Requirements

Mandatory

Autotools

Configuring the project is done with autoconf, and automake. It configures the projects by searching for the necessary dependencies and compiling source code. autoconf should tell you if anything vital is missing.

MPI

Most of the code is in Fortran and is compiled with an MPI script (for example mpif90). A very small part is in C and is compiled likewise (for examplewith a script mpicc). This suppose you have a Fortran and C compiler which are needed for testing purposes mostly. The MPI library should support the MPI2 standard.

You should also be able to run parallel jobs. The code is configured for PBS jobs, but you can also use mpirun and edit the batch file.

Warning

Pangolin has been tested with gfortran, pgf90, ifort for the Fortran compiler and MPICH, OpenMPI, Intel MPI for the MPI library. However, we do not claim to support all implementations and all versions (even if it should eventually).

We only guarantee at the moment the following configurations :

C	Fortran	MPI	Architecture	Machine
icc 13.1.0	ifort	IntelMPI 4.1.2	amd64	Neptune (CERFACS)
gcc 4.5.1	gfortran	OpenMPI 1.4.3	amd64	Pannus (CERFACS, PC)
gcc 4.7.2	gfortran	OpenMPI 1.4.5-1	amd64	Home PC

Table: MPI support

Perl

Needed to start the simulation (even though it can be done by hand). It should be installed by default.

HDF5

An I/O format which allows for parallel I/O. Even though Pangolin can manage ASCII data, it is the preferred I/O format.

netCDF

Input data is given in this format, which must be converted to HDF5 in a preprocessing step.

Recommended

Python 2.7+

A script is available to generate analytical solution into ASCII or HDF5 format. It can also be used to plot data with matplotlib and basemap (ASCII only). This version is only compatible with Python 2.7+ but not Python 3.*.

h5py

A Python package to manage the HDF5 format easily.

Perl modules

The following modules can be installed with cpanm (see ? for more details).

• Config::IniFiles : to read .ini files
• DateTime : to manage date and times
• DateTime::Format::Strptime : to manage date and times
• TAP::Harness  : to run unit and functional tests shipped with Pangolin
• Getopt::Long : to read command-line arguments
• File::Copy : copying files
• File::Slurp : reading files
• File::Find : finding files
• File::Which : finding executables

Docbook

Docbook is actually a format for writing documentation. This manual was generated with Docbook XSL. For that, you will need the packages xsltproc, fop and docbook-xsl. For validating the documentation, you may add xmlstarlet.

This should take care of the latest Docbook, but it also possible to generate documentation using Jade and DSSL. This was not tested and the XSL approach is recommended.

Doxygen

The other half of this documentation is generated from the source code with Doxyegen. It will document everything you should need to know about the source code.

Basemap

A python package to plot data on the sphere with a whole range of projections. The scripts shipped with Pangolin only works for ASCII data at the moment. You should get the latest version and install it from source. Do not forget to install matplotlib with it.

NCL

A plotting program used for publication-quality plotting. It can manage HDF5 files.

Installation help

Perl modules suite

Here, we will configure Perl to install modules without needing root privileges. All of our packages will be installed in ~/perl5 in this example. First, we install the utility cpanminus :

$ wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib

Then we set the local::lib package to use ~/perl5 from now on:

$  eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`

This can be put in .bash_profile (or the equivalent for your shell) for future sessions:

$ echo 'eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`'>> ~/.profile

Now we can install any package easily. For Pangolin, you may want to install everything :

$ cpanm TAP::Harness  Getopt::Long  File::Copy  File::Slurp  File::Find File::Which