installing and running binary INLA on ubuntu cluster

[Hedvig Skirgård]

Hello dearest R-INLA community, 

I come to you with a much simpler question this time than previously. I need to install and run the latest and greatest version of INLA on a Ubuntu-cluster.

From what I've gathered from reading older messages in this group and other threads on the interwebs, what one should do is:

1) install the latest testing (beta) version

install.packages("INLA",repos=c(INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE, lib = "../rlibs")

2) Load INLA

library("INLA")

3) run the binary install pointing at the correct bin dir and with the right os specified

INLA::inla.binary.install(os = "Ubuntu-18.0", path = "../rlibs/INLA/bin/linux/")

But here's where I'm a bit uncertain. Once I've done these steps:

I tried a) setting certain options for inla.call as per a message from inla.binary.install()

inla.setOption(inla.call = " /data/users/skirgard/rlibs/INLA/bin/linux/64bit/inla.run ")

inla.setOption(fmesher.call = " /data/users/skirgard/rlibs/INLA/bin/linux/64bit/fmesher.run ")

Then it crashes because

sh: 1:  /data/users/skirgard/rlibs/INLA/bin/linux/64bit/inla.run

b) not making those settings, and then it seems to be running fine so far in my debug minimal examples.

After the binary install, whether I set those options or not I do

4) set the mode to experimental

INLA::inla.setOption(inla.mode="experimental")

Is this right? I want the latest INLA, I want the testing mode and experimental. In order to run it on the ubuntu-cluster, I need to do the binary install. Am I doing this right if I go with option (b), i.e. not these inla.call options?

Med vänliga hälsningar,

Hedvig Skirgård

PhD,  Australian National University

Postdoc at Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology 

Website

[Helpdesk]

Hi there,

yes install the testing version (with R-4.2) from as you do

do

library(INLA)

do once after each install

inla.binary.install()

you may chose the Ubuntu 1804 one, as we now default build with Ubuntu-
2004

you do not need to set anything else, as it will override the previously
installed binary

if this does not work, let me know

Best
H

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Håvard Rue
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[Hedvig Skirgård]

Thanks Håvard, 

I think it's going well, waiting to inspect some output soon :). Thanks for the help.

Would it be possible for the startup messages displayed by library("INLA") to say something as regard to the binary install and stable vs testing version? Right now it says this for me:

This is INLA_22.05.18-2 built 2022-05-18 09:30:37 UTC.

Med vänliga hälsningar,

Hedvig Skirgård

PhD,  Australian National University

Postdoc at Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology 

Website