The study of solving computational problems by exploiting the use of multiple processors simultaneously.

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Dense distributed matrix

A dense matrix is distributed for parallel computation column-wise, then multiplied from left & right by sparse matrices. What would be appropriate c++ libraries for these tasks?
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1answer
72 views

Best incremental multidimensional Delaunay tessellation algorithm

I'm looking for a specific type of Delaunay tessellation algorithm. The algorithm should be: incremental so that I can add new sites inside known simplexes (i.e. no searching for the right simplex ...
2
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1answer
31 views

Installing GPAW (Python DFT package) on a computing cluster

I'm in the middle of installing GPAW on a cluster but I'm running into problems building the "gpaw-python" interpreter, its job is to allow users to execute parallelised GPAW calculations. Following ...
2
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2answers
113 views

Why is computational cost measured in Floating Pt. Ops. in times of parallel computing?

In times of parallel computing, it seems to me that algorithms (also basic ones, like matrix-vector multiplication) should be measured by their dependent steps (that use results from steps before) ...
3
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0answers
32 views

BLACS context value and multiple MPI communicators

I am reposting here a question previously asked in stackoverflow: as suggested in a reply to my question, scicomp could be a better place to obtain some useful comments/suggestions for my problem. I ...
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5answers
181 views

Is discontinuous Galerkin really any more parallelizable than continuous Galerkin?

I've always heard that easy parallelization was one of the advantages of DG methods, but I don't really see why any of those reasons don't also apply to continuous Galerkin.
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3answers
80 views

Leave openMP theads ready

I have a C++ program that has a double for loop that I'd like to parallelize using opeMP. It is simple (a polynomial product) of varying length (between 100 and ...
3
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1answer
82 views

Increasing thread number degrades performance

I have a problem with parallelization and the brownian dynamics (molecular dynamics) code that I am using. We have our own home-grown framework at the university, and recently we've made the change ...
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1answer
63 views

Optimizing MPICH2 on FX 9370 processor

Short version of question: We have a Opteron 6272 cluster, an we have recently started bilding FX 9370 based small cluster. Problem is that we are not able to get desired speed, i.e scaling with ...
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3answers
215 views

Does IBM LSF facilitate parallel computing?

I have been browsing through the documentation of the IBM Platform Load Sharing Facility, to find out if it supports parallel task computing. Below is what I think is relevant for this question, ...
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3answers
147 views

Is there a general framework for solving PDEs on uniform grid in parallel

Hej, I want to simulate a partial differential equation (a modified Cahn-Hilliard equation, but the details do not matter much. The questions also applies to the diffusion equation). I'm looking for ...
2
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1answer
96 views

Multiple independent random number streams

Having multiple streams of pseudo-random numbers known to be independent and with a uniform distribution I want to do Monte Carlo simulations in parallel. In other words, one thread will have a ...
3
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1answer
118 views

Inverting many small matrices in parallel

I am trying to find a good way to handle the following problem: Let C be an N by 3 array (corresponding to points in $\mathbb{R}^3$). There is a method I am interested in testing which requires ...
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1answer
169 views

Masters in HPC (High Performance Computing)

Is there a master degree in HPC (High Performance Computing) in US? I am asking this question because in my early research I found no direct mentioning of HPC instead invidual courese in parallel ...
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4answers
228 views

Best PARALLEL numerical solver of first order differential equation

I have a system of 256 differential equations that I want to solve numerically. The system represents the Liouville equation, which is a first order, linear differential equation with complex numbers. ...
3
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2answers
196 views

openmp update matrix from neighboring elements (parallelise preconditioner)

Issue of data dependency with stencil code... How to parallelise this using openmp? I looked at the openmp manual, I figured out how to use DO ORDERED to get the same result as the serial version, ...
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1answer
181 views

Exploiting parallelism within a single heterogeneous computing node

I'm looking for a library to exploit parallelism within a single heterogeneous computing node (possibly using Accelerators like Xeon Phi or nVidia's GPGPU's) in a C++ FV/DG code using hierarchical ...
7
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3answers
179 views

