AFNI programs show FAILURE

uwold · October 20, 2016, 7:37pm

Hello,

I am installing the AFNI program. I am able to launch the program. But when I entered the following command:

afni_system_check.py -check_all

Programs such as 3dSkullStrip and 3dRSFC show failure. I don’t understand why because I have entered the folllowing command:

sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0

Both libgsl.so and libgsl.so.0 are present in their respective directory.

The output from the command is shown below. Any help would be much appreciated.

Thank you!

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 4.4.0-42-generic
version: #62-Ubuntu SMP Fri Oct 7 23:11:45 UTC 2016
distribution: Ubuntu 16.04 xenial
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /home/michael/abin/afni
afni version : Precompiled binary linux_openmp_64: Oct 13 2016
AFNI_version.txt : AFNI_16.3.03, linux_openmp_64, Oct 13 2016
which python : /usr/bin/python
python version : 2.7.12
which R : /usr/bin/R
R version : R version 3.3.1 (2016-06-21) – “Bug in Your Hair”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/home/michael/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: Error 40
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.0: cannot open shared object file: Error 40
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 -------------------------------
++ module ‘PyQt4’ found at /usr/lib/python2.7/dist-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /home/michael/bin:/home/michael/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/michael/abin:/home/michael/abin:/home/michael/abin:/home/michael/abin

PYTHONPATH =
R_LIBS = /home/michael/R

LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH = /home/michael/abin

------------------------------ 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/michael/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 ============================

AFNI programs show FAILURE
insufficient data for AFNI bootcamp

dglen · October 20, 2016, 10:10pm

You have to install the gsl library which are probably called gsl-bin on ubuntu. See these instructions and this previous post:

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu.html

https://afni.nimh.nih.gov/afni/community/board/read.php?1,141174,141174

uwold · October 21, 2016, 1:12am

Hello,

Thank you for the help. I have already installed gsl-bin on my computer. And I followed the installation steps listed on this webpage:

https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu.html

But still, I am getting such error. Do I have to start from scratch again? I am using Ubuntu 16.04.

Thank you.

uwold · October 21, 2016, 3:09am

Could it be because I am using Ubuntu 16.04?

rickr · October 21, 2016, 12:05pm

What is the output of these 4 commands?

ls -l /usr/lib/x86_64-linux-gnu/libgsl.*
file  /usr/lib/x86_64-linux-gnu/libgsl.*

ls -l /usr/lib/libgsl.*
file  /usr/lib/libgsl.*

rick

uwold · October 21, 2016, 5:59pm

Thank you for your help Rick! Below is the output from the four commands.

~> ls -l /usr/lib/x86_64-linux-gnu/libgsl.*
lrwxrwxrwx 1 root root 20 Oct 17 17:55 /usr/lib/x86_64-linux-gnu/libgsl.so → /usr/lib/libgsl.so.0
lrwxrwxrwx 1 root root 16 Dec 7 2015 /usr/lib/x86_64-linux-gnu/libgsl.so.19 → libgsl.so.19.0.0
-rw-r–r-- 1 root root 2352808 Dec 7 2015 /usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0

~> file /usr/lib/x86_64-linux-gnu/libgsl.*
/usr/lib/x86_64-linux-gnu/libgsl.so: broken symbolic link to /usr/lib/libgsl.so.0
/usr/lib/x86_64-linux-gnu/libgsl.so.19: symbolic link to libgsl.so.19.0.0
/usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=df4f3d1f505c3f6eff70f86f04fc46bb2027614d, stripped

~> ls -l /usr/lib/libgsl.*
lrwxrwxrwx 1 root root 35 Oct 20 19:32 /usr/lib/libgsl.so.0 → /usr/lib/x86_64-linux-gnu/libgsl.so

~> file /usr/lib/libgsl.*
/usr/lib/libgsl.so.0: broken symbolic link to /usr/lib/x86_64-linux-gnu/libgsl.so

It says broken symbolic link on two occasions. Could that be the problem?

uwold · October 21, 2016, 7:30pm

I removed the symbolic link and then recreated it but that did not seem to work.

