Here is the output of which Xvfb:
lgrande2@node2 AFNI_scripts]$ which Xvfb
/usr/bin/which: no Xvfb in (/usr/local/netpbm/10.73.32/bin:/usr/local/R/3.3.3/bin:/usr/local/gdal/2.1.3/bin:/usr/local/proj/4.9.3/bin:/usr/local/curl/7.53.1/bin:/usr/local/geos/3.6.1/bin:/usr/local/openmpi/1.10.6/gnu/4.8.5-rhel/ib/bin:/usr/local/afni/19.2.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/lgrande2/bin)
Here is the output of: afni_system_check.py -check_all
[lgrande2@node2 AFNI_scripts]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.9.1.el7.x86_64
version: #1 SMP Mon Dec 2 08:31:54 EST 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/19.2.04/afni
afni version : Precompiled binary linux_openmp_64: Jul 19 2019
: AFNI_19.2.04 'Claudius'
AFNI_version.txt : AFNI_19.2.04, linux_openmp_64, Jul 19 2019
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/local/R/3.3.3/bin/R
R version : R version 3.3.3 (2017-03-06) -- "Another Canoe"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/usr/local/afni/19.2.04/afni)
R : 2
/usr/local/R/3.3.3/bin/R
/usr/local/R/3.6.1/bin/R
python : 1 (/usr/bin/python2.7)
python2 : 1 (/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: paran!
These packages are not installed on the computer: psych!
These packages are not installed on the computer: corrplot!
These packages are not installed on the computer: metafor!
checking for $HOME files...
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing
------------------------------ python libs -------------------------------
++ module 'PyQt4' found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /usr/local/netpbm/10.73.32/bin:/usr/local/R/3.3.3/bin:/usr/local/gdal/2.1.3/bin:/usr/local/proj/4.9.3/bin:/usr/local/curl/7.53.1/bin:/usr/local/geos/3.6.1/bin:/usr/local/openmpi/1.10.6/gnu/4.8.5-rhel/ib/bin:/usr/local/afni/19.2.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/lgrande2/bin
PYTHONPATH = /usr/lib64/python2.7
R_LIBS =
LD_LIBRARY_PATH = /usr/local/netpbm/10.73.32/lib:/usr/local/R/3.3.3/lib64:/usr/local/gdal/2.1.3/lib:/usr/local/proj/4.9.3/lib:/usr/local/curl/7.53.1/lib:/usr/local/lapack/3.7.0/lib:/usr/local/blas/3.7.0/lib:/usr/local/geos/3.6.1/lib:/usr/local/openmpi/1.10.6/gnu/4.8.5-rhel/ib/lib:/usr/local/afni/19.2.04:/usr/local/R/3.6.1/lib64:/usr/local/curl/7.64.1/lib:/usr/local/proj/6.0.0/lib:/usr/local/jags/4.3.0/lib:/usr/local/gdal/2.4.1/lib:/usr/local/geos/3.7.1/lib:/usr/local/udunits2/2.2.26/lib:/usr/local/gsl/2.5/lib:/usr/local/lapack/3.8.0/lib64:/usr/local/blas/3.8.0/lib:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/lib:/usr/local/gcc/8.3.0/lib64:/opt2/amd-opencl/lib
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ... [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: ... [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: .../SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /usr/local/afni/19.2.04
------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3
========================= summary, please fix: =========================
* login shell 'bash', trusting user to translate code examples from 'tcsh'
* shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
* missing R packages (see rPkgsInstall)
* please run: cp /usr/local/afni/19.2.04/AFNI.afnirc ~/.afnirc
* please run: "suma -update_env" for .sumarc
* please run: apsearch -update_all_afni_help
I will share the AFNI setup instructions with the IT folks. I am sure we gave it to them in the past, but it would be good to share again as the IT person may be different now.
Thank you for your help!
-Leah
