PACE A Partnership for an Advanced Computing Environment

September 25, 2012

New and Updated Software: GCC, Maxima, OpenCV, Boost, ncbi_blast

Filed under: tech support — Semir Sarajlic @ 4:17 pm

Software Installation and Updates

We have had several requests for new or updated software since the last post on August 14.
Here are the details about the updates.
All of this software is installed on RHEL6 clusters (including force-6, uranus-6, ece, math, apurimac, joe-6, etc.)

GCC 4.7.2

The GNU Compiler Collection (GCC) includes compilers for many languages (C, C++, Fortran, Java, and Go).
This latest version of GCC supports advanced optimizations for the latest compute nodes in PACE.

Here is how to use it:

$ module load gcc/4.7.2
$ gcc <source.c>
$ gfortran <source.f>
$ g++ <source.cpp>

Versions of GCC already installed on RHEL6 cluster are gcc/4.4.5, gcc/4.6.2, and gcc/4.7.0

Maxima 5.28.0

Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, and sets, lists, vectors, matrices, and tensors. Maxima yields high precision numeric results by using exact fractions, arbitrary precision integers, and variable precision floating point numbers. Maxima can plot functions and data in two and three dimensions.

Here is how to use it:

$ module load clisp/2.49.0 maxima/5.28.0
$ maxima
#If you have X-Forwarding turned on, "xmaxima" will display a GUI with a tutorial
$ xmaxima

OpenCV 2.4.2

OpenCV (Open Source Computer Vision) is a library of programming functions for real time computer vision.

OpenCV is released under a BSD license, it is free for both academic and commercial use. It has C++, C, Python and soon Java interfaces running on Windows, Linux, Android and Mac. The library has more than 2500 optimized algorithms.

This installation of OpenCV has been installed with support for Python and NumPy. It has been installed without support for Intel TBB, Intel IPP, or CUDA.

Here is how to use it:

$ module load gcc/4.4.5 opencv/2.4.2
$ g++ <source.cpp> $(pkg-config --libs opencv)


Boost provides free peer-reviewed portable C++ source libraries.
Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.

Here is how to use it:

$ module load boost/1.51.0
$ g++ <source.cpp>


Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

Here is how to use it:

$ module load gcc/4.4.5 ncbi_blast/2.2.27
$ blastn
$ blastp
$ blastx

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