LibBi

From HPC

To install LibBi, run the following command (e.g., on the login node):

curl -L https://git.io/fjPK6 | bash

Make sure you run the "echo..." command at the end of the post-install notes to add a line to your bash profile, which will ensure that all the necessary libraries can be found by LibBi.

You can test your installation using the following qsub script (putting in your email address in the second line):

#!/bin/bash
#$ -M email@lshtm.ac.uk -m be
#$ -N libbi_test
#$ -q short.q
#$ -l mem_free=4G,h_vmem=4.2G
#$ -V -cwd

libbi sample --target prior --model-file $HOME/local/share/LibBi/Test.bi --end-time 1 --nsamples 32 --output-file test.nc

If you save this in a file called, for example, libbi_test.sh, and run

qsub libbi_test.sh

should get an email sometime later saying that the test has succeeded.