Computational Science

Questions tagged [parallel-computing]

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

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Searching for recent code source for "Parallel scientific computing in C++ and MPI "

I am learning C++ scientific computing with "Parallel scientific computing in C++ and MPI A Seamless Approach to Parallel Algorithms and their Implementation" since it kept coming up a lot ...
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114 views

Multi threaded finite element assembly implementation

What is typically the best way to multi thread the assembly loop in a finite element code? Does anyone have experience with implementing this, that they can share? I can think of a couple of ways of ...
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Can you provide an example of an algorithm that has strong scalability but not weak scalability? Can you also provide an example the other way around?

Strong Scaling and Amdahl's Law Strong scaling is a measure of how, for a fixed overall problem size, the time to solution decreases as more processors are added to a system. An application that ...
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MPI vs OPENMP usage for boundary element method

I have an implementation question with MPI and OPENMP. I have a large three-dimensional surface mesh divided into elements. I want to loop over each element (outer loop) and compute an integral over ...
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2answers
112 views

Affecting parts of an array outside MPI process efficiently

This was originally asked on Stackoverflow but instead of migrating it was suggested I repost here and delete that one. I've tried to clarify based on comments there. I'm new to MPI, but I am trying ...
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1answer
94 views

Vectorization Matlab/Octave of Markov Matrix Powers

I have just created a code snippet in Octave/Matlab that aims to create a plot which shows the accuracy of an initial probability vector $\vec{\pi}$ derived from the transition probability matrix $\...
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88 views

Passing in user inputs with mpirun

I am building a quantum circuit simulator using mpi4py. The simulator takes user inputs to build the initial system and quantum gates the system passes through. I can get the code to work if I do not ...
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207 views

OpenMP: parallelizing calculation of pair interaction forces

I recently started to learn OpenMP. Albeit I have developed some intuition I still have some doubts on how to proceed under certain circumstances that are very useful for computational physicists. My ...
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Why does Eigen allocate a temporary to evaluate A.noalias() = B.transpose()*C in parallel?

I wrote a program which iteratively transforms data using matrix multiplications. To minimize the number of large memory allocations, I use two roughly equal-sized ...
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3answers
255 views

How to apply the boundary condition when global stiffness matrix is stored in csr format? [duplicate]

I am solving the poisson equation and I constructed the global stiffness matrix in compressed row storage format. Then I wrote the preconditioned conjugate gradient solver for solving the system of ...
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48 views

MPI_Test not progressing MPI_Isend/MPI_Irecv requests

I am running a CFD simulation with a 200,000-vertex mesh. I've decomposed the mesh into 2 load-balanced sub-domains to test my parallel implementation. In the specific function that I am time-...
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Output solution vector in Petsc

I am using petsc to solve a linear elasticity problem discretized by finite elements.The initial mesh is read by a mesh file and the distribution in each processor is done using METIS.I am using only ...
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161 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://...
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34 views

Methodology to develop parallel GPU simulations

I'm quite new to GPU or in general parallel programming. I am working on a Lattice-Boltzmann simulation that should be parallelized on GPU's. I wanted to asked more experienced people how to attack ...
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200 views

Can one safely use an OpenMP parallel loop with Armadillo?

I have a C++ code performing some Armadillo computations in a loop. I'd like to parallelize this loop with OpenMP. But Armadillo automatically uses OpenMP for some computations. So, would the OpenMP ...
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1answer
88 views

preconditioner for $u''(x)=\sin(x)$

I am interested in finding preconditioner to solve the problem for one dimensional problem $u''(x)=\sin(x), u(0)=u(1)=0$ using Dirichlet-Neumann method. The preconditioner $M$ coming from Dirichlet-...
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325 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 ...
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performance comparison between PETSc and SLATE

We want to start a new project to solve a large-scale inverse problem (O(10^6) number of parameters) to invert for subsurface wave speeds. We will use FEM to solve forward and adjoint PDEs. In our ...
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52 views

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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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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219 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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450 views

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
61 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
117 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
255 views

openmp critical

Following this question, for the code below (from MS OpenMP docs example) ...
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338 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
528 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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1answer
112 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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69 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
93 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
51 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
86 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
91 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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3k 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
76 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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68 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
129 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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105 views

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
102 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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3answers
429 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
56 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
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 ...
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2answers
221 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
458 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
168 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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1answer
71 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
94 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 ...

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