README
¶
Gosl – Go scientific library
Gosl is a library written in Go (golang) to develop high-performance scientific computing with ease. The library tries to be as general and easy as possible. Gosl considers the use of both Go concurrency routines and parallel computing using the message passing interface. Gosl has several modules (sub-libraries/sub-packages) for a variety of tasks in scientific computing, image analysis, and data post-processing. For example, it includes high-performant linear algebra functions (e.g. wrapping MKL/OpenBLAS/LAPACK/SuiteSparse/UMFPACK etc.), fast Fourier transform algorithms (e.g. wrapping FFTW), functions and structures for geometry calculations, random numbers generation and probability distributions, optimisation algorithms, plotting and visualisation using the VTK, and much more. Gosl has also solvers to (stiff or not) ordinary differential equations and several tools for mesh generation to assist on the development of finite element solvers.
See the documentation for more details (e.g. how to call functions and use structures).
Summary
Gosl includes the following subpackages:
- chk – Check code and unit test tools
- io – Input/output, read/write files, and print commands
- utl – Utilities. Lists. Dictionaries. Simple Numerics
- plt – Plotting and drawing (png and eps)
- mpi – Message Passing Interface for parallel computing
- la – Linear Algebra and efficient sparse solvers
- la/mkl – Lower level linear algebra using Intel MKL
- la/oblas – Lower level linear algebra using OpenBLAS
- fdm – Simple finite differences method
- num – Fundamental numerical methods such as root solvers, non-linear solvers, numerical derivatives and quadrature
- fun – Special functions, DFT, FFT, Bessel, elliptical integrals, orthogonal polynomials, interpolators
- fun/dbf – Database of functions of a scalar and a vector like f(t,{x}) (e.g. time-space)
- fun/fftw – Go wrapper to FFTW
- gm – Geometry algorithms and structures
- gm/msh – Mesh structures and interpolation functions for FEA, including quadrature over polyhedra
- gm/tri – Mesh generation: triangles and Delaunay triangulation (wrapping Triangle)
- gm/rw – Mesh generation: read/write routines
- graph – Graph theory structures and algorithms
- ode – Ordinary differential equations (stiff/non-stiff RK methods)
- opt – Solvers for optimisation problems (e.g. interior point method)
- rnd – Random numbers and probability distributions
- rnd/dsfmt – Go wrapper to dSIMD-oriented Fast Mersenne Twister
- rnd/sfmt – Go wrapper to SIMD-oriented Fast Mersenne Twister
- tsr – Tensor algebra and definitions for continuum mechanics
- vtk – 3D Visualisation with the VTK tool kit
- img – Image and machine learning algorithms for images
- img/ocv – Go wrapper to OpenCV
Examples
- Compute (fast) discrete Fourier transform
- Generate and draw a NURBS toroidal surface
- Generating normally distributed pseudo-random numbers
- Solution of sparse linear system
- Solution of sparse linear system with complex numbers
- Numerical differentiation
- Drawing iso-surfaces with VTK
- Plotting a contour
- Solution of Poisson's equation using finite differences
- Root finding problems
- B-splines: curve, control, and basis
- Orthogonal polynomials
See the output of examples here
Installation
Since Gosl needs some other C and Fortran codes, not all sub-packages can be directly installed
using go get .... Nonetheless, Gosl is pretty easy to install! See links below:
The following subpackages are available on Linux only at the moment: mpi, la/mkl, and vtk. The following subpackages are not available for Windows at the moment: gm/tri, rnd/sfmt, and rnd/dsfmt. Help to compile these packages in all platforms is much welcome and appreciated.
About the filenames
t_something_test.gois a unit test. We have several of them! Some usage information can be learned from these files.t_something_main.gois a test with a main function to be run withgo run ...ormpirun -np ? go run ...(replace ? with the number of cpus). There very few of these files.t_b_something_test.gois a benchmark test. There a few of them. Run benchmarks withgo test -run=XXX -bench=.
Design strategies
Here, we call structure any user-defined type. These are simply Go types defined as struct.
One may think of these structures as classes. Gosl has several global functions as well and
tries to avoid complicated constructions.
An allocated structure (instance) is called an object and functions attached to this object are
called methods. In Gosl, the variable holding the pointer to an object is always named o
(lower case "o"). This variable is similar to the self or this keywords in other languages
(Python, C++, respectively).
Functions that allocate a pointer to a structure are prefixed with New; for instance:
NewIsoSurf. Some structures require an explicit call to another function to release allocated
memory. Be aware of this requirement! In this case, the function is named Free and appears in a
few sub-packages that use CGO. Also, some objects may need to be initialised before use. In this
case, functions named Init have to be called.
The directories corresponding to each package has a README.md file that should help with
understanding the library. Also, there are links to godoc.org where all functions, structures, and
variables are well explained.
Bibliography
Gosl is partly included in the following works:
- Pedroso DM (2017) FORM reliability analysis using a parallel evolutionary algorithm, Structural Safety 65:84-99 http://dx.doi.org/10.1016/j.strusafe.2017.01.001
- Pedroso DM, Zhang YP, Ehlers W (2017) Solution of liquid-gas-solid coupled equations for porous media considering dynamics and hysteretic retention behaviour, Journal of Engineering Mechanics 04017021 http://dx.doi.org/10.1061/(ASCE)EM.1943-7889.0001208
- Pedroso DM (2015) A solution to transient seepage in unsaturated porous media. Computer Methods in Applied Mechanics and Engineering, 285:791-816 http://dx.doi.org/10.1016/j.cma.2014.12.009
- Pedroso DM (2015) A consistent u-p formulation for porous media with hysteresis. Int. Journal for Numerical Methods in Engineering, 101(8):606-634 http://dx.doi.org/10.1002/nme.4808
Authors and license
See the AUTHORS file.
