Questions tagged [parallel-computing]

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

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Multigrid Reduction In Time Convergence

I am trying to solve a 2D dynamic linear elasticity model parallel in time using Xbraid. The spatial domain is [0,1]x[0,1] and time domain [0,1]. For time integration I am using a backward Euler ...
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146 views

Parallel In Time with Multigrid

I am trying to solve the linear finite element equation $M\ddot{u}+Ku=F(t)$, where $M$ is the mass matrix ,$K$ the stiffness matrix and $F(t)$ the external load vector, parallel in time using XBraid ...
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1answer
77 views

Dirichlet Boundary Condition finite difference method using sparse-matrix $Ax = b$ system

I am trying to solve the boundary value problem for heat equation: $$ u_{xx} + u_{yy} = f(x,y) $$ where the solution $u(x,y) \in [0,1] \times [0,1]$ and the Dirichlet boundary condition $u(x,y) = ...
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On the reordering of sparse matrices

I have been reading on different techniques used to reorder sparse matrices to achieve better performance, the most popular being the Cuthill-McKee or Reverse Cuthill-McKee algorithm. Most of those ...
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1answer
52 views

Understading memory sharing in a GPGPU using a lattice example

I am new in the GPUs world, I used them in Matlab ambient so I didn't need to appreciate the subtleties of these devices. I know that a GPU can be divided into multiprocessors (also called Streaming ...
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2answers
106 views

Parallelisation strategies for mixed FE formulations

Mixed FE formulations with LBB-stable elements require two different meshes for the primary and the constraint variables, for example, displacement and pressure. With continuous approximation for the ...
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1answer
48 views

openmp critical

Following this question, for the code below (from MS OpenMP docs example) ...
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0answers
68 views

Openmp critical section inside if conditional statement

I have a function like this void foo(x, *y) { some calculations if (x > *y) { *y = x/2; } more calculations } My parallel section is <...
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5answers
283 views

FEM and High Performance Computing

Suppose we want to solve an FEM problem in terms of HPC. What is the most usual way to do it: Using an open-source software like mfem,deal.ii etc.. or, Assembly the system by your own(read mesh file,...
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84 views

How to debug segmentation faults in large problems?

I am sorry if this question seems like off topic or opinion based, but I was not sure how to go about it. I am currently working on a 100k x 100k positive definite linear system and trying to solve it ...
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0answers
58 views

OpenMP inconsistently segfaulting

I parallelized my code with openMP, and now have this bug in my code that's really odd. If it's the first time I run on a computer, it segfaults, but if I run the program again it runs fine. I've ...
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1answer
76 views

How to use 8-cores CPU as a single-core more (8x) powerful CPU?

I use python for my algorithm which uses only one core and I need more processing speed. I have i7 6700K CPU with 8 cores. How to convert them to one core to have a total performance of 8 cores? ...
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Are there any embarrassingly parallel tasks that require a CPU rather than GPU?

I am looking for tasks that are unsuitable for GPUs gain significant speedup as more CPU nodes are added don't require large data transfer or inter-thread communication between nodes. Do any ...
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1answer
49 views

problem in interface operator

https://www.unige.ch/~gander/Preprints/42540.pdf. here I have a problem in section $4,$ of approximating the symbol $\sigma_i(k)$. My understanding is, to get back the operator $S_i$ we have to use ...
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1answer
74 views

Parallel, matrix-free estimate of the trace

What would be the best way to estimate the trace of a large, distributed matrix, if one only know its action on a vector throug a parallel "matvec" routine? In the application I am interested in, the ...
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1answer
66 views

Mesh partition quality

I am working on static FE mesh partitioning and in order to achieve a good quality partitioning I want to know how to drecrease interprocessor communication by increasing the connectivity of elements ...
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3answers
2k views

Why would you need frameworks like MPI when you can multi-task using threads?

MPI is an interface which enables us to create multiple processes to be run on a single machine or on a cluster of machines, and enables message passing or in short sorts of communication between ...
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1answer
71 views

Parallel solution of PDEs

Which is the best approach to solve a PDE in parallel: 1.To split the mesh the mesh in N parts and every processor works on its own part or 2.To take the global linear system Ax=b and solve it in ...
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1answer
59 views

Parallel mesh partitioning

When a mesh partitioning takes place and every process works on a part of the mesh is any way to rename the global numbering of nodes(on each process) into a local numbering?Is there any software that ...
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3answers
107 views

How to store a TB size array in C++ on a cluster

I want to do a huge simulation that requires ~ 1 TB of data to describe a bunch of interacting particles (each has different interactions). Is it possible to store this data in an array in C++, so ...
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0answers
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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
79 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
97 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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2answers
181 views

Parallel output in ASCII-format with MPI

After some parallel computations, I need to write the results in a file and for plotting reasons, I want them in ASCII format. Because of performance issues, I want to avoid to ...
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1answer
35 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 ...
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4answers
392 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 ...
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2answers
183 views

Deep learning using Distributed linear algebra

Is there any deep learning library based on Trillinos or Petsc linear algebra?
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1answer
199 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 ...
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3answers
144 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
98 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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1answer
53 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
85 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
512 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 ...
2
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2answers
153 views

How to compute 16 different simulations on parallel with pbs script on the same machine

I have a 32 cores machine, and I need to run 16 different dynamics simulations in parallel on it. I want the 16 jobs to run in parallel, not sequentially, on the same machine. The 16 dynamics input ...
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1answer
87 views

Access PETSc data in totalview?

Is it possible to view the data stored in the various PETSc data types from within totalview? Ordinarily, PETSc types are integers which act as pointers to the actual data (obviously my understanding ...
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1answer
77 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 ...
2
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1answer
397 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 ...
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2answers
197 views

C standard for computational science

Which C standard should be used for computational science code ? Should we keep compatibility with C89/90/ANSI or jump to C99 or C11 ? Context: Code will use third-party : BLAS, LAPACK, MKL, ...
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2answers
135 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
71 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
70 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
78 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 ...
4
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1answer
129 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
214 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
203 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
242 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
150 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
112 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
168 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
135 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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