Numerical & Mathematical Software Libraries
Intel Math Kernel Library
The Intel Math Kernel Library provides developers of scientific and engineering software with a set of linear algebra, fast Fourier transforms and vector math functions optimized for the latest x86_64 processors from both Intel and AMD. MKL contains LAPACK, the basic linear algebra subprograms (BLAS), and the extended BLAS (sparse). In addition, there is a set of fast Fourier transforms in single- and double-precision, real and complex data types with both Fortran and C interfaces. MKL also includes a set of vectorized transcendental functions in the Vector Math Library (VML), offering both high performance and excellent accuracy compared to the libm functions for most of the processors.
MKL_LDFLAGS=-L/opt/intel/mkl/10.0.4.023/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core MKL_CFLAGS=-I/opt/intel/mkl/10.0.4.023/include
AMD Core Math Library (ACML) (Available Soon)
The AMD Core Math Library (ACML) provides developers of scientific and engineering software with a set of linear algebra, fast Fourier transforms and vector math functions optimized for the latest x86_64 processors from AMD. ACML also works with x86_64 Intel processors. ACML contains LAPACK, the basic linear algebra subprograms (BLAS), and the extended BLAS (sparse). In addition, there is a set of fast Fourier transforms in single- and double-precision, real and complex data types.
ACML_LDFLAGS=-L/nethome/libs/acml/4.3.0/pgi64/lib/ -lacml -lrt ACML_CFLAGS=-I/nethome/libs/acml/4.3.0/pgi64/include/
FFTW - version 3.1.2
FFTW, which stands for the somewhat whimsical title of "Fastest Fourier Transform in the West", is a portable C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). FFTW's performance is typically superior to that of other publicly available FFT software, and is even competitive with vendor-tuned codes. It is installed in /nethome/libs/fftw/3.0.1/gcc/4.1.2
LD_FLAGS=-L/nethome/libs/fftw/3.0.1/gcc/4.1.2/lib/ -lfft3 INC_FLAGS=-I/nethome/libs/fftw/3.0.1/gcc/4.1.2/include
GNU Scientific Libraries
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. Versions of the library compiled with both gcc and Intel compilers are installed in /nethome/libs/gsl.
IO Libraries
Installed IO Libraries are listed below, ordered according to usage.
NetCDF - version 3.6.3
NetCDF (Network Common Data Format) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Both 32 and 64 bit versions are available are installed in /nethome/libs/netcdf/3.6.3/[compiler/version]/32 and /nethome/libs/netcdf/3.6.3/[compiler/version]/64, where [compiler/version] refers to the specific compiler with the version number which has been used to install the NetCDF libarary. For instance, to use 64-bit NetCDF libraries for PGI compiler,
LD_FLAGS=-L/nethome/libs/netcdf/3.6.3/pgi/7.1-5/64/ -lnetcdf INC_FLAGS=-I/nethome/libs/netcdf/3.6.3/pgi/7.1-5/64/include
HDF5 - version 1.8.3
HDF5 is a IO package that provides a versatile data model that can represent very complex data objects and a wide variety of metadata. It uses a completely portable file format with no limit on the number or size of data objects in the collection. The software library runs on a range of computational platforms, from laptops to massively parallel systems, and implementsa high-level API with C, C++, Fortran 90, and Java interfaces. It also provides a rich set of integrated performance features that allow for access time and storage space optimizations with several tools and applications for managing, manipulating, viewing, and analyzing the data in the collection. Version 1.8.3 is installed in /nethome/libs/hdf5/default.
HDF4 - version 4.2r2
Hierarchical Data Format (HDF4) is a general-purpose, machine-independent standard for storing scientific data in files, developed by the National Center for Supercomputing Applications (NCSA). Locally compiled with native IBM compilers. Version 4r2.3 is installed in /nethome/libs/hdf4/default.
Application Software for Data Analysis and Visualization
NCL and NCAR Graphics Package - version 5.0.0
The NCAR Command Language (NCL), a product of the Computational Information Systems Laboratory at the National Center for Atmospheric Research (NCAR), is an interpreted language designed specifically for scientific data processing and visualization. NCL has robust file input and output. It can read and write netCDF-3, netCDF-4, HDF4, binary, and ASCII data, and read HDF-EOS2, GRIB1 and GRIB2 (as of version 4.3.0). It is installed in /nethome/apps/ncarg.
Ferret - version 6.1
Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. It can transparently access extensive remote Internet data bases using OPeNDAP. Ferret offers a Mathematica-like approach to analysis; new variables may be defined interactively as mathematical expressions involving data set variables. Calculations may be applied over arbitrarily shaped regions. Fully documented graphics are produced with a single command. It is installed in /nethome/apps/ferret.
GMT - version 4.3.1
GMT is an open source collection of 60 tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing Encapsulated PostScript File (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views. GMT supports 30 map projections and transformations and comes with support data such as GSHHS coastlines, rivers, and political boundaries. It is installed in /nethome/apps/gmt.
GNUPLOT - version 4.2.3
Gnuplot is a portable command-line driven interactive data and function plotting utility. Gnuplot supports many types of plots in either 2D and 3D. It can draw using lines,points, boxes, contours, vector fields, surfaces, and various associated text. It also supports various specialized plot types. Locally compiled with gcc compilers. Version 4.2.3 is installed in /nethome/apps/gnuplot.
OCTAVE - version 3.2.2
Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language. The latest version, locally compiled with gcc compilers, is installed in /nethome/apps/octave-3.2.2.
Vis5D+ - version 1.2.1
Vis5D+ is a software system that can be used to visualize both gridded data and irregularly located data. Sources for this data can come from numerical weather models, surface observations and other similar sources. Vis5D+ can work on data in the form of a five-dimensional rectangle. That is, the data are real numbers at each point of a "grid" which spans three space dimensions, one time dimension and a dimension for enumerating multiple physical variables. Vis5D can also work with irregularly spaced data which are stored as "records". Each record contains a geographic location, a time, and a set of variables which can contain either character or numerical data. The latest version, locally compiled with gcc compilers, is installed in /nethome/apps/vis5d+.
