dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib

loveH · August 10, 2017, 3:19am

Dear experts,

I’m quite new in AFNI. I got this error when running 3dClustSim:

[zhengmatoMacBook-Pro:~] zhengdang% 3dClustSim -fwhm 7
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/zhengdang/abin/3dClustSim
Reason: image not found

How could I fix it??

Thanks a lot in advance

Dang Zheng

ptaylor · August 10, 2017, 3:27am

Hi, Dang-

We normally recommend that Mac users follow the install instructions here and use the “local” Mac build, which should avoid those problems:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html

That should sort out the libgomp errors? You can check the status of your install by running:


afni_system_check.py -check_all

(as well as your function(s) of choice),

–pt

loveH · August 11, 2017, 1:02am

Thank you.
I update to the latest version like this:

[zhengmatoMacBook-Pro:~] zhengdang% afni -ver
Precompiled binary macosx_10.7_Intel_64: Aug 9 2017 (Version AFNI_17.2.07)

And when I check the status, it showed like this:

[zhengmatoMacBook-Pro:~] zhengdang% afni_system_check.py -check_all
-------------------------------- 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: .tcshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/zhengdang/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Aug 9 2017
: AFNI_17.2.07
AFNI_version.txt : AFNI_17.2.07, macosx_10.7_Intel_64, Aug 09 2017
which python : /Library/Frameworks/Python.framework/Versions/2.7/bin/python
python version : 2.7.13
which R : /usr/local/bin/R
R version : R version 3.3.3 (2017-03-06) – “Another Canoe”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/zhengdang/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 3
/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
/sw/bin/python2.7
/usr/bin/python
python2 : 1 (/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python3 : 1 (/Library/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 : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/zhengdang/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : FAILURE
/bin/sh: SurfMesh: command not found

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

python binaries under /sw/bin:
/sw/bin/python (sym link to /sw/bin/python2.7)
/sw/bin/python2.7

-------------------------------- env vars --------------------------------
PATH = /Library/Frameworks/Python.framework/Versions/2.7/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/sw/bin:/sw/sbin:/opt/local/bin:/opt/local/sbin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/Applications/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Users/zhengdang/abin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH (sub-shell) =
DYLD_FALLBACK_LIBRARY_PATH (sub-shell) =

------------------------------ 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 /Users/zhengdang/abin

------------------------------ OS specific -------------------------------
which fink : /sw/bin/fink
fink version : Package manager version: 0.41.1
which brew : /usr/local/bin/brew
brew version : Homebrew 1.3.1
which port : /opt/local/bin/port
port version : Error: Current platform “darwin 16” does not match expected platform “darwin 13”

++ found ‘brew’ at /usr/local/bin/brew
++ found PyQt4 under /usr/local/lib/python2.7/site-packages
++ found 1 dylib files under ‘/opt/X11/lib/flat_namespace’
– found ‘libXt’ dylib files:
/opt/X11/lib/flat_namespace/libXt.6.dylib
– recent OS X, cannot check DYLD_LIBRARY_PATH in cur shell, cheating …
** env var DYLD_LIBRARY_PATH not set to contain /opt/X11/lib/flat_namespace

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

AFNI programs show FAILURE
insufficient data for AFNI bootcamp
consider adding /usr/local/lib/python2.7/site-packages to PYTHONPATH
please set DYLD_LIBRARY_PATH to /opt/X11/lib/flat_namespace in tcsh