The study of solving computational problems by exploiting the use of multiple processors simultaneously.
3
votes
1answer
70 views
Level scheduling of triangular sparse matrices
Assume one has a triangular sparse matrix and want to solve $Lx=b$ where $b$ and $L$ are known. This can be done easily by using forward substitution when $L$ is a lower triangular matrix. Forward ...
0
votes
1answer
34 views
Matlab parpool on Intel Xeon-Phi (KNL)
I am trying to run my matlab script on a Xeon Phi node with 68 physical cores. Using parpool I allocate 16 cores to enable SMD parallelization with a parfor loop. The script looks something like this.
...
6
votes
1answer
125 views
Solving linear system of the form $ABx=b$
I would like to solve a linear system of the form $ABx=b$ in parallel, where $A$ and $B$ are large, sparse matrices. Currently, I am forming the system matrix $AB$ explicitly, but I would like to ...
0
votes
2answers
38 views
How do I interpret the results from MPI_Wtime()?
Say, I have this code
double start = MPI_Wtime();
ParallelMatrixVectorProductRotuine(...);
double end = MPI_Wtime();
How do I interpret the numbers I am getting. ...
0
votes
1answer
56 views
MPI data broadcast or not in C
I have two slightly different but getting the same results MPI code.
The first one is from an open-source package having several data exchange steps in between:
...
7
votes
0answers
99 views
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,...
5
votes
1answer
99 views
Parallel decomposition of 2D grid with minimal communication
Consider an $M\times N$ grid with periodicity in both dimensions upon which I want to do some local stencil-like computations using distributed-memory parallelism (MPI). I have two options for ...
0
votes
1answer
93 views
Parallelization of FEM calculations
I need to conduct some FEM calculations and I am wondering whether parallelization would be a good idea.
The trouble is that my model is not especially large so it takes few seconds to solve a single ...
1
vote
1answer
61 views
Parallel integration of dynamical systems
I need to solve the following problem:
$$ \begin{cases}
\dot{\vec{x(t)}} = A\vec{x(t)} + u(t)D\vec{x(t)} + u(t)\vec{b}, & x \in (0, T), \\
\vec{x(0)} = \vec{0},
\end{cases}$$
where $u(t)$ is known ...
1
vote
1answer
58 views
PBS: Using different computational resources on different nodes
I am using an HPC cluster to launch parallel simulations. At the moment, there are 48 free cores over 4 nodes but not each node do not have the same number of free cores. The distribution is something ...
1
vote
1answer
108 views
Efficiency of parallel direct linear solver
I am currently working on solving a positive definite symmetric systems in parallel. The parallel direct solver I used is MUMPS. However, the performance and efficiency of the parallel direct solver ...
2
votes
1answer
42 views
Test on a set of high degree polynomials whose coefficients in {-1,0,1}
I'm looking for the best way of implementing the following algorithm: consider the set of all polynomials with a high degree (say, degree 30) whose coefficients ranges from a given set of values (say, ...
0
votes
0answers
34 views
Example of arbitrary precision in Trilinos
I am trying to get Amesos2 in Trilinos working with the arbitrary precision library
GMP. This paper
http://www.sandia.gov/~srajama/publications/Amesos2_Belos_2012.pdf
suggests that it should be ...
2
votes
1answer
78 views
Which iterative method and preconditioner from petsc should be used when solving linear algebra in parallel?
I am currently trying to parallelize the incompressible flow solver code.
However, when I run the code I realise that the parallel code takes much longer time than sequential code to finish one ...
0
votes
1answer
67 views
Why does multithreaded code Segfault in 64-bit but not 32-bit [closed]
I have written some multithreaded code using PyOpenCL, which works fine under the following conditions:
GPU 32-bit floating point values (Intel Iris GPU can only handle single precision values)
CPU ...
0
votes
1answer
195 views
General understanding of Intel MKL, threads and MPI
Preface
I seem to lack a fundamental understanding of best practise recommendations given by Intels MKL user guides for using MKL in threaded applications. So let's clarify it together.
