Questions tagged [parallel-computing]
The study of solving computational problems by exploiting the use of multiple processors simultaneously.
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2answers
85 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
34 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
61 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
97 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
185 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
131 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
60 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
35 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
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2answers
71 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
votes
1answer
102 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
vote
1answer
120 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
150 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
96 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
142 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
108 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
131 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
116 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
81 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
72 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
148 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
48 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
102 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
107 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
576 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
56 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
139 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
124 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
69 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
58 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
534 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
93 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
466 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
47 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
91 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
99 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
109 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
1answer
85 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 ...
3
votes
3answers
1k 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
59 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
98 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 ...
5
votes
2answers
215 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
46 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
574 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
122 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
134 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
...
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0answers
108 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 ...
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1answer
91 views
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0answers
99 views
Irregular data access on CUDA [closed]
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 ...
2
votes
3answers
238 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 ...
