# Tagged Questions

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

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### Parallel SVD via one side Jacobi for distributed memory

I want to build a code executing a parallel SVD via the one sided Jacobi method within a distributed memory approach (MPI). The only possibility therefore seems to be a block method. Sofar it looks ...
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### Block-tridiagonal symmetric parallel solver (software recommendation)

What are the fastest numerical methods / (Fortran) packages to solve in parallel (MPI / OMP) a linear symmetric block - tridiagonal system (double complex) where the RHS is a block vector (complex)? ...
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### Need help understanding cluster process managers and MPI

I apologize if this is a relative simple question. I am very new to setting up a cluster computer and I am attempting to make heads and tails of the information. I was reading on setting up a cluster ...
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### How to determine MPI compatibility [closed]

I have recently acquired a server that I will be using for distributed simulations. However, I was wondering how do I determine which MPI version the server is compatible with? The reason that I am ...
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### PetSc vs Sundials for serial numerical computations?

I am currently working on a physics problem that turns into a non-linear boundary value problem. I need an efficient numerical solver that I could run on my laptop with i5 dual core CPU. I am ...
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I am an undergraduate, and enthusiastic about HPC. I am currently familiar with the tools OpenMP, MPI, CUDA, OpenCL, thrust libraries etc. But I want to know the core functioning of these tools, I ...
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### State of the art in parallel data structures

I'm currently evaluating how I could implement several algorithms on a parallel computer with a large number of nodes, each also equipped with a powerful GPU. It turns out that for many algorithms, it ...
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### Parallel linear algebra without OpenMP

I have searched through the archives without success. Apparently, the question is simple: What linear algebra library can I use that is parallel (shared memory) but without OpenMP? As far as I've ...
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### MPI+OpenMP Scalability

I have a numerical code which is MPI+OpenMP (hybrid) parallelized and an available computational resource of 32 nodes with 16 cores on each node. The code has been tested for MPI scalability up to 16 ...
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### The alternative to using PETSc's SNES solvers in parallel without using the DMDA methods

I am using the PETSc libraries, in particular using the SNES solver package to solve a nonlinear matrix equation. Is there a way of parallelising the solution to this problem problem without using ...
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I'm working on some problems that ultimately boil down into a simple assembly of an overdetermined system of equations, $Ax=b$, where $A$ is $m \times n$ for $m \gg n$. I'm leveraging Armadillo's C++ ...
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### What is “good” parallel scaling?

I often hear the phrase "good" or "bad" parallel scaling/efficiency. What exactly do people mean when they say that? For example, let $p = 1,\ldots 16$ be the number of processing elements, and A and ...
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### What is the best option in terms of library or software to solve this system of hyperbolic PDEs?

I want to solve a system of coupled nonlinear 1-D PDE $(\partial_{tt} + \alpha\partial_t)u_i(x,t)=\partial_{xx}(\sum_{j=1}^{j<i}ju_j(x,t)+i\sum_{j=i}^{n}u_j(x,t))-\sin(u_i(x,t))+f$, using method of ...
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### How to decide how to parallelize nested loops on GPU

Suppose I have an algorithms which I want to implement ona GPU. The algorithm consists of a main loop, and all iterations of the loop can be run in parallel. Also, each iteration of the loop has an ...
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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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### Linear Systems with Multiple Right Hand sides

I am interested in solving a sequence of linear systems of the form: $$A x_i = b_i$$ That is, all the systems use the same matrix $A$ but they have different right hand sides. The matrix $A$ is sparse ...
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### What is the state of the art algorithm for diagonalizing real symmetric matrices?

There are many methods for diagonalizing matrices, probably the most widely used is the combination of Householder transformations and the QR algorithm. Is there any superior method for diagonalizing ...
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### How useful is a Xeon Phi for a general workstation

I do a lot of general processing of data on my desktop computer. It can be stuff like extracting timeseries of point measurements from a large number of NetCDF files, or converting csv-files into ...
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### How does MPI differentiate between two computers?

