Hi Lisa,
Sorry for the delayed response. I've been working on a solution to the
problem you raised.
As you noted, the libnetcdf.so.6 file is no longer available at the
places previously suggested.
Please try the following:
1. Install the hdf5 library files that are prerequisites for libnetcdf6
* Create a directory in your home directory called mylib
$ cd
$ mkdir mylib
* Download libhdf5-serial-1.8.4_1.8.4-patch1-3ubuntu2_amd64.deb
$ cd ~/Downloads
$ wget
http://archive.ubuntu.com/ubuntu/pool/universe/h/hdf5/libhdf5-serial-1.8.4_1.8.4-patch1-3ubuntu2_amd64.deb
o This assumes you are running a 64-bit version of Ubuntu
which hopefully you are. The HCP Pipelines themselves will
not run correctly on a 32-bit version of Ubuntu.
* Extract the shared library files from the .deb file, and put
them in your mylib directory.
$ cd ~/mylib
$ ar xv
~/Downloads/libhdf5-serial-1.8.4_1.8.4-patch1-3ubuntu2_amd64.deb
$ rm control.tar.gz debian-binary
$ tar xvf data.tar.gz
$ mv ~/mylib/usr/lib/* .
$ rm -rf ~/mylib/usr
$ rm data.tar.gz
2. Install libnetcdf6 library files
* Download libnetcdf6_4.1.1-6_amd64.deb
$ cd ~/Downloads
$ wget
http://archive.ubuntu.com/ubuntu/pool/universe/n/netcdf/libnetcdf6_4.1.1-6_amd64.deb
* Extract the shared library files from this .deb file and put
them in your mylib directory.
$ cd ~/mylib
$ ar xv ~/Downloads/libnetcdf6_4.1.1-6_amd64.deb
$ rm control.tar.gz debian-binary
$ tar xvf data.tar.gz
$ mv ~/mylib/usr/lib/* .
$ rm -rf ~/mylib/usr
$ rm data.tar.gz
3. Change your LD_LIBRARY_PATH environment variable
Use a text editor to add the following statements to the
.bash_profile file in your home directory. (If a .bash_profile file
does not exist in your home directory, simply create one with the
following contents.)
if [ -z "${LD_LIBRARY_PATH}" ] ; then
export LD_LIBRARY_PATH=${HOME}/mylib
else
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/mylib
fi
4. Completely log off and log back in again. Try to run FreeSurfer's
mris_make_surfaces binary using the environment set up you use for
running the pipeline.
$ source
/<what//ever-environment-//s//et-up-file-you//-are-using-for-running-this-p//ipeline>/
$ mris_make_surfaces
If the response to the above command is:
mris_make_surfaces: error while loading shared libraries:
libnetcdf.so.6: cannot open ...
then we haven't solved your problem.
On the other hand, if the response is the help information for the
mris_make_surfaces program, something like:
Help
NAME
mris_make_surfaces
SYNOPSIS
mris_make_surfaces [options] <subject name> <hemisphere>
DESCRIPTION
This program positions the tessellation of the cortical
surface at the
...
then I believe you will be able to run mris_make_surfaces and thus the
pipeline.
Either way, please respond to the list to let us know whether this
works. If it does work, then others will be able to find this thread as
you found the previous threads about this topic. If it doesn't work,
we'll investigate further.
Best Regards,
Tim
On 06/27/2017 03:46 AM, Lisa Kramarenko wrote:
Dear experts,
I am getting the following error when the FreeSurferPipeline comes to
the mris_make surfaces step:
mris_make_surfaces: error while loading shared libraries:
libnetcdf.so.6: cannot open shared object file: No such file or directory
It happens when I run it on Ubuntu 14 and 16, however, it works just
fine on Ubuntu 12. I read this thread
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg00782.html
and
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02419.html,
however I cannot find the libnetcdf.so.6 at all in order to install it.
Do you have an idea about how to fix it and enable running this
pipeline on a newer Ubuntu?
Thanks a lot!
Lisa
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--
/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
/
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