AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
July 20, 2020 10:38PM
Thank you! Here you go:

lgrande2@du-hpc ~]$ ssh -X node37
Last login: Sun Jul 19 15:00:27 2020 from du-hpc
[lgrande2@node37 ~]$ module load apps/afni-20.04
[lgrande2@node37 ~]$ module load apps/R-3.6.1
[lgrande2@node37 ~]$
[lgrande2@node37 ~]$ module load tools/netpbm-10.73.32
[lgrande2@node37 ~]$ 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: 16
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/20.04/afni
afni version : Precompiled binary linux_centos_7_64: Jul 12 2020
: AFNI_20.2.02 'Aulus Vitellius'
AFNI_version.txt : AFNI_20.2.02, linux_centos_7_64, Jul 12 2020
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/local/R/3.6.1/bin/R
R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/20.04/afni)
R : 1 (/usr/local/R/3.6.1/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)


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

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

R RHOME : /usr/local/R/3.6.1/lib64/R

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

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib64/python2.7/site-packages/PyQt4/__init__.pyc

** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /usr/local/netpbm/10.73.32/bin:/usr/local/afni/20.04:/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:/home/lgrande2/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/local/netpbm/10.73.32/lib:/usr/local/afni/20.04:/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/20.04

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3


========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE

[lgrande2@node37 ~]$
Subject Author Posted

AFNI preprocessing help

leahariana July 02, 2020 05:01PM

Re: AFNI preprocessing help

ptaylor July 06, 2020 07:38AM

Re: AFNI preprocessing help

leahariana July 14, 2020 02:51PM

Re: AFNI preprocessing help

ptaylor July 14, 2020 03:41PM

Re: AFNI preprocessing help

leahariana July 20, 2020 01:27AM

Re: AFNI preprocessing help

ptaylor July 20, 2020 02:36PM

Re: AFNI preprocessing help

leahariana July 20, 2020 10:38PM

Re: AFNI preprocessing help

ptaylor July 22, 2020 09:43AM

Re: AFNI preprocessing help

ptaylor July 24, 2020 02:06PM