Questions tagged [parallel-computing]
The study of solving computational problems by exploiting the use of multiple processors simultaneously.
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How mature is the "Julia" scientific computing language project?
I'm considering learning a new language to use for numerical/simulation modelling projects, as a (partial) replacement for the C++ and Python that I currently use. I came across Julia, which sounds ...
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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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What's the state of the art in parallel ODE methods?
I'm currently looking into parallel methods for ODE integration. There is a lot of new and old literature out there describing a wide range of approaches, but I haven't found any recent surveys or ...
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Mathematical Libraries for OpenCL?
I am looking for information from anyone that has tried to use OpenCL in their scientific code. Has anyone tried (recently) ViennaCL? If so, how does it compare to cusp?
What about OCLTools? Does it ...
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Are there any famous problems/algorithms in scientific computing that cannot be sped up by parallelisation
Are there any famous problems/algorithms in scientific computing that cannot be sped up by parallelisation? It seems to me whilst reading books on CUDA that most things can be.
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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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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 ...
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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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Parallel I/O options, in particular parallel HDF5
I have an application that can be trivially parallelized but its performance is to a large extent I/O bound. The application reads a single input array stored in a file that is typically 2-5 GB in ...
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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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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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Is there a general-purpose library for structured grid adaptive mesh refinement?
Adaptive mesh refinement (AMR) is a common technique for dealing with the problem of widely varying spatial scales in the numerical solution of PDEs. What general-purpose libraries exist for AMR on ...
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How to Run MPI-3.0 in shared memory mode like OpenMP
I am parallelizing code to numerically solve a 5 Dimensional population balance model. Currently I have a very good MPICH2 parallelized code in FORTRAN but as we increase parameter values the arrays ...
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Parallel optimization algorithms for a problem with very expensive objective function
I am optimizing a function of 10-20 variables. The bad news is that each function evaluation is expensive, approx 30 min of serial computation. The good news is that I have a cluster with a few dozen ...
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Is there a good, easy-to-use, high quality open source CFD solver out there?
My thesis is on developing numerical methods for model reduction in combustion. I run my methods purely on the chemistry part of combustion simulations, and I have plenty of case studies for 0-D ...
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Why isn't my Matrix-Vector Multiplication Scaling?
Sorry for the long post but I wanted to include everything that I thought was relevant in the first go.
What I want
I am implementing a parallel version of Krylov Subspace Methods for Dense Matrices. ...
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What are the advantages and disadvantages of the particle decomposition and domain decomposition parallelization algorithms?
I am running molecular dynamics (MD) simulations using several software packages, like Gromacs and DL_POLY.
Gromacs now supports both the particle decomposition and domain decomposition algorithms. ...
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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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Any recommendations for unit-testing frameworks compatible with code/libraries that use MPI?
Usually, I write serial code, and when I do, I write unit tests with some xUnit-style testing framework (MATLAB xUnit, PyUnit/nose, or Google's C++ testing framework).
Based on a cursory Google ...
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Examples of PDE computations using parallelism in both space and time
In the numerical solution of initial boundary value PDEs, it is very common to employ parallelism in space. It is much less common to employ some form of parallelism in the time discretization, and ...
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Parallel (GPU) algorithms for asynchronous cellular automata
I have a collection of computational models that could be described as asynchronous cellular automata. These models resemble the Ising model, but are slightly more complicated. It seems as if such ...
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Is it preferable to concentrate on studying math or computation?
Concurrent to my research on Krylov Subspace Methods, I have the option of exploring mathematics behind HPC a step ahead or the theory of computation (hardware, OS, compilers etc.).
Currently, I know ...
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I am looking for a parallel dynamic graph library in C++
Hello scicomp community,
I have worked in the area of graph algorithms using frameworks such as NetworkX (Python), JUNG and YFiles (Java). I am now entering the area of parallel and high perfomance ...
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How can one parallelize a multigrid method for solving a linear system of equations?
As I understand it, the multigrid method solves a linear system by solving a coarser version of the same problem (there by eliminating low frequency error) then projecting back to the fine grid to ...
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Guides on Python for shared-memory Parallel Programming
I have experience in coding OpenMP for Shared Memory machines (in both C and FORTRAN) to carry out simple tasks like matrix addition, multiplication etc. (Just to see how it competes with LAPACK). I ...
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Best Methodologies for Managing a Mesh in Parallel Finite Element Computation?
I am currently developing a domain decomposition method for the solution of the scattering problem. Basically I am solving a system of Helmholtz BVPs iteratively. I discretize the equations using ...
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Thrust for GPU programming
I'm very new to GPGPU programming so please forgive me if the question is not particularly appropriate. From what I understand GPU programming is a very intricate piece of engineering work when ...
