Installing INLA on linux sytem

[Yimer Wasihun]

Dear All,

I was trying to use a super computer to do some simulations. It is linux system. So to install r-inla, I just follow the usual procedure like as:

install.packages("INLA", repos="https://www.math.ntnu.no/inla/R/testing")

It works fine for installation and with library(INLA). The problem is that when I use a certain function in the package. For example, when I use inla.nonconvex.hull, I found the following problem:

>   Centroides <-read.delim("centroids_BE.txt")

>   Borders <- as.matrix(Centroides[-1]/10^6)

>   BEdomain <- inla.nonconvex.hull(Borders, convex=-0.05, concave=-0.06) 

/R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/fmesher: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/fmesher)

/R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/fmesher: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/fmesher)

/R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/fmesher: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/libgsl.so.0)

Error in fmesher.read(prefix, "manifold") : 

  File '/tmp/RtmpSc2B8w/fmesher9aca4a15939f.manifold' does not exist.

Would you mind please to let me know how to solve this if you have ever experienced it? 

Sorry if the question is out of the topic or not related to r-inla.

Kind regards,

Yimer

[INLA help]

On Tue, 2016-05-31 at 13:58 -0700, Yimer Wasihun wrote:
> Dear All,
>
> I was trying to use a super computer to do some simulations. It is
> linux system. So to install r-inla, I just follow the usual procedure
> like as:
> install.packages("INLA", repos="https://www.math.ntnu.no/inla/R/testi
> ng")
> It works fine for installation and with library(INLA). The problem is
> that when I use a certain function in the package. For example, when
> I use inla.nonconvex.hull, I found the following problem:
> >   Centroides <-read.delim("centroids_BE.txt")
> >   Borders <- as.matrix(Centroides[-1]/10^6)
> >   BEdomain <- inla.nonconvex.hull(Borders, convex=-0.05, concave=-
> 0.06) 
> /R/x86_64-pc-linux-gnu-library/3.2/INLA/bin/linux/64bit/fmesher:
> /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> (required by /R/x86_64-pc-linux-gnu-
> library/3.2/INLA/bin/linux/64bit/fmesher)
>

you are probably on an older linux system, and you have to revert back
to a simpler build, 

library(INLA)
INLA:::inla.dynload.workaround()



--
Håvard Rue
he...@r-inla.org

[Yimer Wasihun]

Dear Håvard,

Thank you so muchhhh. Now it is working. 

Kind regards,

Yimer

[Mark]

Since this thread has gotten a lot of traffic, and I myself just ran into this issue, I thought I would update it. The following call:

INLA:::inla.binary.install()

is probably the easiest way to get the appropriate linux build. I believe INLA:::inla.dynload.workaround() is deprecated. 

.

[INLA help]

yes,

inla.binary.install()

Is the way to install alternative Linux builds. As now

CentOS 6 (with 2.4 kernel)
CentOS 7
CentOS 8

Ubuntu 16.04
Ubuntu 18.04
Ubuntu 20.04 (recently, obviously)

Is supported. When we transfer to R-4.0, then we will leave Ubuntu 16.04


I also want to mention a recent

inla.prune()


Which will remove (optionally) builds from other OS’s from the installation, hence save quite a lot of disk space.

Like, if you run on a Mac, you do not need to have installed Linux build and various Windows builds.

H

-- 

Håvard Rue 

Helpdesk 

he...@r-inla.org

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[Will]

Working on a Mac, I find that I need to install CentOS 7 when using the R Studio Cloud server and even then INLA crashes with a complicated model that my peers can run on their systems. When I try the same thing on my desktop R Studio, I can't even get to the point of installing CentOS 7 because of Error in inla.binary.install() : inla.os.type() == "linux" is not TRUE. I can't install the dependencies on my Mac that I need and so, it can't run on my machine. Any help you could offer would be much appreciated.

Thanks!

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[INLA help]

Hi,

I have not used R Studio server, the install system assumes you run on the system you’re on. So if you’re on a Mac, it will assume you want to run there. If you then ‘export’ your library to another OS, then it will use that os. You can do this manually, by downloading from 

https://inla.r-inla-download.org/Linux-builds/

And simply replace the 64bit directory you want with the one you download from here. 

I guess you’re on R-4.0 both places? 

-- 

Håvard Rue 

Helpdesk 

he...@r-inla.org

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