How to install deal.II

How to install deal.II

Yanming Wang

May, 2017

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Deal.II is an open Finite Element Method (FEM) code. For detailed description of the code and tutorials, you can refer to their offical website http://www.dealii.org/. Here we explain how to install it on the Sherlock cluster.

System Requirements

The installation of Deal.II requires cmake 3.2 and up, openmpi/1.10.2/gcc and gcc/4.8.1. They have been pre-installed as modules on the cluster, to load them, you can type the following commands on your terminal.

module load cmake/3.2.2
module load gcc/4.8.1
module load openmpi/1.10.2/gcc

Or you can paste the above three lines into your ~/.bashrc file, and type

source ~/.bashrc

Setup

Assuming you want to install the package in the home directory of group's shared space, you can firstly go to the folder by typing

cd /shared/PI/caiwei

From there, you can directly clone the package from Github.

git clone https://github.com/dealii/candi

Now you should have a folder called candi. The next step is to go into the folder and update the following two configuration files candi.cfg and dealii.package.

cd /shared/PI/caiwei/candi
wget -O candi.cfg http://micro.stanford.edu/mediawiki/images/1/1e/Candi.cfg.txt
cd /shared/PI/caiwei/candi/deal.II-toolchain/packages
wget -O dealii.package http://micro.stanford.edu/mediawiki/images/a/aa/Dealii.package.txt

Notice in candi.cfg, there is one line that specifies the installation path,

PREFIX_PATH=/share/PI/caiwei/dealii/

This needs to be modified if you intend to install the package in other places.

References

The below webpages would be useful when you are new to using the clusters.

https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/Main_Page

https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/I%27m_new_%26_don%27t_know_what_to_do

https://www.stanford.edu/group/hpcc/cgi-bin/mediawiki/index.php/New_to_Cluster_Computing