Hi,
I recently installed AFNI on Ubuntu 16.04. When I try to run the superscript afni_proc.py, it gives me an error at 3dSkullStrip (error message: missing a library lib.gsl.so.0); BUT 3dSkullStrip runs fine alone.
I had the exact same issue with Mac OS X El Capitan (becasue of its “System Integrity Protection” feature), which I was able to fix using “csrutil disable” command. Is there something similar that can be done on Ubuntu?
Thank you for starting a different thread with this.
What is the output of:
afni_system_check.py -check_all
Thanks for getting back to me Rick. Here is the output of “afni_system_check.py -check_all”
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-45-generic
version: #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016
distribution: Ubuntu 16.04 xenial
number of CPUs: 36
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/glucksleepstudy/abin/afni
afni version : Precompiled binary linux_openmp_64: Nov 4 2016
AFNI_version.txt : AFNI_16.3.08, linux_openmp_64, Nov 04 2016
which python : /usr/bin/python
python version : 2.7.12
which R : /usr/bin/R
R version : R version 3.3.2 (2016-10-31) – “Sincere Pumpkin Patch”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/glucksleepstudy/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
SurfMesh : 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!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lme4!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
checking for $HOME files…
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /home/glucksleepstudy/bin:/home/glucksleepstudy/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/fsl/5.0:/home/glucksleepstudy/abin
PYTHONPATH =
R_LIBS = /home/glucksleepstudy/R
LD_LIBRARY_PATH = /usr/lib/fsl/5.0
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/glucksleepstudy/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.2.12 (amd64)
have Ubuntu system: Ubuntu 16.04 xenial
============================ summary comments ============================
Try installing libgsl via:
sudo apt-get install libgsl-dev
Then run afni_system_chec.py -check_all again
and see how it goes.
The libgsl-dev install was successful. Here is the output from afni_system_check
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-45-generic
version: #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016
distribution: Ubuntu 16.04 xenial
number of CPUs: 36
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/glucksleepstudy/abin/afni
afni version : Precompiled binary linux_openmp_64: Nov 4 2016
AFNI_version.txt : AFNI_16.3.08, linux_openmp_64, Nov 04 2016
which python : /usr/bin/python
python version : 2.7.12
which R : /usr/bin/R
R version : R version 3.3.2 (2016-10-31) – “Sincere Pumpkin Patch”
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/glucksleepstudy/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
SurfMesh : 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!
These packages are not installed on the computer: snow!
These packages are not installed on the computer: lme4!
These packages are not installed on the computer: paran!
These packages are not installed on the computer: psych!
checking for $HOME files…
.afnirc : found
.sumarc : missing
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4
-------------------------------- env vars --------------------------------
PATH = /home/glucksleepstudy/bin:/home/glucksleepstudy/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/fsl/5.0:/home/glucksleepstudy/abin
PYTHONPATH =
R_LIBS = /home/glucksleepstudy/R
LD_LIBRARY_PATH = /usr/lib/fsl/5.0
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing suma_demo
data dir : missing FATCAT_DEMO
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/glucksleepstudy/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.2.12 (amd64)
have Ubuntu system: Ubuntu 16.04 xenial
============================ summary comments ============================
glucksleepstudy:~>
Hi-
What is the output of:
$ find /usr/lib/ -name “libgsl*”
?
(I believe from previous 16.04 building that they get put under “/usr/lib/x86_64-linux-gnu/”, and not under “/usr/lib/”, and if that is the case we should be able to make a symbolic link to sort it out.)
–pt
Hi,
The output is:
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/lib/x86_64-linux-gnu/libgslcblas.a
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0.0.0
/usr/lib/x86_64-linux-gnu/libgsl.so.19
/usr/lib/x86_64-linux-gnu/libgslcblas.so.0
/usr/lib/x86_64-linux-gnu/libgsl.a
/usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0
Hi-
Talking with Rick, we think that if you make a link by typing:
$ sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0
(and entering your password when prompted), then that should sort things out.
–pt
Afni now works perfectly! Thank you!
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