Body
Quest and Kellogg Linux Cluster Downtime, December 14 - 18.
Quest, including the Quest Analytics Nodes, the Genomics Compute Cluster (GCC), the Kellogg Linux Cluster (KLC), and Quest OnDemand, will be unavailable for scheduled maintenance starting at 8 A.M. on Saturday, December 14, and ending approximately at 5 P.M. on Wednesday, December 18. During the maintenance window, you will not be able to login to Quest, Quest Analytics Nodes, the GCC, KLC, or Quest OnDemand submit new jobs, run jobs, or access files stored on Quest in any way including Globus. For details on this maintenance, please see the Status of University IT Services page.
Quest RHEL8 Pilot Environment - November 18.
Starting November 18, all Quest users are invited to test and run their workflows in a RHEL8 pilot environment to prepare for Quest moving completely to RHEL8 in March 2025. We invite researchers to provide us with feedback during the pilot by contacting the Research Computing and Data Services team at quest-help@northwestern.edu. The pilot environment will consist of 24 H100 GPU nodes and seventy-two CPU nodes, and it will expand with additional nodes through March 2025. Details on how to access this pilot environment will be published in a KB article on November 18.
Installing and Managing R Packages on Quest
R packages are installed, whether system-wide or locally in your own directory, for specific versions of R. If you switch versions of R, you may need to reinstall packages you use. However, packages only need to be installed once on Quest for each version of R. Once installed, a package is available across all log in and compute nodes on Quest for that version of R. On the analytics node, due to technical limitations, there are a limited set of modules that are pre-loaded, and they are, exclusively,
hdf5/1.14.1-2-gcc-12.3.0
gsl/2.7.1-gcc-12.3.0
fftw/3.3.10-gcc-12.3.0
gdal/3.7.0-gcc-12.3.0
nlopt/2.7.1-gcc-12.3.0
If your R package depended on a module that is not one of the above, it will not load properly on the analytics node.
System-wide Packages
A limited number of R packages have been installed centrally for each version of R. These packages can be used without downloading and installing them first. You can get a list of the currently installed packages with the command:
installed.packages()
Package Installation
Users can install additional R packages from CRAN by launching RStudio and using the Packages tab in the bottom-right window, or by running the R command line console and using the install.packages command:
install.packages(c("packagename1", "packagename2"))
with a list of the packages you need. Packages should generally be installed under your home directory. They will be available for you to use across Quest nodes.
First-time Installation
The first time you install an R package on Quest, you may see an error like:
Warning in install.packages("glmnet", repos = "https://cloud.r-project.org/") :
'lib = "/hpc/software/R/4.0.3/lib64/R/library"' is not writable
Would you like to use a personal library instead? (y/n)
Answer "y" to use a personal library. Then it will ask you:
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/4.0
to install packages into? (y/n)
Answer "y" again. The installation should then proceed successfully. This will install the packages in your home directory.
Setting the Repository
If you get an error message indicating that a particular package isn't available for a certain version of R, or you get another error related to the package repository, you may need to explicitly set the mirror from which you want R to download the package. List of CRAN mirrors. Choose an http (instead of https) mirror. You can set the mirror before trying to install packages with the command:
options(repos = "https://cloud.r-project.org/")
or as part of the install.packages call with the repos argument:
install.packages(c("packagename1", "packagename2"), repos = "https://cloud.r-project.org/")
Compiled Packages
For Use on Login and Compute Nodes
Some packages compile underlying code as a part of the installation. To install such packages, you may need to load a newer version of the gcc compiler before starting R and installing the package. Loading a different compiler should NOT be done for packages you intend to use on the Analytics nodes, as the updated gcc modules are not available on those nodes.
For example, if while installing a package, you see an error like:
configure: WARNING: Only g++ version 4.6 or greater can be used with...
try loading the module for a newer version of gcc; For example, after logging into Quest:
module load gcc/5.1.0
module load R/4.4.0
R
then in the R console, issue the package installation commands again.
For Use on Analytics Nodes
R packages intended for use on the Analytics nodes should be installed from within an R session running in RStudio in the web browser on the Analytics nodes. If you encounter compilation or installation errors for a package, please contact quest-help@northwestern.edu with the details for further assistance.
Note
Some compiled packages cannot be successfully installed by individual users. Please contact quest-help@northwestern.edu if you run into trouble with a particular package. Also, you can check out our page on troubleshooting the installation of common R packages in case your package is on this list!
More Options
See the R help page for install.packages for more options, such as installing local (user-created or downloaded) packages or changing the directory where packages are installed. The latter can be used to install packages in your project space instead of your home directory, which might be useful if others on the allocation also need to access the packages. To install packages from GitHub, use the install_github function in the devtools package or use the github install package.
Task Views
CRAN Task Views are collections of packages used frequently in particular fields. They allow you to install all of the packages associated with the task view at once. See the R documentation for more details and the commands to use.
Additional Help
Please contact quest-help@northwestern.edu for additional help with R package installation.