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Questions tagged [parallel-computing]

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

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18 views

Determine non-contiguous elements in a 2D triangular mesh

I am using ParMetis do the repartitioning of the adaptive mesh. However, ParMetis cannot guarantee that the result partition is a contiguous mesh. Hence, I need to check if there are any non-...
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0answers
31 views

Group mpi process based on a flag [closed]

I need to create a sub-communicator (mi_comm_world_2) based on a bigger mpi communicator (mpi_comm_world). In particular, after ...
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1answer
48 views

Writing parallel code for molecular computation [duplicate]

I recently moved towards computational biophysics from an experimental science background. As of now, I am learning the fundamentals and doing some basic monte carlo simulations of LJ fluid on my ...
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48 views

Open source distributed sparse-matrix vector multiplication library

What is the current state-of-the-art open source library that has an efficient implementation distributed memory sparse matrix-vector multiplication? I need to perform repeated SpMVs and I am looking ...
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0answers
31 views

GPGPU/FPGA programming for Combinatorial Analysis

Recently, I have taken an interest in performing combinatorial analysis for the game of 21 (blackjack) and attempted to use my AMD APU to try and thread the program via the 4 cores on the chip. ...
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2answers
62 views

Guaranteed equality between binary results with increasing MPI processes

Testing on an MPI scientific code for compressible flow dynamics I noticed that the results may depend on the number of processors used for the calculation. In fact, comparing the binary files they ...
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1answer
85 views

Level scheduling of triangular sparse matrices

Assume one has a triangular sparse matrix and want to solve $Lx=b$ where $b$ and $L$ are known. This can be done easily by using forward substitution when $L$ is a lower triangular matrix. Forward ...
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1answer
79 views

Matlab parpool on Intel Xeon-Phi (KNL)

I am trying to run my matlab script on a Xeon Phi node with 68 physical cores. Using parpool I allocate 16 cores to enable SMD parallelization with a parfor loop. The script looks something like this. ...
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1answer
134 views

Solving linear system of the form $ABx=b$

I would like to solve a linear system of the form $ABx=b$ in parallel, where $A$ and $B$ are large, sparse matrices. Currently, I am forming the system matrix $AB$ explicitly, but I would like to ...
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2answers
51 views

How do I interpret the results from MPI_Wtime()?

Say, I have this code double start = MPI_Wtime(); ParallelMatrixVectorProductRotuine(...); double end = MPI_Wtime(); How do I interpret the numbers I am getting. ...
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2answers
113 views

MPI data broadcast or not in C

I have two slightly different but getting the same results MPI code. The first one is from an open-source package having several data exchange steps in between: ...
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0answers
102 views

Review of modern homotopy methods and practical techniques

I'm hoping someone can recommend recent literature concerning homotopy methods for solving systems of nonlinear equations. Already by the time of Layne Watson's 1986 paper there were a lot of methods,...
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1answer
114 views

Parallel decomposition of 2D grid with minimal communication

Consider an $M\times N$ grid with periodicity in both dimensions upon which I want to do some local stencil-like computations using distributed-memory parallelism (MPI). I have two options for ...
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1answer
101 views

Parallelization of FEM calculations

I need to conduct some FEM calculations and I am wondering whether parallelization would be a good idea. The trouble is that my model is not especially large so it takes few seconds to solve a single ...
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1answer
64 views

Parallel integration of dynamical systems

I need to solve the following problem: $$ \begin{cases} \dot{\vec{x(t)}} = A\vec{x(t)} + u(t)D\vec{x(t)} + u(t)\vec{b}, & x \in (0, T), \\ \vec{x(0)} = \vec{0}, \end{cases}$$ where $u(t)$ is known ...
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1answer
65 views

PBS: Using different computational resources on different nodes

I am using an HPC cluster to launch parallel simulations. At the moment, there are 48 free cores over 4 nodes but not each node do not have the same number of free cores. The distribution is something ...
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1answer
124 views

Efficiency of parallel direct linear solver

I am currently working on solving a positive definite symmetric systems in parallel. The parallel direct solver I used is MUMPS. However, the performance and efficiency of the parallel direct solver ...
2
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1answer
44 views

