Questions tagged [parallel-computing]

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

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What is the state-of-the-art in parallel sparse matrix and dense vector multiplication?

For sure, there has been many highly optimized library on this. But I am working on a matrix-free context since the problem size does not allow explicit storage of sparse matrix elements. I'd love ...
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1answer
100 views

Full approximation scheme - smoothers - literature recomendation

I would like to use full approximation scheme(FAS) for solving nonlinear PDE. I am looking into practical implementation of FAS in parallel(MPI) settings. I noticed the most common/effective smoother ...
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1answer
104 views

Parareal for particle simulations

Recently I have stumbled upon this video of M. J. Gander https://www.youtube.com/watch?v=dn5vqN8ezuE and the coresponding notes that he wrote on Time Parallel Time Integration and I find it a quite ...
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1answer
52 views

How to compute the mean 2D slice of a 3D set of data in MPI

I have a 3D set of data v(i,j,k), and I want to compute the mean 2D slice vmean(i,j) summing up the ...
3
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1answer
433 views

Parallelizing Newton-method in solving non-linear systems

Circuit simulation software based on SPICE (such as ngspice) uses Newton-Raphson method to solve non-linear system of equations ...
3
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3answers
163 views

GPGPU computing, software selection

I am using an existing GCC C++ x86 Qt application that filters, displays and stores results computed by some C code. Since the computation by now got too complex for CPUs I intend to port the small C ...
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2answers
99 views

simulation outputs differ across hardware platforms

We've recently ported our Python/Fortran simulation code to a new supercomputer. Some (not all) of the tests (simulations) that we've run on the new platform yield results that are significantly ...
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7answers
111k 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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6answers
5k views

How can the gravitational n-body problem be solved in parallel?

How can the gravitational n-body problem be solved numerically in parallel? Is precision-complexity tradeoff possible? How does precision influence the quality of the model?
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8answers
5k views

What software is good to use for parallel debugging?

I'm not running any parallel code right now, but I anticipate running parallel code in the future using a hybrid of OpenMP and MPI. Debuggers have been invaluable tools for me when running serial ...
2
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1answer
69 views

How to pass matrices to parallel workers quickly in matlab?

I am trying to solve many different linear systems in parallel in matlab. The problem is, each linear system has entirely different parts and are fairly large, so passing the information to each of ...
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1answer
92 views

Computer build for scientific or big data computing [closed]

I'm wanting to build a computer for scientific or big data computing (Python, Fortran, Matlab) and I was hoping to get some advice on the type of processor, memory, graphics, etc I would need. I ...
2
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1answer
1k views

Why my parallel code using MPI is much slower than the serial one?

I know that is not the first time someone asks this question but I'm really confused.I'm new to MPI, and I tried to implement the Jacobi solver for a linear system $Ax=b$. I want to compare the time ...
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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 ...
17
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5answers
1k 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 ...
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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, ...
3
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1answer
91 views

Parallelizing FEM for elliptical PDEs with n >1

For a little personal project, I am picking up my FEM skills again. I learned a lot about the theory back in university and I am able to implement a simple FEM solver for specific problems but I was ...
7
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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 ...
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1answer
1k views

How to choose a python parallelization library?

I want to preprocess a relatively large dataset using python. I implemented some Dask parallelization and was stunned by the time reduction. I figure there are other libraries or frameworks I could ...
18
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3answers
2k 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 algorithm/...
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2answers
205 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 ...
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2answers
169 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: ...
3
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2answers
147 views

Parallel assembly of matrix

I have a matrix which I want to assembly quickly, which is in block form: $$ A = \pmatrix{ A_{11} & A_{12} & A_{13} \\ A_{21} & A_{22} & A_{23} \\ A_{31} & A_{32} & A_{33}} $$ ...
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1answer
93 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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1answer
207 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 ...
4
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2answers
866 views

Outputting a distributed vector in PETSc

I'm working with someone else's code that uses PETSc 3.0.0-p9. They have a vector at the end of the computation that is distributed among a number of different processors, and I want to output that ...
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2answers
81 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
257 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
2k views

Masters in HPC (High Performance Computing)

Is there a master degree in HPC (High Performance Computing) in US? I am asking this question because in my early research I found no direct mentioning of HPC instead invidual courese in parallel ...
7
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5answers
271 views

Computational science contests. Why arent there any?

I was wondering why there are no online or offline computational science contests? At least I couldn't find much by googling. I mean, like a topcoder for computational sciences. I assume one reason is ...
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2answers
198 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 ...
4
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1answer
148 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 ...
6
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1answer
294 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 ...
0
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2answers
354 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. ...
9
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0answers
123 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
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 ...
0
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1answer
169 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 ...
3
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4answers
11k views

When is MPI_Wait necessary for non-blocking calls?

I hope this is not too off-topic here -- I've asked it on SO but I'm hoping I'll get better answers here! I'm a little bit confused about when I should call MPI_Wait (or other variants such as: ...
7
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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 ...
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2answers
834 views

How does MPI differentiate between two computers?

I am starting to dabble in MPI. I am fairly new to this area and I am currently reading the MPI standard. I would like to write my first MPI program, a simple hello world program, on a cluster that ...
1
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1answer
131 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 ...
0
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1answer
591 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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1answer
199 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
52 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, ...
0
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1answer
129 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,...
2
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1answer
143 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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2answers
478 views

efficient MPI collective non-blocking communication

I am facing a problem with MPI (Fortran). I have a really big matrix at each node and they differ at different nodes. At some point of my calculations, each node needs the matrix from all other nodes, ...
2
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1answer
160 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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2answers
3k 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 ...
0
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1answer
269 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 ...