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

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2answers
69 views

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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1answer
15 views

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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1answer
37 views

Armadillo Multi-threaded Linear Solve Yielding Different Answers

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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4answers
140 views

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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0answers
55 views

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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0answers
33 views

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 ...
9
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3answers
192 views

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 ...
1
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1answer
87 views

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 ...
8
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1answer
139 views

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 ...
3
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1answer
117 views

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 ...
0
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1answer
56 views

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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1answer
67 views

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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1answer
80 views

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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0answers
72 views

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 ...
0
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0answers
49 views

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 ...
6
votes
2answers
166 views

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 ...
4
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2answers
95 views

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 ...
2
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1answer
76 views

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 ...
3
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3answers
249 views

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 ...
2
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1answer
85 views

Parallel efficiency

I would like to calculate efficiency of parallel alghoritm, using the number of computations instead of time computations. In materials from my studies I have a formula like below: $$ \eta(n,p) = ...
3
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0answers
112 views

What are the career options for computational scientists other than being in software Industry?

I would like to know the career options for a computational scientist other than getting into software industry. I wish to use the my skills of Numerical Linear Algebra,Parallel Programming, ...
2
votes
2answers
241 views

GPU vs CPU calculation

I've been working on calculating large factorials ($N>10^9$) and I was wondering if it wasn't faster to use the GPU to run the calculations on something like openCL. What I realized however was ...
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1answer
119 views

Is there a single C++ IDE packed with necessary scientific libraries for computing purpose?

I am basically looking for a good open source C++ IDE with scientific and visualization libraries built in. Can any one suggest few projects?
2
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0answers
72 views

preconditioned Uzawa method with Petsc

I am trying to improve the resolution of a Stokes problem (P2/P1 on unstructured mesh) defined by the matrix $M$: $M= \begin{pmatrix} A_u & 0 & B_u \\ 0 & A_v & B_v\\ B_u^T & ...
5
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2answers
302 views

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 ...
4
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0answers
76 views

Computing entries of a matrix in parallel using GPU

I am trying to solve $Ax=b$ a system of linear equation. The matrix $A=(a_{ij})$ is constructed as $$a_{ij}=\int_0^1\int_0^1 K(x,y)h_i(x)h_j(y) dxdy.$$ The evaluation of integral takes a lot of time, ...
3
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1answer
125 views

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 ...
0
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1answer
133 views

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 ...
1
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1answer
69 views

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 ...
2
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2answers
255 views

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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2answers
581 views

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 ...
3
votes
1answer
142 views

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 ...
2
votes
1answer
60 views

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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0answers
58 views

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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2answers
167 views

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 ...
4
votes
2answers
151 views

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 ...
12
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4answers
4k views

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 ...
2
votes
1answer
88 views

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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0answers
33 views

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 ...
0
votes
1answer
222 views

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 ...
0
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1answer
79 views

Already exist? parallel computing [closed]

Parallel computing allow us to compute tasks in parallel. And if there was a system like torrent that unlike sharing files, it share computing power? For example I have a gpu and I use only 25% of its ...
3
votes
1answer
73 views

communication penalty when using wide stencils in parallel computations

When reading about discontinuous Galerkin methods one finds the argument that these methods allow higher-order accuracy while maintaining a compact stencil (a cell only communicates with its direct ...
0
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0answers
97 views

FFT parallel processing in MPI

I am working now in Beowulf Cluster and parallel processing, I want code for Fast Fourier transfer functions written in any language, e.g., C/C++. Without using FFTW library based on message passing ...
0
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0answers
204 views

Advantages and Disadvantages of PETSC vs HyPre?

What are some of the differences between using Petsc and using Hypre? Also what are some of the advantages and disadvantages of both? Does Petsc use more memory or run faster? Thank you very much for ...
0
votes
3answers
241 views

Determining efficiency in MFLOPS/s of a parallel program

I am running some scientific (parallel) code and would like to obtain some performance profiling measurements. I want to obtain the "efficiency" of the code in terms of flops/s over theoretical (peak) ...
1
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1answer
72 views

Shared memory parallel computing solutions compared

As of 2015, what shared memory parallel computing solutions are available? What are the advantages and disadvantages of each for various use cases arising in high performance scientific computing? I ...
1
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1answer
83 views

Parallel Monte Carlo simulation using PETSc

I am trying to do Monte Carlo simulation for a large problem which requires eigensolution of a matrix for each sample. The matrix itself is quite large so much so that I want the eigensolution itself ...
2
votes
1answer
224 views

Efficient Successive Over Relaxation using Cuda?

I recently implemented Successive Over Relaxation using Cuda as a part of my course project and was curious to know how I can make the code more efficient. I'm using Red/Black SOR scheme which is ...
4
votes
1answer
151 views

Is solving Verlet constraints parallelizable?

I am a computer science student and I came across the Verlet Cloth simulation. An implementation is here. I was interested in how such computation would lend itself to parallelization. The problem ...
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1answer
431 views

Parallel vs Serial Thomas Algorithm

I am currently writing a code that solves a large tridiagonal matrix every iteration and runs for 1,000's of iterations. I am currently using a Thomas algorithm to solve the matrix serially. I found a ...