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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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1answer
82 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
64 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. ...
6
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1answer
133 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
40 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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1answer
82 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
100 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,...
5
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1answer
109 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 ...
0
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1answer
100 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 ...
1
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1answer
63 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 ...
1
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1answer
113 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
42 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
34 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
87 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 ...
0
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1answer
70 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
310 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
50 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 +...
1
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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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0answers
74 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 ...
0
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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
50 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
47 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
366 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 ,...
0
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1answer
87 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) ...
2
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0answers
428 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
42 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 ...
0
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1answer
78 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 ...
0
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1answer
87 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,...
0
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2answers
82 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
40 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_ ...
0
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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 ...
2
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3answers
988 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, ...
0
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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
81 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 ...
6
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2answers
188 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
0
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1answer
44 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 $...
0
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1answer
439 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
107 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 ...
0
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1answer
89 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
96 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
80 views

Time loop for multiple GPU's

I have a loop that has a similar structure as give below: ...
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0answers
87 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 ...
1
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3answers
170 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 ...
4
votes
3answers
1k views

How do I reliably generate random numbers in Python distributed across multiple nodes?

Consider the following scenario: I want to perform a large Monte Carlo simulation across a compute cluster with several nodes. To avoid excessive transmission of data, I am going to generate random ...
2
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0answers
83 views

Quasi-Newton Optimization with parallel function evaluation

I have a function of many variables (~200-2000) which I am optimizing with some success using L-BFGS. While the function is expensive to evaluate, the gradient can be computed with not much additional ...
2
votes
1answer
68 views

Need help understanding cluster process managers and MPI

I apologize if this is a relative simple question. I am very new to setting up a cluster computer and I am attempting to make heads and tails of the information. I was reading on setting up a cluster ...
0
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2answers
313 views

How to determine MPI compatibility [closed]

I have recently acquired a server that I will be using for distributed simulations. However, I was wondering how do I determine which MPI version the server is compatible with? The reason that I am ...
6
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2answers
348 views

PetSc vs Sundials for serial numerical computations?

I am currently working on a physics problem that turns into a non-linear boundary value problem. I need an efficient numerical solver that I could run on my laptop with i5 dual core CPU. I am ...
4
votes
1answer
120 views

HPC reading material

I am an undergraduate, and enthusiastic about HPC. I am currently familiar with the tools OpenMP, MPI, CUDA, OpenCL, thrust libraries etc. But I want to know the core functioning of these tools, I ...