Test on a set of high degree polynomials whose coefficients in {-1,0,1}

I'm looking for the best way of implementing the following algorithm: consider the set of all polynomials with a high degree (say, degree 30) whose coefficients ranges from a given set of values (say, ...
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0answers
36 views

Example of arbitrary precision in Trilinos

I am trying to get Amesos2 in Trilinos working with the arbitrary precision library GMP. This paper http://www.sandia.gov/~srajama/publications/Amesos2_Belos_2012.pdf suggests that it should be ...
2
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1answer
93 views

Which iterative method and preconditioner from petsc should be used when solving linear algebra in parallel?

I am currently trying to parallelize the incompressible flow solver code. However, when I run the code I realise that the parallel code takes much longer time than sequential code to finish one ...
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1answer
75 views

Why does multithreaded code Segfault in 64-bit but not 32-bit [closed]

I have written some multithreaded code using PyOpenCL, which works fine under the following conditions: GPU 32-bit floating point values (Intel Iris GPU can only handle single precision values) CPU ...
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1answer
401 views

General understanding of Intel MKL, threads and MPI

Preface I seem to lack a fundamental understanding of best practise recommendations given by Intels MKL user guides for using MKL in threaded applications. So let's clarify it together. Wording and ...
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0answers
51 views

Parallel compact schemes using the Parallal Diagonal Dominant (PDD) algorithm

I would like to use the PDD algorithm developed by Sun to solve tridiagonal matrices in parallel for the following compact finite difference scheme: $ \begin{align} \dfrac{1}{4}f^{'}_{i-1} + f^{'}_i +...
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1answer
137 views

Parallel calculation in finite elements

I am trying to solve a 1 Dimensional eigenvalue of poisson problem: $$\nabla \phi ^2 +\nabla \phi = k\phi$$ with the boundary condition: $\phi (0)=0 , \nabla \phi(1) = 0 $. I could solve this ...
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1answer
114 views

Why is FLOP(Floating Point Operations Per Second) mentioned as a specification on every GPU?

Counting FLOP may not be representative of the actual algorithm real world performance but still all the GPU manufacturers mention FLOPS as a metric of Performance on GPU. Is there any way that this ...
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1answer
67 views

How to improve the efficiency when I need to exhaustively pairwise millions of list in Python?

I have a m*n matrix (m>1000000, n>50000). What I want to do now is to pairwise every two rows of the matrix and do some further computation (e.g computing common elements of two rows, or reveal ...
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0answers
51 views

Algorithm design to filter on 5,000 stocks each of which has 4 months worth of data points

I want to filter on 5000 stocks, each of which has 4 month or more worth of data (>= 500 data points each). my filtering criteria will be based on 8 calculated values from the data points. for example,...
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0answers
50 views

Parallel dense solve with submatrices from mesh refinement with Petsc

For a Bounday Element Method problem I require the solution of a system of linear equations with multiple right-hand sides. Though this is a dense system, I still want to do it via Petsc in parallel. ...
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5answers
399 views

c++ Libraries for large linear system of equations

I am looking for libraries for solving large scale linear system (10e5) of equations using parallelization and shared memory. 1. Sparse, complex symmetric, SPD. 2. Suitable for higher order FEM ,...
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1answer
88 views

Need clarification on a piece of book excerpt about spectral element method!

I am reading "Using MPI (3rd edition)" from William Gropp, where in chapter 4 application section 4.13, it introduces an MPI application Nek5000/NekCEM which is based on spectral element method (SEM) ...
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0answers
436 views

Scalability of Julia language [closed]

The Julia language has caught my attention as I am a heavy MATLAB user, but would like more performance. Julia looks attractive as skipping the whole 'prototype in MATLAB then rewrite code in FORTRAN/...
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0answers
44 views

Parallelizing molecular simulation with full configuration energy

First, let just me stress that I'm not a an expert in computation chemistry, so now the problem: We have GCMC molecular simulation, in the Grand Canonical ensemble, using the standard metropolis ...
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1answer
82 views

What exactly is Hardware Acceleration?

