A collection of related programming functions implementing a set of abstract data types, mathematical functions, or other higher level analysis algorithms so that they may be used, and reused, by other programs.

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2answers
100 views

Which C++ Multi-objective Optimization libraries allows the addition of custom problems and custom algorithms?

I'm working on a custom discrete and constrained multi-objective optimization problem and I'd like to know which libraries or platforms that implement algorithms like ...
1
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1answer
52 views

Is OPENFOAM a good idea for direction/operator splitting in parabolic equation

I would like to know if I should switch to OPENFOAM for my task. I work only with Cartesian grids, right now in 2d, rectangular domains only. If $\mathbf{w} = (w_1, w_2)$ and suppose I want to solve ...
3
votes
2answers
178 views

FEM libraries with weak forms

I need to implement a structural analysis code, and I turn to you for advice. My needs are simple: Library must be integrable in a C++ code I want to express a weak form, without manual intervention ...
1
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1answer
55 views

library for arithmetic operations on unstructured xyz

I've got several sets of xyz-data where x,y are coordinates and z is a 'value'. I want to be able to do simple arithmetic operations on these data. The x,y locations are not necessarily the same in ...
6
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0answers
69 views

Library with polylogarithm function

I am looking for a reliable library where I can find polylogarithm function and newton/secant method for solving non-linear equations. Basically I have something like this: ...
5
votes
1answer
63 views

Code to update dense QR and Cholesky factorizations

I am looking for some production-ready code to update dense QR and/or Cholesky factorizations (by adding / removing rows and columns or making small-rank updates -- yes, I need all these cases). I ...
2
votes
1answer
77 views

Templated Numerical Linear Algebra in Parallel

I have to invert large, but densely populated matrices with higher precision arithmetic. Therefore I am looking for something like the PLASMA library, which can do Cholesky or LU factorization in ...
2
votes
1answer
107 views

Kernel of a Sparse Matrix

Given a sparse rectangular matrix $A$ (let's say, with dimension $n,m$ and number of non-zero elements $O(n)\sim O(m)$) with entries in $\mathbb Z/2\mathbb Z$ I'm looking for a basis of the kernel as ...
4
votes
2answers
191 views

Finite element library in fortran

I want to create a finite element code in fortran. There are many libraries out there on internet. Can someone suggest me a good finite element library in fortran? I am looking for Ease of use (...
1
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1answer
142 views

Is there a single C++ IDE packed with necessary scientific libraries for computing purpose?

I am basically looking for a good open source C++ IDE with scientific and visualization libraries built in. Can any one suggest few projects?
2
votes
0answers
37 views

Fast library for parallel n-diagonal matrix inversion

I've tried looking for efficient parallel algorithms to solve banded systems. SPIKE is a good example but it however requires that the band size is large. Is there any efficient library implementing ...
1
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0answers
74 views

Pastix installation [closed]

I'm trying to install Pastix library, but I'm still having problems with missing libraries and I'm really helpless now. I started with copying LINUX-GNU.in as <...
2
votes
2answers
420 views

C++ Library: What is the common libraries that do polynomial arithmetic?

I need to know what libraries (in C++) support polynomial arithmetic specially over a field. So I can give to it an array of coefficients of polynomial over a field and it returns the roots of ...
2
votes
1answer
84 views

How do I make sparse solvers to accept custom matvec function insted of matrix?

I have tried it with Lis, Intel mkl and PETSc. Everywhere you need to pass an actual matrix ...
1
vote
2answers
88 views

Using computational libraries on a machine without root access

If you want to use a computational library on a high-performance computing center where you have no root access to install new software you can use header-only template libraries such as MTL4, Eigen3, ...
1
vote
1answer
73 views

Shared memory parallel computing solutions compared

As of 2015, what shared memory parallel computing solutions are available? What are the advantages and disadvantages of each for various use cases arising in high performance scientific computing? I ...
3
votes
1answer
626 views

Solving Advection (Convection) - Diffusion - Reaction Partial Differential Equation in Python

