psamfass / samoa-chameleon

Sam(oa)^2 application that is able to use chameleon-lib. Based on original repo https://github.com/meistero/samoa

sam(oa)²

Space-Filling Curves and Adaptive Meshes for Oceanic And Other Applications.
Github repository: https://github.com/meistero/Samoa

Contents

1. Prerequisites
2. Installation
3. Local systems
4. SuperMUC
5. Linux Cluster and MAC Cluster
6. Compilation
7. Execution

Prerequisites

The following prerequisites are necessary in order to install and run sam(oa)²:

• git
• scons
• gfortran 4.7 or higher OR Intel Fortran Compiler 13.0 or higher
• (Optional) ASAGI v0.5.0 or higher for external geodata
• (Optional) Netcdf data files for ASAGI: For porous media flow, download the SPE10 data files from SPE10. A script is included in the data directory that converts them to netcdf files. For the tsunami scenario the netcdf files can be generated from our Tsunami repository

Installation

Local Systems

Create a directory (named samoa_dir here) and execute the following steps:

cd <samoa_dir>
git clone https://github.com/meistero/samoa .

This will download the source files for samoa into samoa_dir.

SuperMUC

Create a directory on the SuperMUC (named samoa_dir here). SuperMUC restricts access to outside sources and thus does not allow connections to https servers. However, there are two methods to clone sam(oa)² from github on the SuperMUC:

• By accessing the SuperMUC file system as a remote directory. git can then be executed locally:

    nohup sshfs <login>@supermuc.lrz.de:<samoa_dir> <local_dir>
    cd <local_dir>
    git clone https://github.com/meistero/samoa .
  

• By login with remote port forwarding. In this case an alternative URL must be used to clone the git repository:

    ssh -X <login>@supermuc.lrz.de -R <port>:github.com:9418
    cd <samoa_dir>
    git clone git://localhost:<port>/meistero/Samoa .
  

This will download the source files for samoa into samoa_dir. Additionally, in order to compile and run ASAGI and sam(oa)² on the SuperMUC, we must add the netcdf library to the CMAKE prefix path and load the following modules:

module unload gcc
module load git scons gcc/4.7 cmake/4.1 netcdf
export CMAKE_PREFIX_PATH=$NETCDF_BASE

At this point, you should be able to compile ASAGI and sam(oa)².

Linux Cluster and MAC Cluster

Create a directory (named samoa_dir here) and execute the following steps:

cd <samoa_dir>
git clone https://github.com/meistero/samoa .

This will download the source files for samoa into samoa_dir. The following modules should be loaded before compiling ASAGI and sam(oa)² on the Linux and MAC clusters

module unload gcc python
module load git cmake scons netcdf gcc/4.7
module load gnuplot

sam(oa)² supports both multithreaded and single-threaded MPI. Both ASAGI and sam(oa)² must link to the same respective libraries, thus it is necessary to compile ASAGI twice: once without MT support and once with MT support. Rename the single-threaded library to "libasagi_nomt.so" and the multi-threaded library to "libasagi.so".

At this point, you should be able to compile ASAGI and sam(oa)².

Compilation

In order to view all the compilation options sam(oa)² provides, you can execute the following command now:

scons --help

Typical settings are:

scons asagi_dir=<asagi_dir> compiler=gnu scenario=darcy -j<threads>
scons asagi_dir=<asagi_dir> compiler=intel target=debug scenario=swe -j<threads>

If you wish to simulate simple scenarios that do not require data files you can also disable asagi with the flag

scons asagi=No ...

Executables will be created in the directory samoa_dir/bin and should be run from samoa_dir.

Execution

For execution parameters refer to the online help by calling the executable with '-h' or '--help'.

Build Status