The study of solving computational problems by exploiting the use of multiple processors simultaneously.
3
votes
0answers
39 views
Prediction model on GPU
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
votes
2answers
123 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 ...
4
votes
0answers
48 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 ...
2
votes
1answer
111 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
votes
2answers
41 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 ...
1
vote
0answers
55 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 ...
1
vote
0answers
41 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 ...
-1
votes
0answers
74 views
Why are Computational Fluid Dynamics Problems Difficult to Solve in Parallel Processing? [closed]
I've heard this in distributed computing circles.
Can you tell me why this is so?
Are there any solutions?
P.S: can I use the Finite Element method for a solution?
4
votes
2answers
84 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, ...
1
vote
1answer
78 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
votes
4answers
147 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 ...
7
votes
3answers
158 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 ...
4
votes
1answer
94 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 ...
8
votes
4answers
158 views
Parallel (GPU) algorithms for asynchronous cellular automata
I have a collection of computational models that could be described as asynchronous cellular automata. These models resemble the Ising model, but are slightly more complicated. It seems as if such ...
1
vote
1answer
68 views
Multi-node jobs with Sun Grid Engine without MPI
I am trying to figure out how to write a proper job file for the Sun Grid Engine so I can run a parallel computation using Mathematica on multiple nodes. Unfortunately almost all tutorials on the ...
4
votes
1answer
106 views
MPI-based Implementations of FFT
In a numerical computation, I am required to take a multi-dimensional FFT on a distributed-memory cluster. The data is currently distributed using a distributed array in PETSc (DMDA).
I initial ...
2
votes
0answers
14 views
An asynchronous version of the Covariance Matrix Adaption (CMA)?
Does anyone know of a variant of the CMA algorithm that is suitable for an asynchronous parallel implementation?
The conventional version of the algorithm allows one to evaluate the fitness function ...
4
votes
1answer
151 views
Threaded OpenBlas benchmark slower than system blas?
I'm not sure if I did something wrong or if I just didn't understand the concept of an optimized BLAS.
I'm a FEM engineer trying to optimize my setup on a small cluster computer (six nodes). I'm ...
0
votes
0answers
90 views
Determining Computing Requirements
I am looking at building/buying myself a workstation for scientific computing. I will be doing molecular dynamics simulations that are memory intensive (data on a large number of particles and a ...
3
votes
1answer
105 views
A better Fast Marching Method?
I am using the Fast Marching Method (FMM) to calculate shortest "distance" (traveltime) from some points.
The way FMM works is: I keep a velocity function in RAM: V(xi,yj,zk). I also keep a priority ...
7
votes
1answer
157 views
What algorithm to use for parallel dense matrix inversion on at most 8 cores?
I need to implement parallel dense matrix inversion for a language I am using that appears to not have an existing library for this (specifically IDL using IDL Bridge for message passing). I am ...
2
votes
1answer
84 views
Limitations of Domain Decomposition Method (DDM) in Finite Element Analysis (FEA)?
The use of DDM in FEA makes parallel solution of the whole analysis e.g. assembly, solver etc possible. DDM splits the model in domains and runs them in parallel. Since there are interconnected nodes ...
4
votes
3answers
364 views
I am looking for a parallel dynamic graph library in C++
Hello scicomp community,
I have worked in the area of graph algorithms using frameworks such as NetworkX (Python), JUNG and YFiles (Java). I am now entering the area of parallel and high perfomance ...
2
votes
1answer
121 views
Partitioning of mesh with 20 noded hexahedral elements [closed]
Is there a way to partition a mesh consisting of 20 noded hexahedral elements for parallel processing? I used METIS for partitioning mesh with 8 noded hexahedron elmements, which works fine but i ...
2
votes
1answer
61 views
Cholesky Algorithm loop-Carried
I would like to know how to unroll loop-carried dependency inside the cholesky algorithm. What are the techniques that I should know to accomplish this work?
I need to know it because I want to ...
4
votes
2answers
145 views
Effects of memory speed/architecture on Pardiso scaling
I am using a program that utilizes the PARDISO solver as part of the Intel math kernel library. I am currently in the process of deciding on a new computer to run the simulations on. I have a ...
3
votes
1answer
134 views
Parallelization of LSE solvers using CUDA
I want to know methods which are fully parallelizable on CUDA architecture.
I have implemented the Jacobi and Conjugate Gradient methods and now Im thinking about the Bi-Conjugate gradient method. I ...
7
votes
2answers
186 views
Shared-memory parallel libraries in Scientific Computing
In recent years, several libraries/software projects have appeared that offer some form or another of general-purpose data-driven shared-memory parallelism.
The main idea is that instead of writing ...
8
votes
3answers
384 views
Thrust for GPU programming
I'm very new to GPGPU programming so please forgive me if the question is not particularly appropriate. From what I understand GPU programming is a very intricate piece of engineering work when ...
8
votes
2answers
201 views
Diagonalization of Dense Ill Conditioned Matrices
I am trying to diagonalize some dense, ill-conditioned matrices. In machine precision, results are inaccurate (returning negative eigenvalues, eigenvectors do not have the expected symmetries). I ...