I am looking for library written in Python which will enable me to solve the coupled nonlinear equations which looks like: I need the library which will enable me to couple this solver to other ...
4
votes
2answers
511 views

Solving Lx = b for big sparse Laplacian matrices

What algorithm is more practically suited in terms of performance for solving the $\mathbf{Lx=b}$ equation, where $\mathbf{L}$ is a generic Laplacian matrix (associated to a strongly connected graph, ...
5
votes
2answers
588 views

Looking for Runge-Kutta 8th order in C/C++

I would like to use Runge-Kutta 8th order method (89) in a celestial mechanics / astrodynamics application, written in C++, using a Windows machine. Therefore I wonder if anyone knows a good library / ...
4
votes
4answers
154 views

Measurement error library

Is there a python library that would keep track of uncertainty in measured data? i.e. if I put in a figure of a±b is there an easy way to track the propagation of error through calculations.
0
votes
2answers
586 views

Impact of frequent row major / column major conversions using LAPACK/BLAS?

If you call a library like LAPACK or BLAS (which are written in FORTRAN and use column major order) from a C-like language that uses row major order, won't you lose performance and use a lot of memory ...
2
votes
2answers
131 views

Suggestions for open source C++ library for medium scale non-linear solver

I need to find the root of a nonlinear system (which comes out of collocation, so I will change the order to test). I will likely have about 50-300 variables, and the Jacobian is going to be ...
4
votes
5answers
352 views

Open source auto-differentiation for MATLAB?

Are there any open-source auto-differentiation libraries for MATLAB? I am aware of commerical packages such as http://tomopt.com/tomlab/products/mad/ and plenty of C++ libraries, but I can't find much ...
3
votes
2answers
94 views

Local versus remote development

I know there are similar questions asked on other StackExchange sites, but I think development in Computational Science may work differently because of the computing environments that are common. I ...
0
votes
1answer
219 views

Solver for large non-linear system of equations

I am curently using R package nleqslv for solving a non-linear system of equations with 300 variables. I need to scale this to the system with ~50k variables and naturally this does not scale very ...
1
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0answers
197 views

How to solve sparse linear systems using CPUs and GPUs?

There are several libraries to (iteratively) solve large sparse linear equation systems in parallel on a number of CPUs. Our parallel cluster also has attached powerful GPUs, but so far, I did not ...
1
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1answer
137 views

Solver library for matrix-free linear equation system

I will have to solve a large linear system. I'm now looking for a solver that works "matrix-free" (So that I just have to specify a matrix-vector product, but not the matrix). As far as I understand (...
5
votes
1answer
246 views

Finding closed equipotential surfaces on a 3D grid

In short, I'm looking for either: (1) Publications or other sources dealing with contour/isosurface finding algorithms, so that I can write my own implementation (and parallelize as best I can), or (...
3
votes
2answers
1k views

Developing finite volume (FVM) code in C . General advice

I need to develop a FVM code in C (The multiscale FVM method for heterogeneous media). I know that: Only uniform rectangular grids will be considered (2d now, later 3d) Sparse systems will be large ...
0
votes
1answer
70 views

Harwell-Boeing format for sparse matrices

I'm dealing with SVDLIBC library. In order to compute singular values I need to specify my matrix in the Harwell-Boeing format. On Internet I have found next example: Dense Text Format: ...
0
votes
1answer
52 views

Which version of FFTW

At the moment, I'm installing the "GADGET-2" application. In its documentation it says "Note that the MPI-capable version 2.x of FFTW is required, the new version 3 lacks MPI capability at this point. ...
2
votes
3answers
216 views

R/C/C++ library for N-dimensional arrays

I'm looking for a library that is either in R or easily wrappable with R, that can do the following things: construct and subset N-dimensional arrays perform operations such as ...
4
votes
1answer
160 views

Using PAPI in PETSc code

I am trying to count the number of cache misses, total cycles, etc. per iteration of a for loop inside MatMult_SeqSBAIJ_2() . I'...
4
votes
3answers
317 views

Literature material discussing generic frameworks to solve PDEs

I am trying to gather literature material to study how people propose to implement generic frameworks to solve partial differential equations in C++. Despite my effort to search the web, the only ...
3
votes
3answers
1k views

