Hello,
We're attempting to get RStudio Desktop and Server 2024.04.2+764 deployed on our Linux based High Performance Computing (HPC) cluster. We're currently running 2023.03.1+466 without issue.
We have several versions of R compiled on our HPC system, all installed on a shared file system available to the 200 compute nodes on the cluster and managed using the L-mod (Lmod: A New Environment Module System — Lmod 8.7.47 documentation) environment modules system.
The problem we're having when running either RStudio Desktop or Server is
2024-08-05T13:13:49.046Z DEBUG Ready to run
2024-08-05T13:13:49.169Z DEBUG instance lock: true, project: , file: false
2024-08-05T13:13:49.169Z DEBUG net-ipc: creating new message server; socket=/home/bviviano/.local/share/rstudio/rstudio.socket
2024-08-05T13:13:49.172Z DEBUG No rPath found, scanning for R
2024-08-05T13:13:49.173Z DEBUG Scanning system for R installations
2024-08-05T13:13:49.185Z DEBUG Using /usr/local/apps/R-4.4.0/intel-23.2/bin/R (found by /usr/bin/which/R)
2024-08-05T13:13:49.185Z DEBUG Done choosing R
2024-08-05T13:13:49.185Z DEBUG Preparing environment using R: /usr/local/apps/R-4.4.0/intel-23.2/bin/R
2024-08-05T13:13:49.186Z DEBUG Querying information about R executable at path: /usr/local/apps/R-4.4.0/intel-23.2/bin/R
2024-08-05T13:13:49.197Z DEBUG stdout: [no stdout produced]
2024-08-05T13:13:49.197Z DEBUG stderr: /usr/local/apps/R-4.4.0/intel-23.2/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
2024-08-05T13:13:49.197Z DEBUG status: 127 [failure]
2024-08-05T13:13:49.197Z DEBUG Error querying information about R: no output available
2024-08-05T13:13:49.199Z ERROR An unknown error occurred.
2024-08-05T13:13:49.258Z DEBUG net-ipc: 1914835 taking over as primary instance
All our versions of R are compiled with Intel compilers and we set the LD_LIBARY_PATH according to the version of Intel each R is compiled with, so it can find the needed libraries.
We believe the latest versions of RStdio are manipulating the LD_LIBRARY_PATH in such a way that it is removing our needed settings and therefore causing the
2024-08-05T13:14:49.449Z DEBUG stderr: /usr/local/apps/R-4.4.0/intel-23.2/lib64/R/bin/exec/R: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
error. Because R itself, when run at the CLI works without issue:
$ R
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
I suspect this is related to the newer capabilities of allowing the user to select specific versions of R.
My question is, because we use L-mod to manage the versions of R, in a rather complicated environment. How do we get the old behavior or not having RStudio trying to manage/manipulate the environment? I don't see a command line switch or environment variable setting that would let us just tell RStudio to do it the old way.
We've been using RStudio Desktop and Server for years on our HPC system, but in its current form, it's totally unusable in our environment.
Any suggestions for how we can resolve this situation?
Thanks!