README.md

In richelbilderbeek/peregrine: Work With The Groninger Peregrine Computer Cluster

peregrine

Branch | | ---------|-----------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------- master | | develop||

peregrine is:

• A collection of notes on the Groningen Peregrine computer cluster
• A collection of scripts for the Groningen Peregrine computer cluster
• An R package for some Peregrine functions
• Some presentations on the Groningen Peregrine computer cluster (see below)

Videos

• How to run an R script on Peregrine download (.ogv) YouTube
• How to install the pirouette R package on Peregrine download (.ogv) YouTube
• How to run a pirouette example on Peregrine download (.ogv) YouTube

Presentations

• Running (independent) jobs on the Peregrine computer cluster PDF ODP
• Running jobs with dependencies on the Peregrine computer cluster PDF ODP

Example

The most important function is is_pff: 'Is Peregrine-friendly Filename/Folder'. If this function returns FALSE, one better not uses that path on the Peregrine cluster!

library(peregrine)
library(testthat)

expect_true(is_pff(get_pff_tempdir()))
expect_true(is_pff(get_pff_tempfile()))
expect_false(is_pff("/local/tmp/peregrine_unfriendly"))
expect_false(is_pff("/tmp/peregrine_unfriendly"))

One can use to_pff to convert a filename or folder to its Peregrine-friendly equivalent.

Measurements

Using scripts/test_is_pff.R.

Can create file?

filename | can_create_file ------------------------|------------------ /local/tmp.txt | TRUE /local/tmp/tmp.txt | TRUE /tmp.txt | FALSE /tmp/tmp.txt | TRUE /data/tmp.txt | FALSE /data/p230198/tmp.txt | TRUE /home/p230198/tmp.txt | TRUE /home/tmp.txt | FALSE

Can start BEAST2?

prefix | can_start_beast ----------------|------------------ /local | TRUE /local/tmp | TRUE /tmp | FALSE / | FALSE /data | FALSE /data/p230198 | FALSE /home | FALSE /home/p230198 | FALSE

Can use BEAST2?

folder_name | can_use_beast ---------------|---------------- /tmp | FALSE/local/tmp | TRUE /data/p230198 | FALSE/home/p230198 | TRUE

Can use working dir?

folder_name | can_use_working_dir ----------------|---------------------- /tmp | FALSE /local/tmp | FALSE /data/p230198 | FALSE /home/p230198 | TRUE

richelbilderbeek/peregrine documentation built on Jan. 3, 2024, 7:42 p.m.