9
votes
2answers
758 views
Guides on Python for shared-memory Parallel Programming
I have experience in coding OpenMP for Shared Memory machines (in both C and FORTRAN) to carry out simple tasks like matrix addition, multiplication etc. (Just to see how it competes with LAPACK). I ...
10
votes
5answers
245 views
Examples of PDE computations using parallelism in both space and time
In the numerical solution of initial boundary value PDEs, it is very common to employ parallelism in space. It is much less common to employ some form of parallelism in the time discretization, and ...
9
votes
5answers
187 views
How to address numerical non-associativity for parallel reduction?
A parallel reduction assumes that the corresponding operation is associative. This assumption is violated for addition of floating point numbers. You might ask why I care about this. Well, it makes ...
6
votes
2answers
222 views
What is a robust, iterative solver for large 3-d linear-elastic problems?
I'm diving into the fascinating world of finite element analysis and would like to solve a large thermo-mechanical problem (only thermal $\rightarrow$ mechanical, no feedback).
For the mechanical ...
7
votes
1answer
109 views
Anyone knows references summarizing the history of supercomputing?
Anyone knows references summarizing the history and ideas behind supercomputing including mentioning of developments in parallel programming languages, applications, startup companies (some was ...
3
votes
2answers
255 views
How should I build a 2D 5-point stencil Laplacian matrix in parallel?
I'm making a simple eigenvalue solver with SLEPc, using a 5-point stencil and the finite difference method. I want to be able to assemble the matrix in parallel.
My first thought was just to use ...
4
votes
1answer
92 views
Generating lattice clusters/graphs in parallel
I'm trying to generate all graphs with n or fewer vertices that can be embedded in some lattice, eg square, triangular, Kagome. Do there exist algorithms to both enumerate and draw these graphs? What ...
8
votes
3answers
573 views
What is the best high performance computing platform for engineering simulations?
What is the best platform for high performance computing (HPC)?
Windows is long gone, I think. So only Unix and Linux stand the chance. What platform will strongly back my interest on computational ...
6
votes
1answer
1k views
What are the advantages and disadvantages of the particle decomposition and domain decomposition parallelization algorithms?
I am running molecular dynamics (MD) simulations using several software packages, like Gromacs and DL_POLY.
Gromacs now supports both the particle decomposition and domain decomposition algorithms. ...
5
votes
1answer
92 views
Practical efficacy of parallel back substitution
The fact that the back substitution is not done in parallel is not
important, because it uses a negligible amount of computer time when N
is large, compared to the forward elimination.
This ...
4
votes
1answer
80 views
MatMatMult and KSPSolve for MATMPIDENSE matrices
I'm trying to use MATMPIDENSE matrices to solve a system of type Ax=b, but I have some problems. The KSP documentation says that KSPSolve for dense matrices requires to set a 'gmres' solver and a 'lu' ...
2
votes
2answers
324 views
Contiguous prime numbers with MPI (Want more ideas for an efficient algorithm)
I am a programmer. I am working with Message Passing Interface (MPI) in C. I do a program that consist on finding the contiguous prime from 1 to 10,000,000.
I already do it! but I do it with trial ...
9
votes
3answers
452 views
Why isn't my Matrix-Vector Multiplication Scaling?
Sorry for the long post but I wanted to include everything that I thought was relevant in the first go.
What I want
I am implementing a parallel version of Krylov Subspace Methods for Dense ...
3
votes
2answers
204 views
How can I kill parallel processes running in the background?
I just ran a bash script on a remote computer with a for loop that repeatedly executes the following line of code two hundred times:
...
5
votes
3answers
146 views
Reference Request for Profiling High Performance Computing Codes
I write codes in Fortran and C for various matrix algorithms. However, when I profile my codes using VTune, I usually run into some terminology that I cannot fully appreciate. Is there a good resource ...
3
votes
4answers
300 views
Parallel computing programming paradigms/models not based on a master/slave concept?
Do anyone know if there exist any widely used parallel computing programming paradigms/models not based on a master/slave concept?
6
votes
1answer
177 views
Will upgrading to a 64 bit OS help me any?
Assuming that I am running Intel MKL (BLAS, LAPACK), is there any difference in performance if I run it on a 32 or 64 bit OS? (Of course, assuming that my hardware remains the same).
My processor is ...
8
votes
1answer
500 views
Selection of linear solver for GPGPU computation (OpenCL)
I have already developed a working solution of the Finite Element Method to solve heat transfer problems using GPU and OpenCL using the Conjugate Gradient method. The main disadvantage of this method ...
6
votes
2answers
504 views
Understanding OpenCL performance
I'm using ViennaCL's interface to Eigen as a way to leverage OpenCL. Specifically, I'm using the ::viennacl::linalg::bicgstab_tag with an Eigen sparse matrix. ...
15
votes
4answers
774 views
Are there any famous problems/algorithms in scientific computing that cannot be sped up by parallelisation
Are there any famous problems/algorithms in scientific computing that cannot be sped up by parallelisation? It seems to me whilst reading books on CUDA that most things can be.
