RAVE:UAB
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How to use RAVE on the UAB Cheaha Cluster
First time only (installs RAVE for an account)
- Establish Cheaha account with Office of Research Computing. Be sure to request a 16 gb RAM HPC desktop
- Open Terminal to Cheaha
type
module load FriBidi/1.0.10-GCCcore-10.3.0 module load HarfBuzz/2.8.1-GCCcore-10.3.0 module load R/4.1.0-foss-2021a
type
R
to start R. Then,
install.packages('ravemanager', repos = 'https://beauchamplab.r-universe.dev') ravemanager::install()
To use RAVE (after installation)
module load R/4.1.0-foss-2021a R
Then, start RAVE within R using the commands
rave::start_rave()
or
rave::launch_demo()
This may launch a "graphics device". This can be safely minimized. For analysis of large datasets, you may need to request additional resources. To check on resource usage, type
seff <jobid>
where <jobid> found on My Interactive sessions or
sacct -u <blazerid> -X
After you have loaded RAVE under your personal account, you may need to set your RAVE data dir and raw dir to point to data stored in a shared project directory.
To view your data dir, run in the R console:
raveio::raveio_getopt('data_dir')
To set your data dir:
rave_options(data_dir = 'path/to/shared_data_dir')
To view/set your raw data dir:
raveio::raveio_getopt('raw_data_dir') rave_options(raw_data_dir = 'path/to/shared_raw_data_dir')