DTU HPC setup

Setup R and relevant packages for a DTU HPC account ( http://www.hpc.dtu.dk ) . Update: Now works with new LSF queue system.

Get Started

Login to your account

ssh $USER@login2.gbar.dtu.dk
qrsh

Note that the following instructions will override your ~/.R/Makevars so backup (or ignore if you don't know what this means).

Clone this repo to your home folder and run the main script

git clone https://github.com/DTUAqua/hpc_setup
cd hpc_setup
export PATH=${HOME}/bin:$PATH
MAKE="make -j8" make all

Submitting a script

Say we have an R script

echo "m <- diag(1e3)+1; system.time(for(i in 1:10) m%*%m)" > script.R

We can run the script the usual way by

R --vanilla < script.R

In order to submit this script to the queue replace the above line by

submit "R --vanilla < script.R"

On submission you'll see a list of default parameters attached to the job

Job parameters
==============

MAX_DURATION    = 08:00:00  (hh:mm:ss)
MAX_MEMORY      = 8gb
OMP_NUM_THREADS = 1
MC_CORES        = 1

These four environment variables can be passed to the submit command. We'll see some examples in the following.

Some real examples

• Example 1 Speeding up a single model using the parallel BLAS.
• Example 2 Speeding up residuals using the R package parallel.
• Example 3 Submitting Makefiles to the queue: A toy example.
• Example 4 Submitting Makefiles to the queue: A real example.