Wording and ...
2
votes
0answers
49 views
Parallel compact schemes using the Parallal Diagonal Dominant (PDD) algorithm
I would like to use the PDD algorithm developed by Sun to solve tridiagonal matrices in parallel for the following compact finite difference scheme:
$
\begin{align}
\dfrac{1}{4}f^{'}_{i-1} + f^{'}_i +...
1
vote
1answer
136 views
Parallel calculation in finite elements
I am trying to solve a 1 Dimensional eigenvalue of poisson problem:
$$\nabla \phi ^2 +\nabla \phi = k\phi$$
with the boundary condition: $\phi (0)=0 , \nabla \phi(1) = 0 $.
I could solve this ...
1
vote
0answers
73 views
Why is FLOP(Floating Point Operations Per Second) mentioned as a specification on every GPU?
Counting FLOP may not be representative of the actual algorithm real world performance but still all the GPU manufacturers mention FLOPS as a metric of Performance on GPU. Is there any way that this ...
0
votes
1answer
67 views
How to improve the efficiency when I need to exhaustively pairwise millions of list in Python?
I have a m*n matrix (m>1000000, n>50000). What I want to do now is to pairwise every two rows of the matrix and do some further computation (e.g computing common elements of two rows, or reveal ...
1
vote
0answers
50 views
Algorithm design to filter on 5,000 stocks each of which has 4 months worth of data points
I want to filter on 5000 stocks, each of which has 4 month or more worth of data (>= 500 data points each). my filtering criteria will be based on 8 calculated values from the data points. for example,...
1
vote
0answers
46 views
Parallel dense solve with submatrices from mesh refinement with Petsc
For a Bounday Element Method problem I require the solution of a system of linear equations with multiple right-hand sides. Though this is a dense system, I still want to do it via Petsc in parallel. ...
1
vote
5answers
339 views
c++ Libraries for large linear system of equations
I am looking for libraries for solving large scale linear system (10e5) of equations using parallelization and shared memory.
1. Sparse, complex symmetric, SPD.
2. Suitable for higher order FEM ,...
0
votes
1answer
82 views
Need clarification on a piece of book excerpt about spectral element method!
I am reading "Using MPI (3rd edition)" from William Gropp, where in chapter 4 application section 4.13, it introduces an MPI application Nek5000/NekCEM which is based on spectral element method (SEM) ...
2
votes
0answers
420 views
Scalability of Julia language [closed]
The Julia language has caught my attention as I am a heavy MATLAB user, but would like more performance. Julia looks attractive as skipping the whole 'prototype in MATLAB then rewrite code in FORTRAN/...
1
vote
0answers
41 views
Parallelizing molecular simulation with full configuration energy
First, let just me stress that I'm not a an expert in computation chemistry, so now the problem:
We have GCMC molecular simulation, in the Grand Canonical ensemble, using the standard metropolis ...
0
votes
1answer
76 views
What exactly is Hardware Acceleration?
I'm able to find many definitions and notions to this term including,
Implementing the algorithm (or part of it) in hardware :- Instructions like FMAD; FPGAs
Parallelizing the algorithm at the ...
0
votes
1answer
80 views
Sun Grid Engine peculiarities
I don't know if anyone is using SGE anymore (what is the world of HPC using nowadays?), but I need to work on version 6.2u3, I believe, from sometime back in '11. I'm using it on a cluster of 64 nodes,...
0
votes
2answers
77 views
Halo Region Communication in Unstructured Mesh Problems
I'm currently using ParMETIS and it is required to determine the halo region of the local elements in a parallel unstructured mesh. Assume that the mesh is large and cannot be stored on a single ...
0
votes
0answers
40 views
Alternatives for ScaLAPACK pdgesv_ to reduce solving time [duplicate]
I call ScaLAPACK pdgesv_ inside of my FE code. Now, I have to solve matrices of size more than $20000 \times 20000$ and pdgesv_ ...