I am starting to dabble in MPI. I am fairly new to this area and I am currently reading the MPI standard. I would like to write my first MPI program, a simple hello world program, on a cluster that ...
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### Comparison of US HPC Resources

I was wondering if anyone knows about the differences between the large HPC resources available to US researchers. I am currently using a startup allocation (through the NSF GRFP) on XSEDE but was ...
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### efficient MPI collective non-blocking communication

I am facing a problem with MPI (Fortran). I have a really big matrix at each node and they differ at different nodes. At some point of my calculations, each node needs the matrix from all other nodes, ...
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### Which topics are hot in computational science? [closed]

I am accepted to computational science master program. The master program just started to accept students in our university and today each group of 3 students was assigned to an advisor teacher (we ...
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### Parallel Boost Graph Library (PBGL) and ParMETIS

I want to read a graph from a text file (in parallel) and use the adjacency list data structure to do some computations on it. By computations, I mean doing parallel Jacobi relaxation method. I wanted ...
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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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### Advice on handling many “small” matrices in parallel

I'm working on a small fun project on the side for a numerical method I've been working a bit with. Roughly, the computational problem I have to solve is the following: Assume you have a collection of ...
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### Templated Numerical Linear Algebra in Parallel

I have to invert large, but densely populated matrices with higher precision arithmetic. Therefore I am looking for something like the PLASMA library, which can do Cholesky or LU factorization in ...
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### Does OOP work easily and efficiently in parallel computations? [closed]

I am working on a task for which the object oriented (OO) approach fits well. I am doing it in MATLAB, since I am in the prototyping phase. However, I know that later I will surely have to perform ...
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### Challenges in implementing Algebraic Multigrid on millions of processors

I just implemented an Algebraic Multigrid solver for a Mixed Dirichlet-Neumann Boundary Value problem and was surprised to see the speed-up as compared to a simple iterative solver for a large problem ...
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### Parallel slower than serial

Issue Hello everyone, I have got a program (from the net) that I intend to speed up by converting it into its parallel version thru the use of pthreads ...
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### C++ - Starting paraller instances of an executable from a C++ code

Can I start parallel run of LAMMPS from inside a C++ code. Is it possible to compile my code and then do mpirun with my compiled code. I also have one system command inside the code, which starts ...
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### GPU-enabled Lattice Boltzmann solvers?

Is anybody aware of any GPU-enabled Lattice Boltzmann solvers (preferably on C++/OpenCL and open-source) that would be recommended? I have found Advanced Simulation Library, but it seems to be very ...
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### How to use the basic Sparse matrix operations (multiplication, .etc) in PyCUDA

I try to use sparse matrix operations in GPU in Python and now try to use PyCUDA with theano. But I can't find how to do sparse matrix and vector multiplication. I only got an example showing how to ...
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### Why is MPI/PETSc only showing 1 processor even though it works for helloworld?

I am a beginner with Unix and MPI. For the serial program, I run the program by typing make in /directory/buildagain and then <...
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### Performance based on the Roofline model

To somewhat follow up on the question asked here, I have been told that the Roofline model is one way of assessing the performance of any scientific code. Basically I compute the Arithmetic Intensity (...
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### How come in distributed computing 10X 32GB systems doesn't equal 1 320GB system

is there a mathematical formula to relate how much memory per node is lost when you use parallel computing? for example, when running COMSOL (FEA, MUMPS) in parallel, a problem that would require ...
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### Parallelization of element-wise matrix multiplication

I use Armadillo as an interface to OpenBLAS. In my current program, I have a loop, in which I do multiplications of the form ...
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### Comparing various implementations/software packages for large-scale finite element simulations

I currently use FEniCS and Deal.II to solve various FEM problems. I am also writing my own implementation of these problems by directly implementing the data structures, routines, and solvers within ...
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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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### On an HPC machine, does one compute node equate to one motherboard?

I am using the Hydra Process Manager from MPICH and I plan on running jobs on multiple compute nodes. Currently working with an Intel Xeon E5-2680v2 with a total of 20 cores with 2 sockets (32 GB of ...
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### Minimum effort merging of two sets

I have the following problem. I have two sequences of elements $A = [a_1,a_2,\cdots,a_n]$ and $B = [b_1,b_2,\cdots,b_m]$. I can build a matrix $D[n \times m]$ where $d_{ij} = d(a_i,b_j)$ My greedy ...
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### Armadillo eig_sym() for extracting eigenvalues. Is it parallel at all? [closed]

After wasting 3 days with scalapack, I gave up and moved to Armadillo, considering it uses lapack underneath its beatiful and easy interface. I would like to calculate the eigen values and eigen ...