Running RStudio for R/4.0.0 on a live session on Yggadrasil

HPC Technical
1

Dear admins and users,

I am trying to use RStudio on my Yggdrasil session to request an interactive session and perform some data exploration on a dataset too huge to load and process in a standard computer. I would like to use R 4.0.0 or above.

I read the procedure described here:hpc:applications_and_libraries [eResearch Doc] and performed the following steps:

Obtain Rstudio with:

wget https://download1.rstudio.org/electron/centos7/x86_64/rstudio-2023.06.0-421-x86_64-fedora.tar.gz

Extract it with tar axvf.

Then, I check where is located the RStudio executable and its located at: Downloads/rstudio-2023.06.0+421/rstudio

I then start an interactive session with say:

salloc -p debug-cpu -n 1 -c 16 --x11

Since I want to run R/4.0.0, I do

module spider R/4.0.0

and see that I need to load these modules:

module load GCC/9.3.0  OpenMPI/4.0.3

Then, when I want to run the following (as explained in the documentation):

module load PostgreSQL/11.3-Python-3.7.2

I have an error that these modules cannot be loaded and actually need GCCcore/8.2.0 (obtained with spider)

Hence, I run this command:

module load  GCCcore/8.2.0
module load PostgreSQL/11.3-Python-3.7.2

Then I want to execute RStudio and hence run:

~/Downloads/rstudio-2023.06.0+421/rstudio

and I obtain:

/home/users/v/voirolli/Downloads/rstudio-2023.06.0+421/rstudio: error while loading shared libraries: libatk-bridge-2.0.so.0: cannot open shared object file: No such file or directory

Apparently this library libatk-bridge is missing.

Could you please help me and tell me what modules I need to load to then run RStudio with R/4.0.0 on an interactive session?

Thanks a lot

Best

Lionel

2

Hi,

it seems it is hard to make it working: there is a version for EL7 and EL9 and we are using EL8 :frowning:

I’ve asked the EasyBuild community and they suggest that we launch rstudio-server and connect to it through a browser. If some of you want to share your ideas or script to do so, you are more than welcome.

We’ll see what we we can do to help but unfortunately not in a short delay.

3

Hi Yann,

Thank you for taking a look at it and your reply.

Is this the case because of the R version I am considering (4.0.0) or is it due to RStudio itself?

What I mean is that I could potentially consider an older version of R if it is possible to run RStudio with an older version of R.

If this is not the case, and it’s indeed a problem running RStudio on the server, then I’d be delighted if you could keep me informed of your progress in this direction.

Thanks a lot

Best

Lionel