peregrine

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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