NOTICE: FULL O2 Cluster Outage, January 3 - January 10th

O2 will be completely offline for a planned HMS IT data center relocation from Friday, Jan 3, 6:00 PM, through Friday, Jan 10

  • on Jan 3 (5:30-6:00 PM): O2 login access will be turned off.
  • on Jan 3 (6:00 PM): O2 systems will start being powered off.

This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.

Specifically:

  • The O2 Cluster will be completely offline, including O2 Portal.
  • All data on O2 will be inaccessible.
  • Any jobs still pending when the outage begins will need to be resubmitted after O2 is back online.
  • Websites on O2 will be completely offline, including all web content.

More details at: https://harvardmed.atlassian.net/l/cp/1BVpyGqm & https://it.hms.harvard.edu/news/upcoming-data-center-relocation

Installing Other R packages on O2

Owned by Gaby Rodriguez
Last updated: Dec 19, 2024
3 min read

Please make sure to setup an R Personal Library on O2 to install packages locally.

Here you can find valuable information on how to install R packages requiring some external dependencies.

R package - beachmat and glmGamPoi

# Load modules module purge module load gcc/9.2.0 R/4.3.3 # Launch R R # Install packages install.packages('BiocManager') BiocManager::install('beachmat') BiocManager::install("glmGamPoi")

The beachmat and glmGamPoi packages do not work with recent R versions. To install them on O2, you can load the R/4.3.3 module, which is an older R version compatible with both packages.

R package - curl

# Load modules module purge module load gcc/9.2.0 R/4.4.0 # Install cURL locally mkdir $HOME/CURL_LOCAL && cd $HOME/CURL_LOCAL wget https://curl.se/download/curl-8.7.1.tar.gz tar xvzf curl-8.7.1.tar.gz && cd curl-8.7.1 ./configure --with-openssl --prefix $HOME/CURL_LOCAL make make install # Create a Makevars file with the following output mkdir ~/.R echo "CFLAGS+=-I/home/$USER/CURL_LOCAL/include" >> ~/.R/Makevars echo "CXXFLAGS+=-I/home/$USER/CURL_LOCAL/include" >> ~/.R/Makevars echo "LDFLAGS+=-L/home/$USER/CURL_LOCAL/lib" >> ~/.R/Makevars # Launch R and install rtracklayer R install.packages('remotes') remotes::install_github('jeroen/curl@v4.3.2')

The curl package is needed to install popular R packages such as devtools, rtracklayer and Seurat (v5). You will need to install an older version of curl until the OS for O2 is updated from CentOS to RedHat.

R package - igraph

# Load Modules module purge module load gcc/9.2.0 R/4.3.1 glpk/5.0 # Create ~/.R/Makevars mkdir ~/.R echo "CFLAGS+=-I/n/app/glpk/5.0-gcc-9.2.0/include" >> ~/.R/Makevars echo "CPPFLAGS+=-I/n/app/glpk/5.0-gcc-9.2.0/include" >> ~/.R/Makevars echo "LDFLAGS+=-L/n/app/glpk/5.0-gcc-9.2.0/lib" >> ~/.R/Makevars echo "CPATH+=/n/app/glpk/5.0-gcc-9.2.0/include" >> ~/.R/Makevars # Start R R # Install package install.packages('igraph')

R package - nloptr

You must use an R version compiled against GCC v9.2.0 and load the CMake module. For example:

R package - Devtools

Load the git2 module if using an older R version (e.g., 4.0.1):

If using the R>=4.2.1 module, then it is not required to load the git2 module.


R package - Seurat

R packages - SF and Monocle3

R package - ACTIONet

The R package has not been maintained for the last few years; currently it is only possible to use through a singularity container.

R package - InferCNV

R package - Rmpi

The package must be installed using an sbatch job. For example:

1. Create an sbatch script with the following content

2. Submit script via the sbatch command

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