edanssandes / MASA-OmpSs

The MASA-OpenMP extension is used with the MASA architecture to align DNA sequences of unrestricted size with the Smith-Waterman/Needleman-Wunsch algorithms combined with Myers-Miller. It uses the OmpSs Programming model for accelerating the computation time.

MASA-OmpSs

The MASA-OmpSs extension is used with the MASA architecture to align DNA sequences of unrestricted size with the Smith-Waterman/Needleman-Wunsch algorithms combined with Myers-Miller. It uses the OmpsSs Programming model to accelerate the computation time in CPU.

Download

Latest Version: masa-ompss-1.0.1.1024.tar.gz

Compiling (masa-ompss)

tar -xvzf masa-ompss-1.0.1.1024.tar.gz
cd masa-ompss-1.0.1.1024
./configure
make

In order to compile masa-ompss successfully, you need to install the OmpSs packages (Nanos++ runtime library and Mercurium compiler). See the OmpSs download pages. For Ubuntu, you can download and install all the packages with the following commands (running with root privileges):

# echo 'deb http://pm.bsc.es/ompss/packages/debian wheezy main' > /etc/apt/sources.list.d/OmpSs.list
# wget -O - http://pm.bsc.es/ompss/packages/debian/ompss.gpg.key | apt-key add -
# apt-get update && apt-get install ompss

Executing

./masa-ompss [options] seq1.fasta seq2.fasta

All the command line arguments can be retrieved using the --help parameter. See the wiki for a list of command line examples.

License:

MASA-OmpSs is an open source project with public license (GPLv3). A copy of the LICENSE is maintained in this repository.