Questions tagged [parallel-computing]
The study of solving computational problems by exploiting the use of multiple processors simultaneously.
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Unable to validate hypersonic flatplate case in DSMC SPARTA
I'm trying to learn a software called DSMC SPARTA. I'm validating the hypersonic flatplate case mentioned in one of the tutorials on the website (Page 17). This was my test case:
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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. ...
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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.
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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 ...
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How to decouple nodes and cores with MPI?
I have code currently using multiprocessing with joblib to distribute computations from a loop over multiple cores within one cluster node, like so:
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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 ...
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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 ...
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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 ...
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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
$$\min_{x} \sum_{i = 0}^n |F_i\...
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How can I write a GPGPU program that can run on any GPU?
Here is my objective: I want to code a ray tracing engine in C++ that can be run on any GPU. That means that it should work on NVIDIA GPUs, AMDs, or even Intel Graphics chipsets. The choice of C++ was ...
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Is there a mathematical algorithm that can determine whether a problem is parallelizable?
Is there a mathematical algorithm that can determine whether a problem is parallelizable?
Possibly similar to how the definition for "computable" works out:
https://en.wikipedia.org/wiki/...
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How to find eigvals/eigvecs of huge symmetric tridiagonal matrix using multiple processes or threads?
In python, there is a function in scipy (scipy.linalg.eigh_tridiagonal) which is extremely efficient for an exact diagonalization of a symmetric tridiagonal matrix (...
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Solve a large-scale linear system of equations with millions of unknowns
I have a large-scale system of linear equations: $Ax = b$, where $A$ is an $n\times n$ square symmetric positive definite matrix (not sparse), $b$ is an $n \times 1$ vector and $x$ is $n\times 1$ ...
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Numerical calculation of out-of-time order correlators (OTOCs)
I want to numerically calculate OTOCs for different quantum mechanical systems. Consider the following Hamiltonian
$$H=p_x^2+p_y^2+x^2y^2$$
and I want to calculate the following OTOC
$$C_T(t)=-\left&...
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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 ...
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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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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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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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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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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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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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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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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 ...
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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 ...
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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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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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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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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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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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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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