I also reinstalled gsl-bin using apt-get but that did not seem to help either.

Below is the output from those 4 commands. Your help will be much appreciated.

~> ls -l /usr/lib/x86_64-linux-gnu/libgsl.*
lrwxrwxrwx 1 root root 16 Dec 7 2015 /usr/lib/x86_64-linux-gnu/libgsl.so.19 → libgsl.so.19.0.0
-rw-r–r-- 1 root root 2352808 Dec 7 2015 /usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0

~> file /usr/lib/x86_64-linux-gnu/libgsl.*
/usr/lib/x86_64-linux-gnu/libgsl.so.19: symbolic link to libgsl.so.19.0.0
/usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=df4f3d1f505c3f6eff70f86f04fc46bb2027614d, stripped

~> ls -l /usr/lib/libgsl.*
lrwxrwxrwx 1 root root 35 Oct 21 12:40 /usr/lib/libgsl.so.0 → /usr/lib/x86_64-linux-gnu/libgsl.so

~> file /usr/lib/libgsl.*
/usr/lib/libgsl.so.0: broken symbolic link to /usr/lib/x86_64-linux-gnu/libgsl.so

rickr · October 21, 2016, 8:00pm

So you tried to make a link to /usr/lib/x86_64-linux-gnu/libgsl.so
but that actual file does not exist.

Try pointing the link at the existing so.19.0.0 file:

sudo rm /usr/lib/libgsl.so.0
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0 /usr/lib/libgsl.so.0

rick

uwold · October 21, 2016, 11:09pm

Thank you so much Rick! Now it works. Now the comment ‘AFNI programs show FAILURE’ does not show up anymore when I entered the command afni_system_check.py -check_all

Thank you very much!

giri · November 1, 2016, 3:17pm

Rick/AFNI team -

I just updated to OS Sierra and reinstalled AFNI.

But I now have an AFNI programs show FAILURE problem. Maybe more than one problem, but can you advise how to deal with the error message below when I try to create the .sumarc file with the command suma -update_env. It is looking for the dylib and I don’t know where to get hold of it from. The library doesn’t exist on my system, I assumed it would be installed as part of the overall installation.Much thanks. (Some of the AFNI failures are due to the same missing library.) Giri

dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/gkalamangalam/abin/suma
Reason: image not found
sh: line 1: 19069 Abort trap: 6 suma -environment > ___sumarc
– Error suma (SUMA_suma.c:732):
Failed to create env file.

rickr · November 1, 2016, 3:47pm

What is the output from:

afni_system_check.py -check_all

Have you done homebrew updates since upgrading
your OS?

rick

giri · November 1, 2016, 3:59pm

Rick - thanks for instantaneous response. Yes, I installed Homebrew after installing Sierra. Here is the full output of afni_system_check.py -check_all

-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 16.0.0
version: Darwin Kernel Version 16.0.0: Mon Aug 29 17:56:20 PDT 2016; root:xnu-3789.1.32~3/RELEASE_X86_64
distribution: 10.12 x86_64
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /Users/gkalamangalam/abin/afni
afni version : Precompiled binary macosx_10.7_Intel_64: Oct 31 2016
AFNI_version.txt : AFNI_16.3.06, macosx_10.7_Intel_64, Oct 31 2016
which python : /usr/bin/python
python version : 2.7.10
which R : /usr/local/bin/R
R version : R version 3.3.2 (2016-10-31) – “Sincere Pumpkin Patch”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/Users/gkalamangalam/abin/afni)
R : 1 (/Library/Frameworks/R.framework/Versions/3.3/Resources/bin/R)
python : 1 (/usr/bin/python)

testing ability to start various programs…
afni : success
suma : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/gkalamangalam/abin/suma
Reason: image not found
3dSkullStrip : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/gkalamangalam/abin/3dSkullStrip
Reason: image not found
uber_subject.py : success
3dAllineate : FAILURE
dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
Referenced from: /Users/gkalamangalam/abin/3dAllineate
Reason: image not found
3dRSFC : success
SurfMesh : FAILURE
dyld: Library not loaded: /sw/lib/libglib-2.0.0.dylib
Referenced from: /Users/gkalamangalam/abin/SurfMesh
Reason: image not found

