All Questions

Filter by
Sorted by
Tagged with
6
votes
2answers
98 views

Performance of Lustre filesystems

The cluster I work on has a filesystem labelled as "fast" with no further explanation. But the filesystem type is "lustre", which strongly hints at a Lustre filesystem. While general information about ...
17
votes
5answers
2k views

Is there a good, easy-to-use, high quality open source CFD solver out there?

My thesis is on developing numerical methods for model reduction in combustion. I run my methods purely on the chemistry part of combustion simulations, and I have plenty of case studies for 0-D ...
7
votes
1answer
5k views

How does each process in bag of visual words image classification work?

I hope this is on topic, I found this through the proposal here: https://area51.meta.stackexchange.com/questions/320/shall-we-unite-computational-science-proposals A good visual description of BOW: ...
2
votes
1answer
548 views

Vegas, Monte Carlo multi integration, QCD

To do some calculation on QCD on Lattice, I needed a Monte Carlo multi integration. I wrote a a C++ program according to what I understood from the paper “ Lepage (1978) “ A New Algorith For Adaptive ...
24
votes
8answers
4k views

What software is good to use for parallel debugging?

I'm not running any parallel code right now, but I anticipate running parallel code in the future using a hybrid of OpenMP and MPI. Debuggers have been invaluable tools for me when running serial ...
7
votes
1answer
310 views

Richardson extrapolation for strong rate of convergence of SDE

Is it possible to apply Richardson extrapolation with Euler-Maruyama scheme to improve strong rate of convergence of stochastic differential equations?
11
votes
6answers
2k views

What open source tools are available to visualize molecular vibrations?

I would like to visualize a molecular vibration that is not a normal mode. I'd like to present a static, vectorial representation of the motion, and I would like some flexibility in the vector style (...
26
votes
10answers
711 views

Recommendations and experiences on which license to choose for software?

Developers of software have the choice to choose an appropriate license in accordance with the goal(s) of the work. Can anyone give some recommendations/experiences on which license to pick for ...
13
votes
2answers
450 views

Which time-integration methods should we use for hyperbolic PDEs?

If we employ the Method of Lines for discretization (separate time and space discretization) of hyperbolic PDEs we obtain after spatial discretization by our favorite numerical method (fx. Finite ...
9
votes
2answers
974 views

numerical integration with possible division by 'zero'

I am trying to integrate $$\int^1_0 t^{2n+2}\exp\left({\frac{\alpha r_0}{t}}\right)dt$$ which is a simple transformation of $$\int^{\infty}_1 x^{2n}\exp(-\alpha r_0 x)dx$$ using $t = \frac1{x}$ ...
9
votes
1answer
223 views

Nested dissection on regular grid

When solving sparse linear systems using direct factorization methods, the ordering strategy used significantly impacts the fill-in factor of non-zero elements in the factors. One such ordering ...
7
votes
2answers
5k views

Looking for C/C++ implementations of sampling from multinomial and Dirichlet distributions

I'm looking for C/C++ implementations of functions that return random variates multinomial and Dirichlet distributions. This is in the context of a calculation for posterior predictive p-values, part ...
35
votes
2answers
7k views

Mathematical Libraries for OpenCL?

I am looking for information from anyone that has tried to use OpenCL in their scientific code. Has anyone tried (recently) ViennaCL? If so, how does it compare to cusp? What about OCLTools? Does it ...
6
votes
2answers
620 views

Is it possible to dynamically resize a sparse matrix in the Petsc library?

This may be a Petsc newbie question, but... I'm using Petsc to solve a large sparse linear system. The initial creation of the matrix is fairly slow, which I'm given to understand is largely due to ...
22
votes
6answers
3k views

Future of OpenCL?

The OpenCL programming paradigm promises to be a royalty free opens standard for heterogenous computing. Should we invest our time in developing software based on OpenCL? Pros/cons?
15
votes
2answers
1k views

Estimation of condition numbers for very large matrices

Which approaches are used in practice for estimating the condition number of large sparse matrices?
157
votes
10answers
120k views

Recommendations for a usable, fast C++ matrix library?

