Questions tagged [parallel-computing]
The study of solving computational problems by exploiting the use of multiple processors simultaneously.
260
questions
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0answers
81 views
+50
What is the state-of-the-art in parallel sparse matrix and dense vector multiplication?
For sure, there has been many highly optimized library on this. But I am working on a matrix-free context since the problem size does not allow explicit storage of sparse matrix elements. I'd love ...
1
vote
1answer
72 views
Full approximation scheme - smoothers - literature recomendation
I would like to use full approximation scheme(FAS) for solving nonlinear PDE. I am looking into practical implementation of FAS in parallel(MPI) settings. I noticed the most common/effective smoother ...
4
votes
1answer
85 views
Parareal for particle simulations
Recently I have stumbled upon this video of M. J. Gander https://www.youtube.com/watch?v=dn5vqN8ezuE
and the coresponding notes that he wrote on Time Parallel Time Integration and I find it a quite ...
0
votes
2answers
112 views
Parallel output in ASCII-format with MPI
After some parallel computations, I need to write the results in a file and for plotting reasons, I want them in ASCII format. Because of performance issues, I want to avoid to ...
1
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1answer
32 views
How to compute the mean 2D slice of a 3D set of data in MPI
I have a 3D set of data v(i,j,k), and I want to compute the mean 2D slice vmean(i,j) summing up the ...
3
votes
3answers
115 views
CPU usage when a MPI rank waits during a blocking communication
A typical way of dealing with I/O in MPI parallel programs is to either read all data to a single node and dispatch to the other nodes accordingly, or send all data to a single node and write from ...
3
votes
1answer
106 views
Deep learning using Distributed linear algebra
Is there any deep learning library based on Trillinos or Petsc linear algebra?
3
votes
1answer
125 views
Parallelizing Newton-method in solving non-linear systems
Circuit simulation software based on SPICE (such as ngspice) uses Newton-Raphson method to solve non-linear system of equations ...
3
votes
3answers
132 views
GPGPU computing, software selection
I am using an existing GCC C++ x86 Qt application that filters, displays and stores results computed by some C code. Since the computation by now got too complex for CPUs I intend to port the small C ...
1
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2answers
96 views
simulation outputs differ across hardware platforms
We've recently ported our Python/Fortran simulation code to a new supercomputer. Some (not all) of the tests (simulations) that we've run on the new platform yield results that are significantly ...
0
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0answers
88 views
How to make this parfor loop work properly in Matlab?
I have a code that does some calculations for a given value p (p is between 0 and 1). In theory I should be able to make a parfor loop that runs over the values of p, with p being a vector (for ...
2
votes
1answer
47 views
How to pass matrices to parallel workers quickly in matlab?
I am trying to solve many different linear systems in parallel in matlab. The problem is, each linear system has entirely different parts and are fairly large, so passing the information to each of ...
0
votes
1answer
79 views
Computer build for scientific or big data computing [closed]
I'm wanting to build a computer for scientific or big data computing (Python, Fortran, Matlab) and I was hoping to get some advice on the type of processor, memory, graphics, etc I would need.
I ...
2
votes
1answer
286 views
Why my parallel code using MPI is much slower than the serial one?
I know that is not the first time someone asks this question but I'm really confused.I'm new to MPI, and I tried to implement the Jacobi solver for a linear system $Ax=b$. I want to compare the time ...
1
vote
2answers
130 views
How to compute 16 different simulations on parallel with pbs script on the same machine
I have a 32 cores machine, and I need to run 16 different dynamics simulations in parallel on it. I want the 16 jobs to run in parallel, not sequentially, on the same machine. The 16 dynamics input ...
0
votes
1answer
50 views
Access PETSc data in totalview?
Is it possible to view the data stored in the various PETSc data types from within totalview?
Ordinarily, PETSc types are integers which act as pointers to the actual data (obviously my understanding ...
3
votes
1answer
67 views
Parallelizing FEM for elliptical PDEs with n >1
For a little personal project, I am picking up my FEM skills again. I learned a lot about the theory back in university and I am able to implement a simple FEM solver for specific problems but I was ...
2
votes
1answer
218 views
How to choose a python parallelization library?
I want to preprocess a relatively large dataset using python. I implemented some Dask parallelization and was stunned by the time reduction. I figure there are other libraries or frameworks I could ...
2
votes
2answers
190 views
C standard for computational science
Which C standard should be used for computational science code ?
Should we keep compatibility with C89/90/ANSI or jump to C99 or C11 ?
Context:
Code will use third-party : BLAS, LAPACK, MKL, ...
3
votes
2answers
133 views
Parallel assembly of matrix
I have a matrix which I want to assembly quickly, which is in block form:
$$
A = \pmatrix{ A_{11} & A_{12} & A_{13} \\ A_{21} & A_{22} & A_{23} \\ A_{31} & A_{32} & A_{33}}
$$
...
-1
votes
1answer
68 views
Writing parallel code for molecular computation [duplicate]
I recently moved towards computational biophysics from an experimental science background. As of now, I am learning the fundamentals and doing some basic monte carlo simulations of LJ fluid on my ...
2
votes
0answers
37 views
GPGPU/FPGA programming for Combinatorial Analysis
Recently, I have taken an interest in performing combinatorial analysis for the game of 21 (blackjack) and attempted to use my AMD APU to try and thread the program via the 4 cores on the chip. ...
1
vote
2answers
76 views
Guaranteed equality between binary results with increasing MPI processes
Testing on an MPI scientific code for compressible flow dynamics I noticed that the results may depend on the number of processors used for the calculation. In fact, comparing the binary files they ...
4
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1answer
119 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 ...
1
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1answer
187 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.
...
7
votes
1answer
177 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
191 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. ...
1
vote
2answers
145 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:
...
8
votes
0answers
111 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
159 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
131 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
116 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
83 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
170 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
50 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, ...
2
votes
1answer
129 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
150 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 ...
1
vote
1answer
804 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
60 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
143 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
1answer
141 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
71 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
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0answers
53 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
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0answers
59 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. ...
2
votes
5answers
847 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
100 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
510 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
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0answers
53 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
102 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
108 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,...