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

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

------------------------------ python libs -------------------------------
** python module not found: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/fsl/bin:/Users/gkalamangalam/freesurfer/bin:/Users/gkalamangalam/freesurfer/fsfast/bin:/Users/gkalamangalam/freesurfer/tktools:/Users/gkalamangalam/freesurfer/bin/freeview.app/Contents/MacOS/:/Users/gkalamangalam/freesurfer/mni/bin:/Users/gkalamangalam/AFNIbin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin:/Users/gkalamangalam/abin

PYTHONPATH = /usr/local/lib/python2.7/site_packages

R_LIBS =
LD_LIBRARY_PATH =
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 /Users/gkalamangalam/abin

------------------------------ OS specific -------------------------------
which brew : /usr/local/bin/brew
brew version : Homebrew 1.0.9

============================ summary comments ============================

AFNI programs show FAILURE
consider running “suma -update_env” for .sumarc
insufficient data for AFNI bootcamp
OS X version might be old
consider running: brew install pyqt

rickr · November 2, 2016, 4:54pm

It seems that 10.12 currently is only a 2 number
version right now, which has thrown off the system
check a little.

What is the output of the following commands?

ls -l /usr/local/lib/libgomp*.dylib
ls -l /usr/local/lib/libglib*.dylib

ls -l /usr/local/Cellar/gcc/*/lib/gcc/*/libgomp*.dylib
ls -l /usr/local/Cellar/glib/*/lib/libglib*.dylib

rick

giri · November 2, 2016, 5:09pm

Rick

No match

for all 4 commands.

Giri

rickr · November 2, 2016, 5:47pm

Okay, then you need to install glib and gcc via homebrew.
Please perform step 2d on the OS X install page, which
should be:

brew install gcc --with-all-languages --without-multilib
ln -s /usr/local/Cellar/gcc/6.2.0/lib/gcc/6/libgomp.1.dylib /usr/local/lib/libgomp.1.dylib
brew install glib

Then send me an updated system check output.

Thanks,

rick

giri · November 4, 2016, 2:47pm

Rick - problems here also.

With the first brew command, the system auto-updates a few formulae and then hangs for several hours. I had to exit (^C) it.

It has no problems with the ln -s …command.

But hangs also with the the second brew command. I exited that also after a couple of hours.

Running the afni check commands afterwards just to see gives me the same error messages as last time.

Giri

pmolfese · November 4, 2016, 6:03pm

What’s the output of:


brew doctor

rickr · November 4, 2016, 6:28pm

Hi Giri,

Given that you had to terminate the processes, I would
not expect the libraries to be available for AFNI yet.

I don’t recall how much text output there is during the
installation, but I would have guessed it to be a fair
amount. And while gcc does take hours to install, glib
usually just takes a few moments. Do you have a reliable
network right now?

Hopefully Peter’s “brew doctor” output will suggest
something useful. A second attempt to install might too.
Once you are ready to try agagin, try “brew install glib”
first, since that is a much simpler install than gcc.

rick

giri · November 4, 2016, 8:50pm

Rick/Peter - thanks for suggestions. The command

brew doctor

also hangs.

I will try installing all the packages again, and try installing gcc first as Rick suggests.

Hopefully there will be a resolution before too long.

Giri

pmolfese · November 4, 2016, 11:35pm

If it continues to hang, you can try removing all of homebrew (and probably everything in /usr/local) and then starting the installation instructions over again. Good luck! Upgrading is always an interesting process in terms of the UNIX side of things.