Questions tagged [performance]

Questions about the execution speed and memory usage of algorithms, data structures, languages and libraries.

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6
votes
2answers
546 views

Why performance is given in Gflop/s rather than actual time in seconds

While reading many research-papers comparing parallel implementations of algorithms on different machines/architectures, I have noticed that the performance comparison is always listed in terms of ...
11
votes
2answers
351 views

What is the underlying structure of scientific code performance?

Consider two computers with different hardware and software configurations. When running the exact same serial Navier-Stokes code on each platform it takes x and y time to execute one iteration for ...
6
votes
1answer
111 views

Measures of parsimony for numerical models?

There are hundreds of different types of performance measures for numerical models, many of which are applicable to many different types of models. But a good model doesn't just perform well, it ...
10
votes
3answers
8k views

Nvidia K20X vs GeForce Titan for GPGPU acceleration

Im trying to understand the difference between these two graphics cards for academic computing, specifically for the DGEMM component. If we look at the raw statistics, both have the same GK110 chip, ...
14
votes
3answers
1k views

Comparison of iteration methods: number of iterations vs. cpu time

I am comparing two iterative methods for inverting random square matrices. Since the matrices are random, every test case takes both different amounts of iterations and different elapsed times. My ...
13
votes
3answers
1k views

Is there any benefit to compiling LAPACK from source versus installing the prebuilt package from Ubuntu?

I know that ATLAS is able to optimize itself for the machine it is compiled on and thus maximum benefits are found by compiling from source. Is there any benefit to compiling LAPACK from source? It ...
14
votes
2answers
12k views

What is the fastest way to compute all eigenvalues of a very big and sparse adjacency matrix in python?

I'm trying to figure out if there is a faster way to compute all the eigenvalues and eigenvectors of a very big and sparse adjacency matrix than using scipy.sparse.linalg.eigsh As far as I know, this ...
6
votes
1answer
437 views

Reference BLAS/LAPACK from NETLIB is twice as fast as MKL for complex numbers

I'm solving the Helmholtz equation using PETSc. I found with the PETSc configure option --download-f-blas-lapack my program runs twice as fast over running it with ...
2
votes
0answers
454 views

Prediction model on GPU [closed]

I am doing a small project at school. I have done my code implementations in CUDA and did some performance measurements with real values, i.e. running the program with different number of threads, ...
2
votes
2answers
214 views

Speedup prediction of rotating mask filter

I am trying to do the speed up analysis of the rotating mask filter (section 4.2.3). Let $N^2$ be the pixels in the image and let $m^2$ be the neighborhood of a given pixel, what I have for my ...
8
votes
2answers
402 views

How do Volkov and Demmel experimentally determine the latencies, line sizes, and page sizes of a GPU?

In "LU, QR and Cholesky Factorizations using Vector Capabilities of GPUs", by Vasily Volkov and James Demmel, there is an interesting way to interpret the latencies, line sizes, and page sizes of a ...
2
votes
2answers
4k views

Matlab element within ranges and distance between two points

I have a $53534\times 3$ matrix with $x$, $y$, and $z$ coordinates. I want to find the element of matrix within ranges as follows: ...
3
votes
3answers
296 views

How do I get reliable timing data for time spent in function calls in my code?

This question is a follow-up to Fortran: Best way to time sections of your code?. If I want to time functions in my code, I know I could use gprof or kcachegrind. I also know that the results from ...
4
votes
1answer
1k views

Effecient CFD programming techniques

I'm trying to make highly efficient CFD programming complex for solving combustion problems. I've finished writing core which realises mathematical model, and now I'm concerned about code performance. ...
10
votes
1answer
711 views

What is the impact of C++11 move semantics in the context of scientific computing?

C++11 introduces move semantics which can, for example, improve code performance in situations where C++03 would need to perform a copy construction or copy assignment. This article reports that ...
21
votes
1answer
2k views

How does the performance of Python/Numpy array operations scale with increasing array dimensions?

