RE: gearing up for bootcamp

AFNI Message Board
1

Hi,
Trying to get my laptop all set up for next week’s bootcamp. I ran afni_system_check.py with the following output. Can’t seem to get rid of the 3dAllineate error – could someone please help with that, and any other red flags that popped up here?
Thanks,
Chuck

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 8
apparent login shell: tcsh

--------------------- AFNI and related program tests ---------------------
which afni : /Users/cfg2/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Aug 27 2015
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.0 (2017-04-21) – “You Stupid Darkness”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/cfg2/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/cfg2/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : success

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

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

------------------------------ python libs -------------------------------

** python module not found: PyQt4

 -> please see the output of "uber_subject.py -help_install"

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/cfg2/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: 25 Aug 2017 [rickr]: PPI scripts are now based on FT_analysis/s05.ap.uber
data dir : found suma_demo under $HOME
top history: Archive created by @PrepArchives in eomer.nimh.nih.gov : /Users/ziad/SUMA_Class_New/data/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found FATCAT_DEMO under $HOME/AFNI_demos
top history: Archive created on eomer: /Volumes/Data/ziad/SUMA_test_dirs/FATCAT/FATCAT_DEMO.Distro, Wed Apr 8 12:41:00 EDT 2015
atlas : found TT_N27+tlrc under /Users/cfg2/abin

------------------------------ OS specific -------------------------------
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
(consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH)

---------------------------- general comments ----------------------------

2

Hi, Chuck-

You have an older version of the Mac binaries, where linking libraries was more painful. Rick has wrapped up a lot of that in a newer distribution; so, if you move your current abin/ somewhere else, and then follow the “Install AFNI binaries” instructions here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html#install-afni-binaries

… that should sort things out, I think.

–pt

3

Thank you! I did as suggested (as well as follow some previously posted instructions related to El Capitan). Below is now the output of afni system check. Looks like there’s still something to do related to linking libraries (at the bottom)? How do I do this? Also, does everything else look OK?
Thanks,
Chuck

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.7.0
version: Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
distribution: 10.12.6 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/cfg2/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Sep 19 2017
: AFNI_17.2.16
AFNI_version.txt : AFNI_17.2.16, macosx_10.7_Intel_64, Sep 19 2017
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.4.0 (2017-04-21) – “You Stupid Darkness”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/cfg2/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.4/Resources/bin/R)
python : 1 (/usr/bin/python)
python2 : 1 (/usr/local/Cellar/python/2.7.14/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/usr/local/Cellar/python3/3.6.2/Frameworks/Python.framework/Versions/3.6/bin/python3.6)

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 : success

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

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

-------------------------------- env vars --------------------------------
PATH = /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/cfg2/abin

PYTHONPATH = /usr/local/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH = /opt/X11/lib/flat_namespace

DYLD_FALLBACK_LIBRARY_PATH = /Users/cfg2/abin

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: …PPI scripts are now based on FT_analysis/s05.ap.uber
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 /Users/cfg2/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.3.4

++ found valid link /usr/local/lib/libglib-2.0.dylib
to …/Cellar/glib/2.54.0/lib/libglib-2.0.dylib
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
++ yay, env var DYLD_LIBRARY_PATH contains /opt/X11/lib/flat_namespace

========================= summary, please fix: =========================

  • consider linking /usr/local/Cellar/gcc/7.2.0/lib/gcc/7/libgomp.1.dylib under /usr/local/lib
4

I didn’t think this had to be done if you were using the “local” version for the Mac, but the problem you run into can be solved pretty simply. Unfortunately, the brew install doesn’t update this library link, so it needs to be done separately with this command:

sudo ln -s /usr/local/Cellar/gcc/7.2.0/lib/gcc/7/libgomp.1.dylib /usr/local/lib/libgomp.1.dylib