GPU libraries to use for Linear Algebra operations

I am looking for GPU libraries to accelerate a code I have, whose primary "high performance" regions have singular value decomposition, QR factorization and Eigen values, Eigenvectors computation. I ...
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2answers
203 views

Why performance is given in Gflop/s rather than actual time in seconds

While reading many research-papers comparing parallel implementations of algorithms on different machines/architectures, I have noticed that the performance comparison is always listed in terms of ...
6
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3answers
242 views

Any recommendations for unit-testing frameworks compatible with code/libraries that use MPI?

Usually, I write serial code, and when I do, I write unit tests with some xUnit-style testing framework (MATLAB xUnit, PyUnit/nose, or Google's C++ testing framework). Based on a cursory Google ...
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4answers
156 views

Computational science contests. Why arent there any?

I was wondering why there are no online or offline computational science contests? At least I couldn't find much by googling. I mean, like a topcoder for computational sciences. I assume one reason is ...
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3answers
315 views

When is MPI_Wait necessary for non-blocking calls?

I hope this is not too off-topic here -- I've asked it on SO but I'm hoping I'll get better answers here! I'm a little bit confused about when I should call MPI_Wait (or other variants such as: ...
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0answers
57 views

Computational science and related energy research [closed]

I want to understand how energy related researches benefit from computational science. I have work on large scale computing and thus curious to know how I can use my skills in renewable and ...
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1answer
205 views

Is there some good mailing list for `Computational Science`?

I am wondering whether there is some very good mailing list or google groups for Computational Science, where we can discuss questions instead of only asking and replying questions. In fact, I am ...
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1answer
104 views

MPI policy for multiple asynchronous transfers

What is the policy of multiple overlapping asynchronous transfers in MPI? I have a program with several open asynchronous irecv operations. I find that transfers ...
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1answer
228 views

Solving a large non-hermitian generalised eigenvalue problem from a linear stability analysis using SLEPc

I have a generalised matrix problem: $A x = \lambda B x$ from a spectral method on a linear stability analysis problem. My matrix B is diagonal and positive semi-definite. A is non-hermitian and ...
7
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1answer
119 views

What are the differences between Parareal, PITA, and PFASST?

The Parareal, PITA, and PFASST algorithms are all across-the-domain techniques for parallelizing the solution of time-dependent problems in time. What are the guiding principles behind these ...
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1answer
48 views

Can you give me a detailed description of (spetral) deferred correction method?

I have just read "Accelerating the convergence of spectral deferred correction methods". The link is here: http://www.unc.edu/~junjia/papers/sdcgmres.pdf‎. But I wonder how to understand deferred ...
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3answers
221 views

Performance optimization or tuning possible for Scalapack Gemm?

I'm comparing the performance of distributed gemm, using Scalapack over OpenBLAS, with threaded gemm, using OpenBLAS. It seems quite hard for me to get scalapack to give better results than ...
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1answer
145 views

What kinds of size of matrix A that CHOLMOD can solve Ax=b

CHOLMOD is very fast, but I am just wondering what kinds of size A such that it can solve Ax=b. I have a A of 200,000 * 200,000, but it outputs errors" problem too large". I am very appreciated if ...
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2answers
196 views

How to make Elemental Gemm run quickly?

How to make Elemental Gemm run quickly? I have the following code: ...
1
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1answer
62 views

How to convert a Matrix to a DistMatrix in Elemental?

I have a Matrix<double> on a single core, the result of doing an MPI_Reduce. I want to do the Cholesky, so I need to ...
24
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2answers
401 views

What's the state of the art in parallel ODE methods?

I'm currently looking into parallel methods for ODE integration. There is a lot of new and old literature out there describing a wide range of approaches, but I haven't found any recent surveys or ...
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1answer
96 views

Optimal Scheduling of Parallel Tasks with Known Dependencies

This is maybe a trivial question, but I am stuck with the problem. Suppose we have a general graph: $$G=(V,E)$$ Each edge represents a task, each vertex represents a data for the task (hence each ...
4
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1answer
188 views

Libraries for distributed-memory Cholesky factorization?