How do Python/Numpy arrays scale with increasing array dimensions? This is based on some behaviour I noticed while benchmarking Python code for this question: How to express this complicated ...
6
votes
5answers
286 views

Evaluate the sum

I want to evaluate the sum $$\sum_{k=1}^\infty \left(\frac{i+1}{\sqrt{2}}\right)^k\cdot k^{-\alpha}$$ where $i=\sqrt{-1}$ and $\alpha\in[\frac{3}{4},1]$ with 8 digits accuracy. If I am willing to ...
13
votes
5answers
2k views

Calculation of the sparsity structure for finite element matrices

Question: What methods are available to accurately and efficiently calculate the sparsity structure of a finite element matrix? Info: I'm working on a Poisson Pressure Equation solver, using Galerkin'...
2
votes
0answers
591 views

Cusp Library performance worse than PETSC (GMRES 200 iterations) Why?

I wanted to compare the speeds of the GMRES implementations in the CUSP and the PETSc libraries. The matrix (A) used for testing was a 3d Laplacian matrix obtained by using the 7 point stencil on a ...
11
votes
1answer
254 views

Statistical models for local memory/compute, network latency, and bandwidth jitter in HPC

Parallel computation is frequently modeled using a deterministic local rate of computation, latency overhead, and network bandwidth. In reality, these are spatially variable and non-deterministic. ...
10
votes
3answers
270 views

Literature references for modeling current and future energy costs of floating-point operations and data transfers

I am searching for the most important literature and slide references for modeling current and future energy costs of floating-point operations and data transfers across the CPU, memory, network, and ...
13
votes
3answers
6k views

Memory usage in fortran when using an array of derived type with pointer

In this sample program I'm doing the same thing (at least I think so) in two different ways. I'm running this on my Linux pc and monitoring the memory usage with top. Using gfortran I find that in the ...
8
votes
1answer
2k views

How to get sparse complex matrices from my code to PETSc efficiently

What is the most efficient way to get a complex sparse matrix from my Fortran code to PETSc? I understand that this is problem dependent, so I tried to give as many relevant details as possible below. ...
15
votes
2answers
1k views

Open source implementation of rational approximation to a function

I am looking for some open source implementation (any of Python, C, C++, Fortran is fine) of rational approximation to a function. Something along the article [1]. I give it a function and it gives me ...
4
votes
1answer
126 views

Efficient way to find max height repetitive sub-trees in an object tree

I am trying to solve a problem of finding a max repetitive sub-tree in an object tree. By the object tree I mean a tree where each leaf and node has a name. Each leaf has a type and a value of that ...
9
votes
2answers
391 views

Fastest way to find eigenpairs of a small nonsymmetric matrix on a GPU in shared memory

I have a problem where I need to find all positive (as in the eigenvalue is positive) eigenpairs of a small (usually smaller than 60x60) nonsymmetric matrix. I can stop calculating when the eigenvalue ...
3
votes
2answers
210 views

Efficiently changing basis on many diagonal matrices

I have to perform a [complex] basis transformation on a large number of [real] diagonal matrices: $$ \langle b_i | A | b_j \rangle = \sum_k \langle b_i | \bar{b}_k\rangle \langle\bar{b}_k | A | \bar{b}...
8
votes
2answers
230 views

How should I report profiling/timing information about my code?

I've seen a lot of publications in Computational Physics journals use different metrics for the performance of their code. Especially for GPGPU code, there seems to be a great variety of timing ...
30
votes
4answers
2k views

What tools or approaches are available to speed up code written in Python?

Background: I think I might want to port some code that calculates matrix exponential-vector products using a Krylov subspace method from MATLAB to Python. (Specifically, Jitse Niesen's expmvp ...
5
votes
1answer
455 views

Intersection of hyperplanes

A very basic question but i couldn't find another post about it: Given $p$ non parallel hyper-plane in $\mathbb{R}^p$: $\left(\begin{array}{cccc} c_{11} & a_{11} & .... & a_{1p} \\ ... &...
11
votes
3answers
3k views

What is the overhead in sparse matrix multiplication

Does matrix multiplication (both Mat*Mat, and Mat*Vec) scale with number of non-zeros, or with the size of the matrix? Or some combination of the two. What about with shape. For example, I have a ...
4
votes
2answers
1k views

How should I build a 2D 5-point stencil Laplacian matrix in parallel?

I'm making a simple eigenvalue solver with SLEPc, using a 5-point stencil and the finite difference method. I want to be able to assemble the matrix in parallel. My first thought was just to use <...
11
votes
3answers
308 views

How to implement efficient indexing function for two particle integrals <ij|kl>?