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Best choice of solver for a large sparse symmetric (but not positive definite) system
I am presently working on solving very large symmetric (but not positive definite) systems, generated by some certain algorithms. These matrices have a nice block sparsity which can be used for ...
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Parallel Mersenne Twister for Monte Carlo
Recently, I came across a comment claiming that almost all researchers doing Monte Carlo methods are doing it wrong. It went on to elaborate that merely choosing different seeds for different ...
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What is a robust, iterative solver for large 3-d linear-elastic problems?
I'm diving into the fascinating world of finite element analysis and would like to solve a large thermo-mechanical problem (only thermal $\rightarrow$ mechanical, no feedback).
For the mechanical ...
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Task-based shared-memory parallel libraries in Scientific Computing
In recent years, several libraries/software projects have appeared that offer some form or another of general-purpose data-driven shared-memory parallelism.
The main idea is that instead of writing ...
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Diagonalization of Dense Ill Conditioned Matrices
I am trying to diagonalize some dense, ill-conditioned matrices. In machine precision, results are inaccurate (returning negative eigenvalues, eigenvectors do not have the expected symmetries). I ...
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What are the differences between Parareal, PITA, and PFASST?
The Parareal, PITA, and PFASST algorithms are all across-the-domain techniques for parallelizing the solution of time-dependent problems in time.
What are the guiding principles behind these methods?...
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How to assemble and solve a matrix system in parallel from values generated in different processors?
I am solving a multiscale problem using the Heterogeneous Multiscale Method (HMM). Essentially, my particular procedure uses the following iterative process:
Solve many local matrix systems.
...
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Selection of linear solver for GPGPU computation (OpenCL)
I have already developed a working solution of the Finite Element Method to solve heat transfer problems using GPU and OpenCL using the Conjugate Gradient method. The main disadvantage of this method ...
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cuda and numerical methods with implicit time discretization
I am looking to port some code that resolves a set of partial differential equations (PDE) by the finite volume method in IMPLICIT form (for the time discretization).
As result there is a tridiagonal ...
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Is discontinuous Galerkin really any more parallelizable than continuous Galerkin?
I've always heard that easy parallelization was one of the advantages of DG methods, but I don't really see why any of those reasons don't also apply to continuous Galerkin.
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Parallel computation of big covariance matrices
We need to compute covariance matrices with sizes ranging from $10000\times10000$ to $100000\times100000$. We have access to GPUs and clusters, we wonder what is the best parallel approach for ...
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GPU libraries to use for Linear Algebra operations
I am looking for GPU libraries to accelerate a code I have, whose primary "high performance" regions have singular value decomposition, QR factorization and Eigen values, Eigenvectors computation. I ...
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How do I compute the parallel overhead of a parallel code run on a single processor when no sequential code is available?
I'm profiling the performance of PETSc's linear solvers. As I understand it,
$$\text{speedup}=\frac{\text{Sequential Time}}{\text{Parallel Time}}.$$
I know that running the parallel code on one ...
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Is there some good mailing list for `Computational Science`?
I am wondering whether there is some very good mailing list or google groups for Computational Science, where we can discuss questions instead of only asking and replying questions.
In fact, I am ...
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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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How can I seed a parallel linear congruential pseudo-random number generator for maximal period?
Normally when I seed a sequential random number generator in C, I use the call
srand(time(NULL))
then use
rand() mod N
...
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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 ...
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Intel Knights Landing work loads vs NVIDIA GeForce
There are lot of articles being written about how the newly launched Intel Xeon Phi will steal the HPC\Super Computer market share from the competitors. Intel Knights is equipped with 72 cores and 4 ...
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Reference Request for Profiling High Performance Computing Codes
I write codes in Fortran and C for various matrix algorithms. However, when I profile my codes using VTune, I usually run into some terminology that I cannot fully appreciate. Is there a good resource ...
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MPI policy for multiple asynchronous transfers
What is the policy of multiple overlapping asynchronous transfers in MPI?
I have a program with several open asynchronous irecv operations. I find that transfers ...
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What algorithm to use for parallel dense matrix inversion on at most 8 cores?
I need to implement parallel dense matrix inversion for a language I am using that appears to not have an existing library for this (specifically IDL using IDL Bridge for message passing). I am ...
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Solving a large non-hermitian generalised eigenvalue problem from a linear stability analysis using SLEPc
I have a generalised matrix problem: $A x = \lambda B x$ from a spectral method on a linear stability analysis problem. My matrix B is diagonal and positive semi-definite. A is non-hermitian and ...
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Anyone knows references summarizing the history of supercomputing?
Anyone knows references summarizing the history and ideas behind supercomputing including mentioning of developments in parallel programming languages, applications, startup companies (some was ...
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