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Questions tagged [parallel-computing]

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

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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,...
OskarM's user avatar
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6 votes
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290 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, ...
Madhav Gumma's user avatar
5 votes
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119 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, ...
spm's user avatar
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4 votes
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How amenable is this 2D Frenkel–Kontorova-like energy minimization problem in Python to the use of a modest PC + GPU? (Heavy reliance on indexing)

@Richard's answer to Going to try to move some of my scipy/numpy calculation to a new GPU, how to avoid disappointing results? is quite helpful, and as promised I've added a simple running example ...
uhoh's user avatar
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4 votes
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387 views

Can you provide an example of an algorithm that has strong scalability but not weak scalability? Can you also provide an example the other way around?

Strong Scaling and Amdahl's Law Strong scaling is a measure of how, for a fixed overall problem size, the time to solution decreases as more processors are added to a system. An application that ...
hzhaoc's user avatar
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3 votes
0 answers
161 views

Numerical calculation of out-of-time order correlators (OTOCs)

I want to numerically calculate OTOCs for different quantum mechanical systems. Consider the following Hamiltonian $$H=p_x^2+p_y^2+x^2y^2$$ and I want to calculate the following OTOC $$C_T(t)=-\left&...
ghost's user avatar
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3 votes
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One cancels the other qsub semantics atop SGE?

Is there a way to achieve "one cancels the other" semantics (http://www.investopedia.com/terms/o/oco.asp) for qsub jobs submitted to Sun Grid Engine? That is, I submit two (or more) jobs and when one ...
Rhys Ulerich's user avatar
3 votes
0 answers
37 views

An asynchronous version of the Covariance Matrix Adaption (CMA)?

Does anyone know of a variant of the CMA algorithm that is suitable for an asynchronous parallel implementation? The conventional version of the algorithm allows one to evaluate the fitness function ...
Toon Verstraelen's user avatar
2 votes
0 answers
80 views

Diagonalization of large sparse matrix, computational programme recommendation and methods

According to this link, All eigenpairs of large sparse symmetric matrix. The guy @Baranas seems to have given a very confident answer about solving the whole Eigen spectrum. May I know if anyone has ...
Lee Zhi Yan's user avatar
2 votes
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83 views

OpenMP Fortran array operations in target regions

I am asking this here for the possibility that someone here is familiar with OpenMP offloading. Is there some other way to parallelise Fortran array operations outside of unrolling the loops of the ...
Touko Puro's user avatar
2 votes
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171 views

Why GPU scaling (speedup) is usually worse than CPU scaling?

Let's define scaling, as how linear the speedup of using more than one GPU or CPU is. For example, having 2 GPUs gives you 2x faster execution time. I have noticed that in many software (e.g. ...
Daniel Wiczew's user avatar
2 votes
0 answers
99 views

How to find eigvals/eigvecs of huge symmetric tridiagonal matrix using multiple processes or threads?

In python, there is a function in scipy (scipy.linalg.eigh_tridiagonal) which is extremely efficient for an exact diagonalization of a symmetric tridiagonal matrix (...
Stelladuck's user avatar
2 votes
0 answers
159 views

Parallel In Time with Multigrid

I am trying to solve the linear finite element equation $M\ddot{u}+Ku=F(t)$, where $M$ is the mass matrix ,$K$ the stiffness matrix and $F(t)$ the external load vector, parallel in time using XBraid ...
spyros's user avatar
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2 votes
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OpenMP inconsistently segfaulting

I parallelized my code with openMP, and now have this bug in my code that's really odd. If it's the first time I run on a computer, it segfaults, but if I run the program again it runs fine. I've ...
EMP's user avatar
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2 votes
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128 views

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 ...
Izzy Vang's user avatar
2 votes
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76 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 +...
user26633's user avatar
2 votes
0 answers
159 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 ...
danny's user avatar
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2 votes
0 answers
161 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 ...
Phil Reinhold's user avatar
2 votes
0 answers
217 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 & B_v^...
RYegavian's user avatar
1 vote
0 answers
353 views

Why does Eigen allocate a temporary to evaluate A.noalias() = B.transpose()*C in parallel?