0
votes
1answer
80 views
Generate a set of random x,y,z numbers, with a minimum difference between them, between defined limits
So I am trying a molecular dynamics simulation, and trying to populate a 3D rectangular volume with random particles which are uniformly distributed throughout the volume. Each molecule has a fixed ...
2
votes
3answers
895 views
A good, simple book/resource on Parallel Programming in C++ for scientific computing
I am a Mechanical Engineering grad student, currently working on a project which will be scaled up in the new future to require quite some processing power. I am using C++ for the code that I have, ...
0
votes
1answer
55 views
simple and fast graph-clustering for paralelization of finite element simulations
I'm learning to use OpenCL to optimize some of my simulations. I realized that I need some sort of Graph-clustering or graph-partitioning to exploit efficiently local memory for un-ordered meshes.
...
2
votes
0answers
78 views
scalable parallel mesh/amr on unstructured grid
I am trying to code a scalable parallel AMR for unstructured grid. There seems to be three approaches for this
a) Store some global grid info on each processor and partition with parmetis (The ...
6
votes
2answers
179 views
Speeding up a linear transform using Python
In an optical wavefront propagation problem, I need to do excessive Fourier-type computations:
...
0
votes
1answer
44 views
Balancing core load when number of particles in cells vary (PIC on GPU)
Consider this basic scheme for particle in cell simulations ( with just short-range interactions ):
assign particles to disjunct cells
for cell $A$ go over neighboring cells $B$
for each particle $...
0
votes
1answer
412 views
Best books and notes for beginners in the parallel FORTRAN 90 programming
I am a PhD student and my field of study is Quantum Information and Computation in the theoretical aspect. Actually I write the computer codes/program in FORTRAN 90 which are serial codes but now I ...
2
votes
1answer
106 views
Parallel processing ability of popular commercial software
I recently scaled my dynamic model based on an open source FEM solver, to run a mesh containing nearly 34 million cells successfully on 800 cores. I have very limited experience using commercial ...
0
votes
1answer
79 views
checksum of a distributed variable
Let say I have N computers and 2 N-by-N matrices distributed across them called A and B. Matrix A is row distributed while B is column distributed. Therefore, processor i knows
...
1
vote
0answers
95 views
Porting from MPI to GPU
Assuming that the underlying algorithm can be ported to multi GPU, what aspects should one consider while porting from MPI (on multiple nodes) to multi GPU (again on multiple nodes)?
Making use of ...
1
vote
1answer
79 views
1
vote
0answers
85 views
Irregular data access on CUDA
I am trying to parallelize a program with CUDA that has irregular memory access. To explain what I am talking about, I have attached two figures. In the first figure, I have plotted the indices of the ...
1
vote
3answers
163 views
MPI in C, all processor run outside of the MPI envir created
I am new to MPI and am trying to figure out the subtleties in it, and for that reason I am just playing around with an easy example. The question I have is that when I run the code below with 2 ...
1
vote
2answers
1k views
What makes a computer fast and powerful to run numerical simulations?
I need to compare two computers and decide which one I want. My goal is to run faster simulations. The current run time is 3.5 hours and I would like to reduce that as much as possible. The code I am ...
4
votes
3answers
1k views
How do I reliably generate random numbers in Python distributed across multiple nodes?
Consider the following scenario: I want to perform a large Monte Carlo simulation across a compute cluster with several nodes. To avoid excessive transmission of data, I am going to generate random ...
2
votes
0answers
80 views
Quasi-Newton Optimization with parallel function evaluation
I have a function of many variables (~200-2000) which I am optimizing with some success using L-BFGS. While the function is expensive to evaluate, the gradient can be computed with not much additional ...
2
votes
1answer
66 views
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 ...
0
votes
2answers
252 views
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 ...
6
votes
2answers
340 views
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 ...
4
votes
1answer
120 views
HPC reading material
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 ...