Can anyone recommend a library in C++ which has the most efficiency in doing sparse matrix operations under Windows system

I have download sparselib++, but it seems that it can't be complied in Windows, only in Unix, I don't know. So can anyone recommend some which can be used in Visual Studio 2010? I want to do a large ...
4
votes
5answers
533 views

FEM library with support of simplex elements

My question can be rephrased as "FEM library like deal.II but for simplex elements". Our scientific group works with very complicated 3D geometries, so usually we prefer tetrahedral meshes for our ...
1
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1answer
838 views

software request for solving acoustic wave equation

I am searching some libraries or toolboxes (preferred MATLAB) for solving acoustic wave equation in heterogeneous media with time varying source term, i.e. $$\nabla^2 \psi(\vec{r},t) - \frac{1}{c(\vec{...
5
votes
1answer
118 views

Use Butterworth and Chebychev filters

I need to calculate frequency response, phase response and apply to signals the Butterworth, Chebychev1 and Chebychev2 band-pass filters. I'm developing in C++ with Qt, and I'm looking for algorithms ...
5
votes
3answers
163 views

Where do I find data to start a graph data structure to practice on?

I am interested in learning firsthand about graph data structures but have no data to put into the database. Can anyone recommend a source for a beginner to find graph data? (Preferably a source that ...
9
votes
3answers
3k views

I am looking for a parallel dynamic graph library in C++

Hello scicomp community, I have worked in the area of graph algorithms using frameworks such as NetworkX (Python), JUNG and YFiles (Java). I am now entering the area of parallel and high perfomance ...
8
votes
4answers
460 views

Hosting site for a small scientific library

For my research work I have been developing a small C++ library aimed at facilitating the communication between C++ computational codes and Octave/Matlab (when the latter is used for post-processing ...
9
votes
3answers
616 views

Recommendations for a lightweight/no-install C or C++ based dense linear algebra solver

Most of my programming is one-off research codes in C for my own use. I have never distributed any code to other than close collaborators. I have developed an algorithm that I am publishing in a ...
10
votes
2answers
342 views

Task-based shared-memory parallel libraries in Scientific Computing

In recent years, several libraries/software projects have appeared that offer some form or another of general-purpose data-driven shared-memory parallelism. The main idea is that instead of writing ...
5
votes
2answers
406 views

Recommendations for a usable, fast GPL-compatible derivative-free numerical optimization library that can be interfaced to C++

I am dealing with optimization of functions for which I do not have derivatives available, and the optimization is not constrained. I am searching for a high quality GNU Public License-compatible ...
6
votes
1answer
1k views

What are the strategies for local Adaptive Mesh Refinement (local AMR) on unstructured meshes?

I am interested in local AMR on unstructured meshes. Currently, I'm working with the OpenFOAM library - it supports completely unstructured local AMR: cell refinement criteria determine a list of ...
6
votes
3answers
920 views

How to quickly implement and test a turbulence model?

What is the best software for quickly implement and test a Reynolds Averaged Navier-Stokes turbulence model ?
2
votes
3answers
1k views

What modern OOP features should a computational scientist use? [closed]

Many computational scientists that I know of, including myself for example, are not computer scientists. As such they are often not very well aware more advanced techniques in OOP. On the other hand, ...
7
votes
1answer
510 views

C++ library for graphs with maximum common subgraph solver

I'm looking for a convenient, free C++ library for graphs that include a solver for the maximum common subgraph (MCS) problem. I'm aware of the Boost Graph Library and LEMON , but neither includes an ...
15
votes
1answer
635 views

Are there any open source inverse-based multilevel ILU implementations?

I am very impressed with the serial performance of multilevel inverse-based ILU preconditioners, particularly for heterogeneous Helmholtz, but I am surprised to not be able to find any open source ...
4
votes
1answer
435 views

Outputting a distributed vector in PETSc

I'm working with someone else's code that uses PETSc 3.0.0-p9. They have a vector at the end of the computation that is distributed among a number of different processors, and I want to output that ...