What libraries can compute dense Cholesky factorizations in distributed-memory environments (preferably using MPI). I'm using C/C++, and have access to a cluster of between 1 and 40 nodes, where each ...
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1answer
82 views

Does scalapack need threaded or unthreaded blas?

I'm compiling a blas to use with scalapack. Some blases, such as openblas, are naturally multithreaded, but scalapack uses mpi, so maybe needs a single-threaded blas? My questions then are: does ...
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288 views

Best Methodologies for Managing a Mesh in Parallel Finite Element Computation?

I am currently developing a domain decomposition method for the solution of the scattering problem. Basically I am solving a system of Helmholtz BVPs iteratively. I discretize the equations using ...
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2answers
61 views

Reshaping a MultiVector in Trilinos

I'm using Trilinos for a problem and I have an Epetra_MultiVector object with 1 vector of length m*n*nFrames. I need to turn it ...
2
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0answers
81 views

Prediction model on GPU [closed]

I am doing a small project at school. I have done my code implementations in CUDA and did some performance measurements with real values, i.e. running the program with different number of threads, ...
4
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2answers
286 views

Computing matrix exponential with PETSc/SLEPc

My question is basically the best way to compute the matrix exponential in parallel. I've got a sequential code written in Python (https://github.com/hadsed/AdiaQC) and I need to extend it to run in a ...
8
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0answers
166 views

cuda and numerical methods with implicit time discretization

I am looking to port some code that resolves a set of partial differential equations (PDE) by the finite volume method in IMPLICIT form (for the time discretization). As result there is a tridiagonal ...
4
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1answer
216 views

Any useful application for smartphones in the world of computational science?

I was having this discussion with a colleague of mine a week ago and thought I might as well bring it here to a broader audience. That said, I am not certain this is a kind of question that is ...
2
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2answers
104 views

Speedup prediction of rotating mask filter

I am trying to do the speed up analysis of the rotating mask filter (section 4.2.3). Let $N^2$ be the pixels in the image and let $m^2$ be the neighborhood of a given pixel, what I have for my ...
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145 views

CUDA Mandelbrot Set effective bandwidth and optimization

I was reading through this article (very good article and excellent blog BTW) to do some measurements in my (very simple) implementation of the Mandelbrot Set. I'm using a Quadro 2000D card which has ...
2
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2answers
95 views

Is there MPI_Star instead of MPI_Win (window) for MPI_Get?

In FEM applications, each processor needs only data from neighboring processors, which gives a stencil or star pattern of communication. In MPI_Win for MPI_Get, one needs to setup a group of ...
5
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2answers
121 views

Under which conditions is better OMP_NUM_THREADS = 4 or 2 for multithread two-core CPU?

I am running my Fortran 95 numerical codes, whose structure is most times easily parallelized by little more than simply adding the corresponding OpenMP instruction before some critical DO sentences, ...
2
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1answer
201 views

Memory management in time-domain simulation

I develop a parallel time-domain DAE simulation software using OpenMP and Fortran 2003. The main algorithm is: ...
6
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4answers
913 views

Best choice of solver for a large sparse symmetric (but not positive definite) system

I am presently working on solving very large symmetric (but not positive definite) systems, generated by some certain algorithms. These matrices have a nice block sparsity which can be used for ...
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3answers
330 views

Log-log parallel scaling/efficiency plots

A lot of my own work revolves around making algorithms scale better, and one of the preferred ways of showing parallel scaling and/or parallel efficiency is to plot the performance of an ...
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1answer
334 views

Parallel computation of big covariance matrices

We need to compute covariance matrices with sizes ranging from 10000x10000 to 100000x100000. We have access to GPUs and clusters, we wonder what is the best parallel approach for speeding up these ...