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

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2answers
82 views

Using Trilinos and/or Petsc in Windows with Visual Studio?

I am currently working on a project of building a simulator. Up till now I have mostly played around with very simple examples, but with regards to the future I have been thinking that it might be a ...
3
votes
1answer
124 views

Parallel Gram-Schmidt algorithms

I've heard that classical Gram-Schmidt is more amenable to parallelization than modified Gram-Schmidt; apparently the reason has something to do with "level 2 BLAS", which I'm not familiar with. ...
2
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1answer
60 views

Optimal Discontinuous Galerkin (DG) solver on a parallel system

I am seeking the optimal method for implementing DG on a parallel system. For my research, I come across two types of problems. For the first problem, I am solving a time-independent (steady-state) ...
0
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1answer
46 views

Using OpenMP in Fortran for common array operations

In Fortran, given arrays A(1000000) and B(1000000), and to compute the sum you simply write: C = A + B However, when I want to implement OpenMP, I have to write ...
1
vote
1answer
54 views

Fast way to compute all eigenvalues of a dense Hermitian matrix

I am finding the eigenvalues of dense NxN Hermitian matrix which is calculated from a density operator in quantum physics. All the eigenvalues are needed as I need to calculate the sum of the absolute ...
1
vote
1answer
37 views

Solving a problem using multiple threads using CLP

Is it possible to run Clp on multiple threads using Julia and JuMP?
3
votes
1answer
91 views

How does matrix-matrix product scale with multiple CPUs?

These days, one can have 64 cores in a single node. I wonder how well the dense matrix-matrix product (SGEMM and DGEMM) scales ...
4
votes
1answer
136 views

Python: Multistart optimization using parallel programming

[I previously asked my question on StackOverflow but this site may be more appropriate] In Matlab, I am currently using the MultiStart as an optimization algo in a parallel setup for a computer ...
2
votes
1answer
101 views

Maxwell vs Kepler for GPU computation

I am looking at the Nvidia GT-860M which comes in both the old Kepler and new Maxwell architecture. The old one (1152) seems to have almost twice the cores as the new one (640). The new one has a ...
3
votes
2answers
138 views

C - OpenMP, MPI, Serial Program

I'm part of a Computational Science course and come from a non-programming background, so please forgive me my ignorance. I'm working on a set of code in C to numerically solve the Navier Stokes ...
3
votes
2answers
69 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 ...
3
votes
1answer
75 views

Threaded QR with column pivoting

My program needs to perform pivoted QR decomposition on tall (e.g. 1e9 by 100) matrices. I run into the bottleneck that the major computational time of my program is spent on doing serial pivoted-QR ...
1
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0answers
75 views

Why would this a pair of E5-2670 cpus be faster than 4 E5-2640 cpus for large matrix diagonalisation problems?

Not really much more to say; Of several computers available for use, these are two of the larger ones; one has 2x E5-2670, and the other has 4x E5-4640. The problems we're looking at essentially boil ...
4
votes
4answers
103 views

Removing non-determinism from molecular dynamics code

I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing ...
1
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0answers
89 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 ...
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vote
3answers
185 views

Scripting for High Performance Computing

I would like links to resources which provide codes for scripting (preferably in python) for high performance computing. I'm looking for sample codes and examples which can, (1) automatically create ...
1
vote
1answer
98 views

Is it possible to simulate fluid dynamics in a time-based and deterministic manner?

The Problem Domain I have a number of network-connected PCs. I want to be able to simulate and replicate the same simple fluid dynamics simulation (E.g. Navier-Stokes), in real-time, between them. ...
4
votes
2answers
526 views

GPU Computing: Which GPU Brand and Type gives best value for money?

Recently I started to get interested in GPU-computing. I am considering buying a GPU and am inclined to buy an NVIDIA GPU since this allows for coding in both OpenCL and CUDA. But is NVIDIA really the ...
2
votes
3answers
195 views

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?
3
votes
1answer
184 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
votes
1answer
83 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 ...
3
votes
2answers
175 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
votes
0answers
44 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 ...
6
votes
5answers
227 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.
3
votes
3answers
118 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
votes
1answer
101 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 ...
2
votes
1answer
74 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
235 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, ...
4
votes
3answers
164 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
votes
1answer
102 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
votes
1answer
131 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 ...
1
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1answer
236 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
386 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
votes
2answers
201 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, ...
7
votes
1answer
210 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
239 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 ...
6
votes
2answers
225 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
votes
3answers
380 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 ...
5
votes
4answers
161 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 ...
2
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3answers
647 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
59 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 ...
9
votes
1answer
223 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 ...
7
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1answer
144 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 ...
7
votes
1answer
294 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
votes
1answer
202 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
50 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 ...
3
votes
3answers
318 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 ...
1
vote
1answer
174 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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votes
2answers
231 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
69 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 ...