Questions tagged [c]

C is a general purpose programming language. Originally intended for implementing system software, C and its close relatives are the principle languages used in most modern operating systems. Due to its thin layer of abstraction and low overhead, C allows efficient coding of algorithms and data structures useful for scientific computation. Use this tag for questions involving the C programming language.

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What sparse solver supports diagonal storage format

I'm writing finite-difference method program using C. The stiffness matrix is symmetrical and band. For its storage I'd like to use Sparse Diagonal Storage format. Could someone tell please, what ...
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1answer
513 views

PETSc's makefile system can't find MKL

I'm learning PETSc and trying to make the examples written in C. However, when I use the provided makefile, I get the following error: ...
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2answers
115 views

Are matlab C library versions backwards compatible?

I have some C++ code that links to matlab2008b. Are matlab 2012a and 2012b backwards compatible with 2008b? If it's not trivially compatible, are there some simple steps to make it compatible?
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1k 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 ...
4
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2answers
2k views

Extracting a 2D matrix from a multidimensional array in C

In my c language program, I have to store multiple dense $m\times m$ matrices corresponding to gridpoints $x_i$ with $i=1,...,n$. I decided to create a three dimensional array $A\in R^{n\times m\...
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1answer
2k views

Open-source, thread-safe implementation of convex optimization solvers in C/C++?

Is there an open-source, thread-safe implementation of convex optimization solvers in C/C++? Some libraries such as NLopt, Ipopt, OPT++ don't meet my requirements. OPT++ and Ipopt aren't thread-safe,...
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3answers
3k views

How do I know if my code is being vectorized by the compiler?

As exemplified by Jed Brown's answer to Costs of lookups versus calculations, using vectorized vs non-vectorized floating point operations results in much faster code. Many modern compilers claim ...
13
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4answers
2k views

Is C slower than Fortran on the spectral norm shootout (using gcc, intel and other compilers)?

The conclusion here: How much better are Fortran compilers really? is that gfortran and gcc are as fast for simple code. So I wanted try something more complicated. I took the spectral norm shootout ...
2
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1answer
561 views

Implicitly casting PetscReal to the real part of PetscComplex

The version of Petsc installed on my machine has PetscScalar set to be complex. I am making a matrix which has all real entries. Something like the following code compiles: ...
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3answers
2k views

I/O Strategies for computational problems with large data sets?

My research group focuses on molecular dynamics, which obviously can generate gigabytes of data as part of a single trajectory which must then be analyzed. Several of the problems we're concerned ...
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3answers
437 views

How to obtain finite difference, which is continuous

I want to calculate a finite difference (something like this SO Post). My data is as follows: I have x-values that are powers of two (4, 8, 16, 32 and 64). Corresponding to them are y-values, such ...
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2answers
2k views

Is there an open source set of ODE solvers for C that use the native C99 complex type?

I've been using GSL as the foundation of many of my simulations, but it's a little bit overkill for my purposes and it defines its own complex type for legacy reasons. Rather than code my own Runge-...
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8answers
2k views

Parsing protein structure data in C

My background is in genomics, but I have recently been working with problems related to protein structure. I wrote a few relevant programs in C, building my own PDB file parser from scratch in the ...

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