INLA (cgeneric) implementation for alpha=2 now available

[AlexandreBSimas]

We now have an implementation for exact Whittle-Matern fields with alpha = 2 in INLA and inlabru.

See INLA vignette or inlabru vignette.

[AlexandreBSimas]

Observe that to run alpha=2 now, you will need to install the rSPDE package from source.

The details on how to do it are given here: https://davidbolin.github.io/rSPDE/articles/build_source.html

[AlexandreBSimas]

Hi Karina,

Really good that you are going to use it!!

From what I see it is not finding g++ on /usr/local/bin folder:

/usr/local/bin/g++: No such file or directory

I updated the instructions here https://davidbolin.github.io/rSPDE/articles/build_source.html recently, so maybe when you saw, it was not updated.

Basically, you need to make sure you have gcc-14 installed (for instance, using brew):

brew install gcc@14

Then, you need to link it to that folder /usr/local/bin to be able use our Makefile:

sudo ln -s $(brew --prefix gcc@14)/bin/gcc-14 /usr/local/bin/gcc
sudo ln -s $(brew --prefix gcc@14)/bin/g++-14 /usr/local/bin/g++

This only creates a symbolic link to that folder.

You will also need eigen:

brew install eigen

and the following symbolic links:

sudo ln -s $(brew --prefix eigen)/include/eigen3 /usr/local/include/eigen3
sudo ln -s $(brew --prefix)/lib /usr/local/brewlib
sudo ln -s $(brew --prefix)/include /usr/local/brewinclude

With all of this, you should be able to install.

Please, let me know if you encounter any problems.

[karinalilleborge]

Thank you for clarifying, Alexandre! I was missing the dependencies, indeed. The error when trying to install rSPDE with remotes::install_github is now related to Eigen instead of g++.
I am trying to follow the instructions, but when I try to install it with brew, I get the following

Warning: eigen 3.4.0_1 is already installed and up-to-date.

Then when I try to link it with
sudo ln -s $(brew --prefix eigen)/include/eigen3 /usr/local/include/eigen3
it cannot find the file/directory:

ln: /usr/local/include/eigen3: No such file or directory

I also tried to do the brew reinstall eigen as it suggested that with the warning, but nothing changed.

I checked the location of eigen with brew --prefix eigen and got

/opt/homebrew/opt/eigen

but I must admit I am not sure if I understand what I should change in the linking (or if I should change something in the linking at all?).
Also, I don't understand the section about the Makefile. Where is this Makefile located? In rSPDE (that you can clone from git) or is it related to something else?

[AlexandreBSimas]

Hi Karina,

From the error: ln: /usr/local/include/eigen3: No such file or directory

you probably don't have an include folder inside /usr/local. So, you can try

sudo mkdir -p /usr/local/include

and then try to link again. After that, you can try to install again.

All you need to do is to create the link, because the Makefile, used to compile (it is inside the src folder from the devel-src branch). If you link like that, you probably will not need to touch the Makefile.

There is only one possibility, which is related to the intrinsic models, that sometimes make it annoying to compile, if you face that, the easiest way is to adjust the Makefile indeed. But let's not worry about this now, and there is a very good chance it will directly work.

Please, let me know if you still run into some problem.

[karinalilleborge]

I managed to make the link and also successfully downloaded rSPDE. 🥳 Thank you so much for the quick response and help.

[AlexandreBSimas]

Great!!! My pleasure!!