I'm able to find many definitions and notions to this term including, Implementing the algorithm (or part of it) in hardware :- Instructions like FMAD; FPGAs Parallelizing the algorithm at the ...
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1answer
88 views

Sun Grid Engine peculiarities

I don't know if anyone is using SGE anymore (what is the world of HPC using nowadays?), but I need to work on version 6.2u3, I believe, from sometime back in '11. I'm using it on a cluster of 64 nodes,...
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2answers
87 views

Halo Region Communication in Unstructured Mesh Problems

I'm currently using ParMETIS and it is required to determine the halo region of the local elements in a parallel unstructured mesh. Assume that the mesh is large and cannot be stored on a single ...
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0answers
41 views

Alternatives for ScaLAPACK pdgesv_ to reduce solving time [duplicate]

I call ScaLAPACK pdgesv_ inside of my FE code. Now, I have to solve matrices of size more than $20000 \times 20000$ and pdgesv_ ...
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1answer
81 views

Generate a set of random x,y,z numbers, with a minimum difference between them, between defined limits

So I am trying a molecular dynamics simulation, and trying to populate a 3D rectangular volume with random particles which are uniformly distributed throughout the volume. Each molecule has a fixed ...
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3answers
1k views

A good, simple book/resource on Parallel Programming in C++ for scientific computing

I am a Mechanical Engineering grad student, currently working on a project which will be scaled up in the new future to require quite some processing power. I am using C++ for the code that I have, ...
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1answer
55 views

simple and fast graph-clustering for paralelization of finite element simulations

I'm learning to use OpenCL to optimize some of my simulations. I realized that I need some sort of Graph-clustering or graph-partitioning to exploit efficiently local memory for un-ordered meshes. ...
2
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0answers
86 views

scalable parallel mesh/amr on unstructured grid

I am trying to code a scalable parallel AMR for unstructured grid. There seems to be three approaches for this a) Store some global grid info on each processor and partition with parmetis (The ...
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2answers
194 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
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1answer
45 views

Balancing core load when number of particles in cells vary (PIC on GPU)

Consider this basic scheme for particle in cell simulations ( with just short-range interactions ): assign particles to disjunct cells for cell $A$ go over neighboring cells $B$ for each particle $...
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1answer
475 views

Best books and notes for beginners in the parallel FORTRAN 90 programming

I am a PhD student and my field of study is Quantum Information and Computation in the theoretical aspect. Actually I write the computer codes/program in FORTRAN 90 which are serial codes but now I ...
2
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1answer
113 views

Parallel processing ability of popular commercial software

I recently scaled my dynamic model based on an open source FEM solver, to run a mesh containing nearly 34 million cells successfully on 800 cores. I have very limited experience using commercial ...
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1answer
103 views

checksum of a distributed variable

Let say I have N computers and 2 N-by-N matrices distributed across them called A and B. Matrix A is row distributed while B is column distributed. Therefore, processor i knows ...
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0answers
98 views

Porting from MPI to GPU

Assuming that the underlying algorithm can be ported to multi GPU, what aspects should one consider while porting from MPI (on multiple nodes) to multi GPU (again on multiple nodes)? Making use of ...
1
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1answer
84 views

Time loop for multiple GPU's

I have a loop that has a similar structure as give below: ...
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0answers
89 views

Irregular data access on CUDA

I am trying to parallelize a program with CUDA that has irregular memory access. To explain what I am talking about, I have attached two figures. In the first figure, I have plotted the indices of the ...
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3answers
179 views

MPI in C, all processor run outside of the MPI envir created

I am new to MPI and am trying to figure out the subtleties in it, and for that reason I am just playing around with an easy example. The question I have is that when I run the code below with 2 ...
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2answers
1k views

What makes a computer fast and powerful to run numerical simulations?

I need to compare two computers and decide which one I want. My goal is to run faster simulations. The current run time is 3.5 hours and I would like to reduce that as much as possible. The code I am ...