wyntonquery: Query the UCSF Wynton Environment

An R package that provides utility functions for querying the UCSF Wynton environment, in order to gather system details used to populate the information on the Wynton website.

Usages

Query compute node information via job submissions

To gather the information, in R, run:

> source(system.file(package="wyntonquery", "scripts", "system_info.R"), echo = TRUE)

This will identify all compute nodes on the cluster (by querying qhost) and launch a job on each one that gathers details on that particular node. Depending on the amount and type of jobs currently occupying the cluster nodes, this may take anywhere from a few minutes to hours to complete.

When completed, a tab-delimited file .data/host_table,{date}.tsv will be produced. To deploy this to Wynton website, copy this file to docs/assets/data/host_table.tsv, then commit and push.

Internal notes

How to Rebuild Wynton HPC Specification Database

  1. Query recently added nodes
cd .data
export R_WYNTONQUERY_EXCLUDE="$(cut -f 1 host_table.tsv | tail -n +4) qb3-hmid1"
qsub -v R_WYNTONQUERY_EXCLUDE="$R_WYNTONQUERY_EXCLUDE" ../inst/scripts/system_info.sge
  1. Update current database
Rscript merge_all.R
  1. Deploy
cp host_table.tsv ../../wynton/docs/assets/data/

Installation

R package wyntonquery is only available via GitHub and can be installed in R as:

remotes::install_github("ucsf-wynton/wyntonquery", ref="master")

Pre-release version

To install the pre-release version that is available in Git branch develop on GitHub, use:

remotes::install_github("ucsf-wynton/wyntonquery", ref="develop")

This will install the package from source.