This is a simple symmetry enumeration problem. I give the full background here, but no knowledge of quantum chemistry is needed. The two particle integral $\langle ij|kl\rangle$ is: $$ \langle ...
10
votes
3answers
6k views

MATLAB matrix multiplication (the best computational approach)

I have to make a coordinates transformation between two reference systems (axes). For that, three matrices ($3\times3$) have to be multiplied due to some intermediate axes being used. I have thought ...
67
votes
10answers
14k views

What are some good strategies for improving the serial performance of my code?

I work in computational science, and as a result, I spend a non-trivial amount of my time trying to increase the scientific throughput of many codes, as well as understanding the efficiency of these ...
17
votes
4answers
5k views

Portable multicore/NUMA memory allocation/initialization best practices

When memory bandwidth limited computations are performed in shared memory environments (e.g. threaded via OpenMP, Pthreads, or TBB), there is a dilemma of how to ensure that the memory is correctly ...
4
votes
3answers
122 views

Whats wrong with my running time calculation?

I am running a linear algebra iterative method (PCG) for solving Ax=b, the dimension of the matrix is 10000x10000. So, I did 2 preliminary analyses: Memory Analysis The size of the matrix dominates ...
9
votes
4answers
4k views

Are DAXPY, DCOPY, DSCAL overkills?

I have implemented CG in FORTRAN by linking it to Intel MKL. When there are statements like: (Refer Wikipedia) p=r; x=x+alpha*p r=r-alpha*Ap; or similar ...
2
votes
2answers
2k views

Contiguous prime numbers with MPI (Want more ideas for an efficient algorithm)

I am a programmer. I am working with Message Passing Interface (MPI) in C. I do a program that consist on finding the contiguous prime from 1 to 10,000,000. I already do it! but I do it with trial ...
17
votes
6answers
3k views

To what extent is generic and meta-programming using C++ templates useful in computational science?

The C++ language provides generic programming and metaprogramming through templates. These techniques have found their way into many large-scale scientific computing packages (e.g., MPQC, LAMMPS, CGAL,...
25
votes
4answers
2k views

When should I use C++ expression templates in computational science, and when should I *not* use them?

Suppose that I'm working on a scientific code in C++. In a recent discussion with a colleague, it was argued that expression templates could be a really bad thing, potentially making software ...
12
votes
2answers
12k views

Octave: calculate distance between two matrices of vectors

Suppose I have two matrices Nx2, Mx2 representing N, M 2d vectors respectively. Is there a simple and good way to calculate distances between each vector pair (n, m)? The easy but inefficient way is ...
7
votes
2answers
1k views

Understanding OpenCL performance

I'm using ViennaCL's interface to Eigen as a way to leverage OpenCL. Specifically, I'm using the ::viennacl::linalg::bicgstab_tag with an Eigen sparse matrix. ...
9
votes
2answers
2k views

How do I compute the parallel overhead of a parallel code run on a single processor when no sequential code is available?

I'm profiling the performance of PETSc's linear solvers. As I understand it, $$\text{speedup}=\frac{\text{Sequential Time}}{\text{Parallel Time}}.$$ I know that running the parallel code on one ...
2
votes
1answer
1k views

How to measure the overall performance of a PETSc program using the -log_summary flag?

When I run a PETSc example in parallel with the flag "-log_summary", the first two tables of information look something like this: ...
39
votes
4answers
32k views

How does the MATLAB backslash operator solve $Ax=b$ for square matrices?

I was comparing a few of my codes to "stock" MATLAB codes. I am surprised at the results. I ran a sample code (Sparse Matrix) ...
13
votes
4answers
7k views

FLOP counting for library functions

When evaluating the number of FLOPs in a simple function, one can often just go down the expression tallying basic arithmetic operators. However, in the case of mathematical statements involving even ...
8
votes
2answers
446 views

Filtering a dataset to get a more uniform distribution for neural network training

I'm looking into using artificial neural networks (ANN) to predict the reaction rates in my fluid instead of solving the full system of stiff ODEs. Some people from my lab have already done some work ...
9
votes
2answers
901 views

Which Sparse Matrix Solver Libraries can I run on Android?

The title says most of it. I'm looking for a lightweight and easy-to-use library that I can use for Android (NDK) projects. For dense stuff I like using Eigen but I haven't found many comprehensive (...
2
votes
1answer
122 views

Low performance on sge cluster

I'm having an issue with my project. When I run the code of Monte-Carlo simulation, on the local server (the machine in my office) it runs on a rate of roughly 100000 steps per 24 hours. When I run it ...