Dear Timothy, thanks a lot for your effort and this detailed description!!
Best, Lisa On 28 June 2017 at 19:59, Timothy B. Brown <[email protected]> wrote: > 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 > > <http://archive.ubuntu.com/ubuntu/pool/universe/h/hdf5/libhdf5-serial-1.8.4_1.8.4-patch1-3ubuntu2_amd64.deb> > > - 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/[email protected]/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 > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > -- > > > > > * Timothy B. Brown Business & Technology Application Analyst III Pipeline > Developer (Human Connectome Project) tbbrown(at)wustl.edu > <http://wustl.edu> * > ------------------------------ > The material in this message is private and may contain Protected > Healthcare Information (PHI). If you are not the intended recipient, be > advised that any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited. If you have received this email in error, please immediately > notify the sender via telephone or return mail. > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