Unless otherwise noted, the Gosl source files are distributed under the BSD-style license found in the LICENSE file.
Directories
¶
| Path | Synopsis |
|---|---|
|
Package chk contains functions for checking and testing computations
|
Package chk contains functions for checking and testing computations |
|
package fdm implements functions and structures to assist on the development of finite difference solutions of problems involving partial differential equations
|
package fdm implements functions and structures to assist on the development of finite difference solutions of problems involving partial differential equations |
|
Package fun (functions) implements special functions such as elliptical, orthogonal polynomials, Bessel, discrete Fourier transform, polynomial interpolators, and more.
|
Package fun (functions) implements special functions such as elliptical, orthogonal polynomials, Bessel, discrete Fourier transform, polynomial interpolators, and more. |
|
dbf
Package dbf implements a database of f(t,{x}) functions (e.g.
|
Package dbf implements a database of f(t,{x}) functions (e.g. |
|
fftw
Package fftw wraps the FFTW library to perform Fourier Transforms using the "fast" method by Cooley and Tukey
|
Package fftw wraps the FFTW library to perform Fourier Transforms using the "fast" method by Cooley and Tukey |
|
gm (geometry and meshes) implements auxiliary functions for handling geometry and mesh structures
|
gm (geometry and meshes) implements auxiliary functions for handling geometry and mesh structures |
|
msh
package msh defines mesh data structures and implements interpolation functions for finite element analyses (FEA)
|
package msh defines mesh data structures and implements interpolation functions for finite element analyses (FEA) |
|
rw
package rw implements reader and writers for geometry files such as the STEP file format
|
package rw implements reader and writers for geometry files such as the STEP file format |
|
tri
package tri wraps Triangle to perform mesh generation a Delaunay triangulation
|
package tri wraps Triangle to perform mesh generation a Delaunay triangulation |
|
package graph implements solvers based on Graph theory
|
package graph implements solvers based on Graph theory |
|
package img provides tools to manipulate images including some machine learning techniques (e.g.
|
package img provides tools to manipulate images including some machine learning techniques (e.g. |
|
ocv
package ocv connects with the OpenCV library for image analyses and machine learning, in particular for computer vision algorithms.
|
package ocv connects with the OpenCV library for image analyses and machine learning, in particular for computer vision algorithms. |
|
Package io (input/output) implements auxiliary functions for printing, parsing, handling files, directories, etc.
|
Package io (input/output) implements auxiliary functions for printing, parsing, handling files, directories, etc. |
|
Package la implements routines and structures for linear algebra with matrices and vectors in dense and sparse formats (including complex)
|
Package la implements routines and structures for linear algebra with matrices and vectors in dense and sparse formats (including complex) |
|
mkl
package mkl implements lower level linear algebra using Intel MKL for max efficiency
|
package mkl implements lower level linear algebra using Intel MKL for max efficiency |
|
oblas
package oblas implements lower level linear algebra using OpenBLAS for max efficiency
|
package oblas implements lower level linear algebra using OpenBLAS for max efficiency |
|
package mpi wraps the Message Passing Interface for parallel computations
|
package mpi wraps the Message Passing Interface for parallel computations |
|
package num implements fundamental numerical methods such as numerical derivative and quadrature, root finding solvers (Brent's and Newton's methods), among others.
|
package num implements fundamental numerical methods such as numerical derivative and quadrature, root finding solvers (Brent's and Newton's methods), among others. |
|
package ode implements solvers for ordinary differential equations, such as the ones based on the Runge-Kutta method; e.g.
|
package ode implements solvers for ordinary differential equations, such as the ones based on the Runge-Kutta method; e.g. |
|
package opt implements routines for solving optimisation problems
|
package opt implements routines for solving optimisation problems |
|
plt contains functions for plotting, drawing in 2D or 3D, and generationg PNG and EPS files
|
plt contains functions for plotting, drawing in 2D or 3D, and generationg PNG and EPS files |
|
package rnd implements random numbers generators (wrapping the standard functions or the Mersenne Twister library).
|
package rnd implements random numbers generators (wrapping the standard functions or the Mersenne Twister library). |
|
dsfmt
package dsfmt wraps the dSFMT Double precision SIMD-oriented Fast Mersenne Twister
|
package dsfmt wraps the dSFMT Double precision SIMD-oriented Fast Mersenne Twister |
|
sfmt
package sfmt wraps the SFMT SIMD-oriented Fast Mersenne Twister
|
package sfmt wraps the SFMT SIMD-oriented Fast Mersenne Twister |
|
tsr implements routines to conduct tensor operations and solve problems in Continuum Mechanics
|
tsr implements routines to conduct tensor operations and solve problems in Continuum Mechanics |
|
package utl implements functions for simplifying calculations and allocation of structures such as slices and slices of slices.
|
package utl implements functions for simplifying calculations and allocation of structures such as slices and slices of slices. |
|
package vtk wraps the visualisation tool kit (VTK) for drawing 3D surfaces (scalar fields, vector fields, etc.)
|
package vtk wraps the visualisation tool kit (VTK) for drawing 3D surfaces (scalar fields, vector fields, etc.) |