Does anyone have recommendations on a usable, fast C++ matrix library? What I mean by usable is the following: Matrix objects have an intuitive interface (ex.: I can use rows and columns while ...
8
votes
3answers
434 views

What should be the criteria for accepting/rejecting singular values?

I am solving a system using singular value decomposition. The singular values (before scaling) are: ...
35
votes
6answers
3k views

What attributes make a figure “professional-quality”?

I've heard people say that plots produced by ORIGIN tend to look polished and "professional," whereas plots produced by Mathematica do not. However, most plot-creation programs are quite configurable ...
7
votes
6answers
6k views

Python implementations of Gillespie's direct method

I'm looking for a decent implementation of Gillespie's Direct Method in Python, as if I code the algorithm myself I'm nigh positive I'll do it inefficiently. Anyone have a favorite?
8
votes
2answers
192 views

Is there one general approach to build a projection methods for different problems?

My question is probably going to be too general to answer it with a couple words. Could you please suggest a good reading in that case. Projection methods are used to reduce size of the solution space ...
44
votes
8answers
2k views

What are good ways to document scientific software?

Many times, when I've inherited or encountered scientific code written by other people (or occasionally, even my own work), I've noticed that documentation is either sparse or nonexistent. If I'm ...
3
votes
3answers
244 views

Evaluating $\binom{100}{i}a^i(1-a)^{(100-i)}$ in GMP-GNU

I want to calculate $\binom{100}{i}a^i(1-a)^{(100-i)}$ for different $i$ with $a=0.001$ using GMP-GNU. How can this be done?
8
votes
4answers
355 views

(How) do you take into account memory fragmentation?

I use an example from finite element theory, but anybody who maintains a large datastructure and successively extends it will find something similar. Suppose I have an unstructured mesh of points and ...
6
votes
1answer
448 views

An efficient 'drizzle' algorithm?

What efficient implementations of a 'drizzle' algorithm are available? The problem is, given a timestream of data in which each element is associated with a pixel in a map, how do you create that map?...
3
votes
2answers
1k views

Applying same feature selection to multiple data sets with Weka

I am using the Weka workbench to train a protein fold classifier. I imported my training data into Weka and performed PCA-based feature selection. This seems to have worked fine, but now I cannot ...
56
votes
12answers
32k views

C++ vs Fortran for HPC

In my computational science PhD program, we are working almost exclusively in C++ and Fortran. It seems like some professors prefer one over the other. I am wondering which one is 'better' or if one ...
12
votes
3answers
304 views

In what application cases are additive preconditioning schemes superior to multiplicative ones?

In both domain decomposition (DD) and multigrid (MG) methods, one may compose the application of the block updates or coarse corrections as either additive or multiplicative. For pointwise solvers, ...
46
votes
5answers
8k views

What are criteria to choose between finite-differences and finite-elements

I am used to thinking of finite-differences as a special case of finite-elements, on a very constrained grid. So what are the conditions on how to choose between Finite Difference Method (FDM) and ...
5
votes
5answers
816 views

Introductions to hp-FEM

do you know good introductions into or surveys $hp$-adaptive finite elements? In particular I do not know how the heuristics for choosing spatial refinement or increased polynomial degree are ...
11
votes
2answers
5k views

How to work with function pointers in Fortran in scientific programs

Here is a typical usage of function pointers in C. I would like to do something similar in Fortran. I have some ideas, but I would like to know if there is some canonical way to do so. The function ...
13
votes
1answer
1k views

What are possible methods to solve compressible Euler equations

I would like to write my own solver for compressible Euler equations, and most importantly I want it to work robustly in all situations. I would like it to be FE based (DG is ok). What are the ...
14
votes
4answers
347 views

How to deal with too much data?

Our plasma dynamics simulations often produce too much information. During the simulations we record various physical properties on a grid (x,y,z,t) that is as large as (8192x1024x1024x1500), for at ...
1
vote
0answers
57 views

Assembled human ESTs for annotation

I am annotating protein-coding genes in a region of the human genome and am looking for a set of assembled ESTs I can use as evidence for constructing gene models. A quick search of NCBI's SRA shows 4,...
16
votes
3answers
560 views

How should I study creating and programming HPC systems?

