Questions tagged [parallel-computing]

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

Filter by
Sorted by
Tagged with
7
votes
3answers
2k 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 ...
7
votes
4answers
798 views

When analyzing a parallel algorithm, how do you take communication costs into account?

My question is related in spirit to "Is algorithmic analysis by flop counting obsolete?". Counting the number of computational operations in an algorithm is commonly used as a first-order model to ...
7
votes
4answers
201 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 ...
7
votes
2answers
325 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 ...
7
votes
3answers
608 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 ...
7
votes
3answers
6k 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 ...
7
votes
1answer
2k views

What is the state of the art algorithm for diagonalizing real symmetric matrices?

There are many methods for diagonalizing matrices, probably the most widely used is the combination of Householder transformations and the QR algorithm. Is there any superior method for diagonalizing ...
7
votes
2answers
1k 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. ...
7
votes
2answers
148 views

Can quantum methods be applied to the protein-ligand docking problem?

In the problem of protein-ligand docking, most of the time people are happy if they can just predict the final conformation the ligand adopts into the protein's binding pocket. Most of the time one ...
7
votes
1answer
222 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 ...
7
votes
1answer
357 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 ...
6
votes
3answers
1k views

Krylov Subspace Methods for Dense Systems

I am currently researching on the viability of using KS methods for solving large dense systems. What I wish to prove (or disprove) is that methods like CG, BiCG and QMR are as good (if not better) ...
6
votes
1answer
295 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 ...
6
votes
2answers
6k 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 ...
6
votes
2answers
423 views

How can I reduce the communication bottleneck of a parallel explicit finite difference scheme?

Suppose i was trying to solve a parabolic PDE (heat equation) on a rectangular domain using an explicit finite difference scheme. I am storing my solution vector in a matrix form (because it closely ...
6
votes
2answers
385 views

What guidelines should I use when choosing a scalable linear solver?

There are many different linear solvers, some which work best for diagonally dominant matrices, some for symmetric, some for positive definite ones, some for banded matrices, etc... There are direct ...
6
votes
2answers
547 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
1answer
2k 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 ...
6
votes
1answer
940 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 is a ...
6
votes
1answer
285 views

Parallelize Scipy iterative methods for linear equation systems(bicgstab) in Python

I need to solve linear equations system Ax = b, where A is a sparse CSR matrix with size 500 000 x 500 000. I'am using scipy.bicgstab and it takes almost 10min to solve this system on my PC and I need ...
6
votes
1answer
4k 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 ...
6
votes
2answers
1k views

Starting multiple processes from a single PBS job and distributing them on the free cluster nodes

I'm not very familiar with PBS (we have torque installed here), and I have only used it to run one process per job so far, so bear with me. The actual problem I am trying to use Mathematica on a ...
5
votes
4answers
2k views

What is "good" parallel scaling?

I often hear the phrase "good" or "bad" parallel scaling/efficiency. What exactly do people mean when they say that? For example, let $p = 1,\ldots 16$ be the number of processing elements, and A and ...
5
votes
2answers
1k 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 ...
5
votes
3answers
247 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, ...
5
votes
3answers
456 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, ...
5
votes
3answers
1k 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 ...
5
votes
2answers
544 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
5
votes
2answers
425 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 ...
5
votes
2answers
489 views

How to parallelize a banded direct solver?

I have a linear system whose matrix that is diagonally dominant, non-symmetric, but banded. Since the band-radius is 2 (producing only 5 variables per equation), a banded direct solver (gaussian ...
5
votes
1answer
152 views

Solving PDEs in parallel

I have read different approaches on how to solve pdes in parallel which are discretized using finite element method. For example: Non-overlapping domain decomposition approach as mentioned in https://...
5
votes
1answer
188 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 ...
5
votes
2answers
551 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 ...
5
votes
1answer
3k 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 ...
5
votes
1answer
449 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 ...
5
votes
2answers
1k 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 ...
5
votes
1answer
1k 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. Also,...
5
votes
0answers
269 views

What are the career options for computational scientists other than being in software Industry?

I would like to know the career options for a computational scientist other than getting into software industry. I wish to use the my skills of Numerical Linear Algebra,Parallel Programming, ...
5
votes
0answers
113 views

Computing entries of a matrix in parallel using GPU

I am trying to solve $Ax=b$ a system of linear equation. The matrix $A=(a_{ij})$ is constructed as $$a_{ij}=\int_0^1\int_0^1 K(x,y)h_i(x)h_j(y) dxdy.$$ The evaluation of integral takes a lot of time, ...
5
votes
0answers
198 views

BLACS context value and multiple MPI communicators [closed]

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 ...
4
votes
3answers
2k 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, ...
4
votes
2answers
477 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) ...
4
votes
4answers
1k views

CPU usage when a MPI rank waits during a blocking communication

A typical way of dealing with I/O in MPI parallel programs is to either read all data to a single node and dispatch to the other nodes accordingly, or send all data to a single node and write from ...
4
votes
2answers
111 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 ...
4
votes
2answers
2k views

How do I compile a program that contains both MPI and OPENMP

I have a fortran 90 code that distributes blocks of computations (from a matrix) to multiple nodes in a cluster using MPI, but in each node, the for loops are executed in parallel using openmp. I ...
4
votes
2answers
777 views

COMSOL on Ubuntu (10.04 LTS and 11.04)

I am running into a problem with COMSOL 4.2.0.187 on Ubuntu (both 10.04 LTS and 11.04). When using the option -np x with x > 1, ...
4
votes
1answer
745 views

Libraries for distributed-memory Cholesky factorization?

What libraries can compute dense Cholesky factorizations in distributed-memory environments (preferably using MPI). I'm using C/C++, and have access to a cluster of between 1 and 40 nodes, where each ...
4
votes
2answers
1k 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
2answers
186 views

What mapping strategy should I use when solving many large linear systems of equations?

I am working on a problem that involves solving many (thousands) of distinct linear systems of equations, each with thousands of variables. Let's assume that the size of each matrix is exactly the ...
4
votes
3answers
353 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 ...