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

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GPU-enabled Lattice Boltzman solvers?

Is anybody aware of any GPU-enabled Lattice Boltzman solvers (preferably on C++/OpenCL and open-source) that would be recommended? I have found Advanced Simulation Library, but it seems to be very ...
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52 views

How to use the basic Sparse matrix operations (multiplication, .etc) in PyCUDA

I try to use sparse matrix operations in GPU in Python and now try to use PyCUDA with theano. But I can't find how to do sparse matrix and vector multiplication. I only got an example showing how to ...
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23 views

Why is MPI/PETSc only showing 1 processor even though it works for helloworld?

I am a beginner with Unix and MPI. For the serial program, I run the program by typing make in /directory/buildagain and then ...
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27 views

Performance based on the Roofline model

To somewhat follow up on the question asked here, I have been told that the Roofline model is one way of assessing the performance of any scientific code. Basically I compute the Arithmetic Intensity ...
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42 views

How come in distributed computing 10X 32GB systems doesn't equal 1 320GB system

is there a mathematical formula to relate how much memory per node is lost when you use parallel computing? for example, when running COMSOL (FEA, MUMPS) in parallel, a problem that would require ...
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77 views

Parallelization of element-wise matrix multiplication

I use Armadillo as an interface to OpenBLAS. In my current program, I have a loop, in which I do multiplications of the form ...
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109 views

Comparing various implementations/software packages for large-scale finite element simulations

I currently use FEniCS and Deal.II to solve various FEM problems. I am also writing my own implementation of these problems by directly implementing the data structures, routines, and solvers within ...
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175 views

Parallelizing a for-loop in Python

Are there any tools in Python that are like Matlab's parfor? I found this thread, but it's four years old. I thought maybe someone here might have more recent experience. Here's an example of the ...
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77 views

On an HPC machine, does one compute node equate to one motherboard?

I am using the Hydra Process Manager from MPICH and I plan on running jobs on multiple compute nodes. Currently working with an Intel Xeon E5-2680v2 with a total of 20 cores with 2 sockets (32 GB of ...
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21 views

Minimum effort merging of two sets

I have the following problem. I have two sequences of elements $A = [a_1,a_2,\cdots,a_n]$ and $B = [b_1,b_2,\cdots,b_m]$. I can build a matrix $D[n \times m]$ where $d_{ij} = d(a_i,b_j)$ My greedy ...
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57 views

Armadillo eig_sym() for extracting eigenvalues. Is it parallel at all? [closed]

After wasting 3 days with scalapack, I gave up and moved to Armadillo, considering it uses lapack underneath its beatiful and easy interface. I would like to calculate the eigen values and eigen ...
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77 views

parallel computatioan of a PDE in MATLAB

I want to solve a 1-D PDE $(\partial_{tt} + \alpha\partial_t)u(x,t)=\partial_{xx}u(x,t)-\sin(u(x,t))+f$, using method of lines and for this I defined a spatial grid of about n~1000 points. Since my ...
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73 views

Already exist? parallel computing [closed]

Parallel computing allow us to compute tasks in parallel. And if there was a system like torrent that unlike sharing files, it share computing power? For example I have a gpu and I use only 25% of its ...
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67 views

communication penalty when using wide stencils in parallel computations

When reading about discontinuous Galerkin methods one finds the argument that these methods allow higher-order accuracy while maintaining a compact stencil (a cell only communicates with its direct ...
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55 views

FFT parallel processing in MPI

I am working now in Beowulf Cluster and parallel processing, I want code for Fast Fourier transfer functions written in any language, e.g., C/C++. Without using FFTW library based on message passing ...
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82 views

Advantages and Disadvantages of PETSC vs HyPre?

What are some of the differences between using Petsc and using Hypre? Also what are some of the advantages and disadvantages of both? Does Petsc use more memory or run faster? Thank you very much for ...
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109 views

Determining efficiency in MFLOPS/s of a parallel program

I am running some scientific (parallel) code and would like to obtain some performance profiling measurements. I want to obtain the "efficiency" of the code in terms of flops/s over theoretical (peak) ...
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60 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 ...
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1answer
66 views

Parallel Monte Carlo simulation using PETSc

I am trying to do Monte Carlo simulation for a large problem which requires eigensolution of a matrix for each sample. The matrix itself is quite large so much so that I want the eigensolution itself ...
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1answer
106 views

Efficient Successive Over Relaxation using Cuda?

I recently implemented Successive Over Relaxation using Cuda as a part of my course project and was curious to know how I can make the code more efficient. I'm using Red/Black SOR scheme which is ...
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114 views

Is solving Verlet constraints parallelizable?

I am a computer science student and I came across the Verlet Cloth simulation. An implementation is here. I was interested in how such computation would lend itself to parallelization. The problem ...
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217 views

Parallel vs Serial Thomas Algorithm

I am currently writing a code that solves a large tridiagonal matrix every iteration and runs for 1,000's of iterations. I am currently using a Thomas algorithm to solve the matrix serially. I found a ...
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164 views

Designing a preconditioner for a very Ill-conditionned matrix

I am a physicist with limited numerical methods knowledge and I am trying to speed up the inversion of a very ill-conditioned problem ($rcond>10^{30}$). The same sparse square matrix is used ...
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133 views

Are there any popular (paralleled) implementations of Lanczos methods for SVD/eigendecomposion?

I want to use it in Matlab or Java. Will these two languages be much slower for computing the algorithm compared to C, C++, in case efficiency is an important factor? I'm aware of that there's a ...
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1answer
65 views

Efficiently swap vectors in PETSC

The PETSC function VecSwap after a few layers of abstraction calls the BLAS primitive swap, which essentially copies data around (unless I am missing something). ...
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49 views

Any book or teaching material on computational neuroscience using hardware acceleration?

I am looking for some material (be it in the form of a book, reader notes, teaching material freely available etc.) on the topic of computational neuroscience employing hardware acceleration? I guess ...
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285 views

Parallel optimization algorithms for a problem with very expensive objective function

I am optimizing a function of 10-20 variables. The bad news is that each function evaluation is expensive, approx 30 min of serial computation. The good news is that I have a cluster with a few dozen ...
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243 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 ...
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149 views

Parallel solver for sparse matrices on unstructured grids

I am trying to solve Euler equations on unstructured grids. Consequently, the problem reduces to solving Ax=b where A is a ...
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2answers
207 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 ...
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1answer
192 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. ...
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1answer
92 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) ...
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169 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 ...
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102 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 ...
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104 views

Solving a problem using multiple threads using CLP

Is it possible to run Clp on multiple threads using Julia and JuMP?
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107 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 ...
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382 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 ...
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1answer
206 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 ...
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187 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 ...
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80 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
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1answer
76 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 ...
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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 ...
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122 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 ...
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119 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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235 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 ...
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1answer
106 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. ...
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1k 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 ...
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3answers
202 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?
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274 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 ...
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1answer
155 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 ...