Questions tagged [parallel-computing]

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

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Parallel vs Serial computing using Python Qutip. Why is serial faster?

I am trying to learn parallel computing using qutip's parallel_map function. I've tried to write a basic and simple code to understand the differences between parallel and serial calculation of ...
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Is it possible to run a Metropolis Monte Carlo simulation in parallel?

Is it possible to run a Metropolis Monte Carlo simulation in parallel? Suppose I perform a Metropolis Monte Carlo simulation using four threads. Suppose, the programming source code divides a ...
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Non-dimensionalizing the Ideal MHD System

Non-dimensionalization is a really frustrating topic for me, and I imagine many others, because in school it was glossed over while being really important to implementing a simulation. I'm writing a ...
Ashamandarei's user avatar
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What is the name of the theory that combines 3d discretized surfaces and distributed numerical algebra

I've looked into distributed numerical computation work before, but I've realized that 3D applications are all about 3d surfaces and meshes.So I'd like to look into related work on mesh and parallel ...
Haitao Xiao's user avatar
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row and column based distributed LU factorization

The LU parallel computation theories I've seen are based on $M\times N$ mesh computations, is there a theory for one dimensional device mesh LU parallel decomposition? For example, $A$ is a matrix. we ...
Haitao Xiao's user avatar
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Iteration counts of AMG solver changes in parallel

I am solving the linear elasticity equation within a FEM library with a complex 3D geometry. The resulting linear system is solved with CG, preconditioned by AMG (Algebraic Multigrid). The computed ...
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Diagonalization of large sparse matrix, computational programme recommendation and methods

According to this link, All eigenpairs of large sparse symmetric matrix. The guy @Baranas seems to have given a very confident answer about solving the whole Eigen spectrum. May I know if anyone has ...
Lee Zhi Yan's user avatar
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PhD in scientific computing to be a scientific programmer

Intro and disclaimer: this question concerns developing a career in Scientific Computing in industry, starting from an (applied) mathematics background, say an MSc. It definitely arises from my ...
Lilla's user avatar
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Lattice Boltzmann method parallelization

I'm learning about the lattice Boltzmann method (LBM) and how it can be parallelized. On Wikipedia, they say, "The LBM was designed from scratch to run efficiently on massively parallel ...
Medulla Oblongata's user avatar
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OpenMP Fortran array operations in target regions

I am asking this here for the possibility that someone here is familiar with OpenMP offloading. Is there some other way to parallelise Fortran array operations outside of unrolling the loops of the ...
Touko Puro's user avatar
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Parallel Block-Structured class abstraction for FDM

I’m currently developing a FDM/FVM (using contravariant coordinates) code using Fortran and Co-Arrays (SIMD, in general), and so far I have all sparse matrix (BiCGStab, working on AMG) solvers and ...
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Under what circumstances is parallel scaling of the finite element method not "solved"?

I see things like this deal.II example, (ctrl + f for "superMUC") which seems to show some pretty impressive scaling (nearly twice as fast for twice as many CPU cores for a wide range of ...
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Where to find datasets to research the optimal parameter search space for HPC systems? [closed]

I am a student researcher who is new to the HPC domain. I have recently taken a project where I am working on optimizing the parameter search space (both application level and hardware level ...
Abrar Hossain's user avatar
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Why GPU scaling (speedup) is usually worse than CPU scaling?

Let's define scaling, as how linear the speedup of using more than one GPU or CPU is. For example, having 2 GPUs gives you 2x faster execution time. I have noticed that in many software (e.g. ...
Daniel Wiczew's user avatar
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Parallelize pseudo inverse of a matrix using Lapacke

I am currently using the protocol described in https://stackoverflow.com/questions/55599950/computation-of-pseidoinverse-with-svd-in-c-using-blas-and-lapacke to compute the pseudo inverse of a matrix. ...
Filippo Caleca's user avatar
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How to define a global index from local index and rank in parallel computing

Suppose I have 4 processes and each process has $n_i, i=0,1,2,3$ elements. In particular, with rank $0$, we have loc indices list $[0,1,\ldots, n_{0}-1]$ and $1$, we have loc indices list $[0,1,\ldots,...
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How does a blocking MPI all to all synchronization work?