I'm in a field that doesn't necessarily do a great deal of HPC work, and when it does encounter it, it's often the result of researchers from other fields exploring new applications to their methods ...
4
votes
1answer
889 views

Sampling from posterior predictive distribution

First post. I'm working on this problem using Bayesian methods. In desperation I'm considering using p-values (shock horror), specifically posterior predictive p-values. So I need to simulate from the ...
4
votes
4answers
349 views

Approximate a distribution function from a finite sample

Say I have a simulation that produces a single floating point number as a result, and a different number is produced each time the simulation runs. These numbers are randomly distributed according to ...
4
votes
2answers
717 views

COMSOL on Ubuntu (10.04 LTS and 11.04)

I am running into a problem with COMSOL 4.2.0.187 on Ubuntu (both 10.04 LTS and 11.04). When using the option -np x with x > 1, ...
21
votes
3answers
18k views

Intel Fortran Compiler: tips on optimization at compilation

I will start with my personal experience in our lab. Back in the ifort 9 and 10 days, we used to be quite aggressive with the optimizations, compiling with -O3 and processor specific flags (-xW -xSSE4....
3
votes
1answer
166 views

Global optimal sequence alignment algorithms

As far as global optimal sequence alignment goes, is the Needleman-Wunsch and Hirschberg's algorithm still state of the art? Or have there been any improvements to these algorithms since they were ...
5
votes
4answers
4k views

Where can I find a database of simple chemical structures in XYZ format?

As from Title. Where can I find a database of simple chemical structures in XYZ format, possibly with a simple CAS -> XYZ or InChi -> XYZ REST service ?
23
votes
1answer
1k views

Is there a numerical algorithm for finding an asymptotic slope?

I have a series of data points $(x_i,y_i)$ which I expect to (approximately) follow a function $y(x)$ that asymptotes to a line at large $x$. Essentially, $f(x) \equiv y(x) - (ax + b)$ approaches zero ...
14
votes
3answers
227 views

Best practices for describing agent-based models

I work fairly heavily in mathematical biology/epidemiology, where most of the modeling/computational science work is still dominated by sets of ODEs, admittedly sometimes fairly elaborate sets of them....
7
votes
1answer
202 views

Optimal way to find stationary solutions of the PDE

I am researching heat diffusion in an optical element irradiated by laser. This problem is described by the PDE which I wrote down in this question. I am using an implicit numerical scheme to model ...
3
votes
1answer
160 views

Artificial RNA 3D folding

I have a 50-base, artificially created RNA sequence and I would like to obtain its 3D structure. What software should I use for this purpose?
12
votes
2answers
622 views

Quickly finding rough lines in sets of points

In a particular class of detectors, our data comes out as pairs of points in two dimensions, and we want to string these points into lines. The data is noisy, and is binned in one direction but not ...
3
votes
2answers
712 views

Linear regression via SVD not producing best fit with escalating polynomial degree

I am using a basic singular value decomposition (via LAPACK) routine in FORTRAN to solve an overdetermined system in the form of $A\cdot X = B$ where $\mathrm{size}(A) = [m,n]$ with $m > n$. My ...
31
votes
5answers
10k views

Performance differences between ATLAS and MKL?

ATLAS is a free BLAS/LAPACK replacement that tunes itself to the machine when compiled. MKL is the commercial library shipped by Intel. Are these two libraries comparable when it comes to performance, ...
5
votes
2answers
226 views

Enumerating hexahedral cell vertices and faces in arbitrary dimension

I have a Cartesian mesh in $d$ dimensions, and I would like to enumerate all the subcells of a given hexahedral cell. If I am just enumerating the vertices of a cell (or cells that contain a vertex) I ...
8
votes
1answer
981 views

How can I compute the Schur complement in PETSc?

How can I compute the Schur complement: $$ S = K_{bb} - K_{ba} K_{aa}^{-1} K_{ab} $$ where $$ K=\begin{pmatrix} K_{aa} & K_{ab} \\ K_{ba} & K_{bb} \end{pmatrix} $$ (in some ordering) is a ...

15 30 50 per page