I wrote a program which iteratively transforms data using matrix multiplications. To minimize the number of large memory allocations, I use two roughly equal-sized ...
Wout12345's user avatar
1 vote
0 answers
215 views

performance comparison between PETSc and SLATE

We want to start a new project to solve a large-scale inverse problem (O(10^6) number of parameters) to invert for subsurface wave speeds. We will use FEM to solve forward and adjoint PDEs. In our ...
user2348209's user avatar
1 vote
0 answers
73 views

Multigrid Reduction In Time Convergence

I am trying to solve a 2D dynamic linear elasticity model parallel in time using Xbraid. The spatial domain is [0,1]x[0,1] and time domain [0,1]. For time integration I am using a backward Euler ...
spyros's user avatar
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1 vote
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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,...
stucash's user avatar
  • 111
1 vote
0 answers
78 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. ...
Toon's user avatar
  • 31
1 vote
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68 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 ...
dual0's user avatar
  • 11
1 vote
0 answers
138 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 ...
Mathnoob's user avatar
  • 111
1 vote
0 answers
85 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 ...
Ahmad Sheikhzada's user avatar
1 vote
0 answers
55 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 ...
Ramón's user avatar
  • 11
1 vote
0 answers
128 views

Why would this a pair of E5-2670 cpus be faster than 4 E5-2640 cpus for large matrix diagonalisation problems?

Not really much more to say; Of several computers available for use, these are two of the larger ones; one has 2x E5-2670, and the other has 4x E5-4640. The problems we're looking at essentially boil ...
will's user avatar
  • 131
1 vote
0 answers
512 views

CUDA Mandelbrot Set effective bandwidth and optimization

I was reading through this article (very good article and excellent blog BTW) to do some measurements in my (very simple) implementation of the Mandelbrot Set. I'm using a Quadro 2000D card which has ...
BRabbit27's user avatar
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0 votes
0 answers
53 views

Parallel vs Serial computing using Python Qutip. Why is serial faster?

I am trying to learn parallel computing using qutip's parallel_map function. I've tried to write a basic and simple code to understand the differences between parallel and serial calculation of ...
muzbi's user avatar
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0 votes
0 answers
30 views

Parallel Block-Structured class abstraction for FDM

I’m currently developing a FDM/FVM (using contravariant coordinates) code using Fortran and Co-Arrays (SIMD, in general), and so far I have all sparse matrix (BiCGStab, working on AMG) solvers and ...
Kbzon's user avatar
  • 251
0 votes
0 answers
58 views

Calculate the time taken to run an algorithm on GPU

I want to calculate the total time taken for a fixed code run using an NVIDIA GPU (for instance, Tesla K40). The code has to run 1 million single-bit comparisons. All the comparisons are independent ...
guptasonal's user avatar
0 votes
0 answers
87 views

where to use multiprocessing in multi-loop program

I am running a program that uses [a lot of] looping to perform a type of bootstrap analysis. The computational step - PCA - can take a long time (60+) seconds, which means that collectively this ...
Brian Barry's user avatar
0 votes
0 answers
69 views

Is there a mathematical algorithm that can determine whether a problem is parallelizable?

Is there a mathematical algorithm that can determine whether a problem is parallelizable? Possibly similar to how the definition for "computable" works out: https://en.wikipedia.org/wiki/...
mavavilj's user avatar
  • 427
0 votes
0 answers
86 views

Output solution vector in Petsc

I am using petsc to solve a linear elasticity problem discretized by finite elements.The initial mesh is read by a mesh file and the distribution in each processor is done using METIS.I am using only ...
Spy123's user avatar
  • 21
0 votes
0 answers
50 views

Methodology to develop parallel GPU simulations

I'm quite new to GPU or in general parallel programming. I am working on a Lattice-Boltzmann simulation that should be parallelized on GPU's. I wanted to asked more experienced people how to attack ...
enco909's user avatar
  • 11
0 votes
0 answers
845 views

Openmp critical section inside if conditional statement

I have a function like this void foo(x, *y) { some calculations if (x > *y) { *y = x/2; } more calculations } My parallel section is <...
user123's user avatar
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