I was trying to understand more in detail how a blocking MPI all to all really work. Of course, the actual all to all traffic is pretty straightforward, what I can't understand is how it is able to &...
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Calculate the time taken to run an algorithm on GPU

I want to calculate the total time taken for a fixed code run using an NVIDIA GPU (for instance, Tesla K40). The code has to run 1 million single-bit comparisons. All the comparisons are independent ...
guptasonal's user avatar
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where to use multiprocessing in multi-loop program

I am running a program that uses [a lot of] looping to perform a type of bootstrap analysis. The computational step - PCA - can take a long time (60+) seconds, which means that collectively this ...
Brian Barry's user avatar
3 votes
1 answer
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Measurement of observables in Parallel Tempering Monte Carlo simulations

I'm doing Metropolis-Hastings Monte Carlo simulations of a classical spin Hamiltonian at different temperatures using the parallel tempering algorithm. I have managed to obtain constant exchange rates ...
David Leonardo Ramos's user avatar
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Pythonic way of finding RMS in large dataset

I am working on a fluid mechanics problem with a 4-D dataset (time,x,y,z). I am trying to find the RMS values such as $\overline{u^\prime u^\prime}$,$\overline{v^\prime v^\prime}$,$\overline{w^\prime ...
Ykrath_TheReader's user avatar
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Distributed Optimization of Least Powers

I have $F_i \in \mathbb{R}^{m}$, $y_i \in \mathbb{R}$, $\beta_i \in (1,\infty)$ for $i = 1,\ldots, n$. I would like to solve the following convex optimization problem $$\min_{x} \sum_{i = 0}^n |F_i\...
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How can I write a GPGPU program that can run on any GPU?

Here is my objective: I want to code a ray tracing engine in C++ that can be run on any GPU. That means that it should work on NVIDIA GPUs, AMDs, or even Intel Graphics chipsets. The choice of C++ was ...
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Is there a mathematical algorithm that can determine whether a problem is parallelizable?

Is there a mathematical algorithm that can determine whether a problem is parallelizable? Possibly similar to how the definition for "computable" works out: https://en.wikipedia.org/wiki/...
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How to find eigvals/eigvecs of huge symmetric tridiagonal matrix using multiple processes or threads?

In python, there is a function in scipy (scipy.linalg.eigh_tridiagonal) which is extremely efficient for an exact diagonalization of a symmetric tridiagonal matrix (...
Stelladuck's user avatar
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Solve a large-scale linear system of equations with millions of unknowns

I have a large-scale system of linear equations: $Ax = b$, where $A$ is an $n\times n$ square symmetric positive definite matrix (not sparse), $b$ is an $n \times 1$ vector and $x$ is $n\times 1$ ...
Math_Lover's user avatar
3 votes
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Numerical calculation of out-of-time order correlators (OTOCs)

I want to numerically calculate OTOCs for different quantum mechanical systems. Consider the following Hamiltonian $$H=p_x^2+p_y^2+x^2y^2$$ and I want to calculate the following OTOC $$C_T(t)=-\left&...
ghost's user avatar
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How amenable is this 2D Frenkel–Kontorova-like energy minimization problem in Python to the use of a modest PC + GPU? (Heavy reliance on indexing)

@Richard's answer to Going to try to move some of my scipy/numpy calculation to a new GPU, how to avoid disappointing results? is quite helpful, and as promised I've added a simple running example ...
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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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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 ...
lijas's user avatar
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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 ...
Debasish Das's user avatar
1 vote
2 answers
291 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 ...
tmph's user avatar
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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 $\...
david david's user avatar
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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 ...
Orphea12's user avatar
3 votes
2 answers
378 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 ...
CLP's user avatar
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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 ...
Wout12345's user avatar
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3 answers
761 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 ...
Resa's user avatar
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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-...
niran90's user avatar
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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 ...
Spy123's user avatar
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5 votes
1 answer
287 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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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 ...
enco909's user avatar
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2 votes
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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 ...
Stéphane Laurent's user avatar
1 vote
1 answer
92 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-...
420's user avatar
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6 votes
1 answer
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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 ...
I.P.'s user avatar
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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 ...
user2348209's user avatar
1 vote
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66 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 ...
spyros's user avatar
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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 ...
spyros's user avatar
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3 votes
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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) = ...
Dong Le's user avatar
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3 answers
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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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