The GotoBLAS codes are a fast implementation of the Basic Linear Algebra Subroutines. The advantage is fast calculation. Note that the actual performance depends in part on the code from which you call the GotoBLAS subroutine(s), and on the combination of architecture and operating system under which you are running. Your own tuning can make a big difference.
PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.
The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. It provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.
MathGL is a library for making high-quality scientific graphics under Linux and Windows, fast data plotting and handling of large data arrays, working in window and console modes, and easily embedding into other programs. It has more than 40 general types of graphics for 1d, 2d, and 3d data arrays. It can export graphics to raster and vector (EPS or SVG) formats. It has an OpenGL interface and can be used from console programs. It has functions for data handling and MGL language scripting for simplification of data plotting. It has several types of transparency and smoothed lightning, vector fonts and TeX-like formula drawing, an arbitrary curvilinear coordinate system, and many other useful things.
LAPACK is a linear algebra library, based on LINPACK and EISPACK, designed to provide routines for handling simultaneous equations and matrix algebra efficiently, particularly on shared memory vector processors, parallel processors, and clusters. The code is written in Fortran, and requires the BLAS (Basic Linear Algebra Subprograms) library.
Parallel Three-Dimensional Fast Fourier Transforms, dubbed P3DFFT, is a library for computing 3D FFTs using 2D (pencil) decomposition. It is written using Fortran with MPI, and is tuned to work on multiple single-CPU systems (up to 32768 of them). It is built to leverage high-performance serial 1D FFT libraries, such as FFTW or ESSL.
The FLASH code is a modular, adaptive, parallel simulation code capable of handling general compressible flow problems in astrophysical environments. It has been designed to allow users to configure initial and boundary conditions, change algorithms, and add new physical effects with minimal effort. It uses the PARAMESH library to manage a block-structured adaptive grid, placing resolution elements only where they are needed most. It uses the Message-Passing Interface (MPI) library to achieve portability and scalability on a variety of different message-passing parallel computers.