.3/lib/:/N/soft/rhel7/r/3.3.1/lib64/R/lib:/N/soft/rhel7/nlopt/2.4.2/lib:/N/soft/rhel7/curl/intel/7.54.0/lib:/N/soft/rhel7/gsl/gnu/2.3/lib:/N/soft/rhel7/perl/gnu/5.24.1/lib:/N/soft/rhel7/python/2.7.13a/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/mic/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/ipp/lib/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/tbb/lib/intel64/gcc4.7:/N/soft/rhel7/intel/18.0.2/debugger_2018/iga/lib:/N/soft/rhel7/intel/18.0.2/debugger_2018/libipt/intel64/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/daal/lib/intel64_lin:/N/soft/rhel7/gcc/6.3.0/lib64:/N/soft/rhel7/gcc/6.3.0/lib:/N/soft/rhel7/matlab/MATLAB_Compiler_Runtime/v92/runtime/glnxa64:/N/soft/rhel7/matlab/MATLAB_Compiler_Runtime/v92/bin/glnxa64:/N/soft/rhel7/matlab/MATLAB_Compiler_Runtime/v92/sys/os/glnxa64
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 /N/soft/rhel7/afni/18.0.13
------------------------------ OS specific -------------------------------
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* missing R packages (see rPkgsInstall)
* consider running: cp /N/soft/rhel7/afni/18.0.13/AFNI.afnirc ~/.afnirc
* consider running: apsearch -update_all_afni_help
* insufficient data for AFNI bootcamp
* consider installing PyQt4
Loading SUMA by typing suma on the command line only brings up the GUI, but no image is displayed. The command line output is:
suma:
No input specified, loading some toy surfaces...
Use '.' and ',' to cycle between them.
See suma -help for assistance.
libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
SUMA_Engine: Starting to listen ...
