Questions tagged [hpc]

High Performance Computing generally uses large arrays of computers connected in clusters or grids.

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98 views

Pricing of HPC resources in terms of power usage

Following the latest trends in linear algebra, power consumption is quickly becoming an important factor to consider when designing and using an algorithm. I've even heard that over time, the ...
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2answers
119 views

How to begin writing scientific codes in C++ in Trilinos or PETSC style?

My background: I have taken some courses on numerical analysis during my PhD and read a few books on the topic as well. I mostly work on low Reynolds number fluid mechanics and use boundary element ...
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1answer
218 views

Can Julia be used to create a large-scale CFD software like OpenFOAM?

I have some experience with some programming languages like C/C++, Fortran, Python, etc but recently, I am getting interested in Julia. But, I am wondering if Julia could be used to create some large ...
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1answer
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what do I need to know to get started in HPC?

I have a huge interest in HPC, cloud computing and quantum computing since years. I'm currently a CS student with bachelor degree and I only have some basic knowledge about HPC from online articles ...
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2answers
71 views

Distributed computation with computers around me

I know for large amounts of data there are online computation services or supercomputers or Beowulf cluster. For a small quantity of data, a good computer is enough. But sometimes, for medium qty of ...
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3answers
105 views

How to store a TB size array in C++ on a cluster

I want to do a huge simulation that requires ~ 1 TB of data to describe a bunch of interacting particles (each has different interactions). Is it possible to store this data in an array in C++, so ...
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3answers
1k views

Flush output in Torque scheduler?

I'm trying the Torque scheduler. I have previous experience with the LSF scheduler, and I quite like being able to use 'bsub -I make -j 12' to compile a program really quickly, i.e. running an '...
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3answers
19k views

Intel Fortran Compiler: tips on optimization at compilation

I will start with my personal experience in our lab. Back in the ifort 9 and 10 days, we used to be quite aggressive with the optimizations, compiling with -O3 and processor specific flags (-xW -xSSE4....
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5answers
3k views

Parallel Scientific Computation Software Development Language?

I want to develop a parallel scientific computation software from scratch. I want some thoughts on which language to start. The program involves reading/writing data to txt files and doing heavy ...
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1answer
33 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 ...
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2answers
215 views

How to simulate over 1 billion particles?

I want to simulate human erythrocytes in capillaries. I calculated, that for a 1 meter long and 1 mm in diameter capillary there are about 3 billion blood cells. Erythrocytes are actually discs, but ...
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host vs nodes vs sockets vs thread vs processors vs cores in cluster computing [duplicate]

I am new to the computer cluster and I am so confused with these terms, could you please explain them? Regards, Vricc
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2answers
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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 ...
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2answers
2k views

Boost::mpi or C MPI for high performance scientific applications?

The thing I dislike most about MPI is dealing with datatypes (i.e. data maps/masks) because they don't fit that nicely with object oriented C++. boost::mpi only ...
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19 views

Regarding Amdahl's balanced system law [closed]

One of the paper titled "Rules of Thumb in Data Engineering" (Jim Gray et. el.) mentions some calculations based on Amdahl's balanced system law. Link to paper: https://www.microsoft.com/en-us/...
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1answer
78 views

Relation between IPC and number of cores? Which spec mention theis number?

In multicore architecture, are Instructions Per Second (IPS) and Instructions Per Cycle (IPC) parameters of a single core or the whole CPU? Where to look out for this value? And does it change as the ...
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1answer
85 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 ...
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4answers
196 views

Removing non-determinism from molecular dynamics code

I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing ...
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0answers
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Is it Grid/Cluster/Cloud Computing? How are those terms defined?

There are three very connected and widely used terms: Grid and grid computing Cluster and cluster computing Cloud and cloud computing In many situations, it is not obvious which term to use, as I ...
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2answers
193 views

Using computational libraries on a machine without root access

If you want to use a computational library on a high-performance computing center where you have no root access to install new software you can use header-only template libraries such as MTL4, Eigen3, ...
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0answers
527 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/...
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90 views

Super Computer cluster service for students [duplicate]

I would like to ask whether there is a free of charge supercomputer for students, in my current institution they don't have a supercomputer, I am running MD simulations, I would be grateful for ...
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1answer
256 views

MPI support for discrete Fourier transform (DFT) in Python

I am looking for a discrete Fourier transform (DFT) library that can be run with MPI on Python. Usually, in other languages (C, Fortran) FFTW is used. There's a Python wrapper for FFTW called pyFFTW, ...
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1answer
143 views

Fast and free server for computing

I have to calculate a huge differential equation. With my laptop, it's going to be computed for several days. Is there a free (I need just for 3 days) fast server for scientific calculations? My ...
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7answers
12k views

Is it a good idea to use vector<vector<double>> to form a matrix class for high performance scientific computing code?

Is it a good idea to use vector<vector<double>> (using std) to form a matrix class for high performance scientific computing code? If the answer is no. ...
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1answer
49 views

Weak scaling for N-body simulations

I'm going to be doing some weak scaling of an $N$-body integrator on AWS. In the past when I've done weak scaling for this integrator I've fixed the number of particles per core ($N/n = {\rm const}$). ...
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2answers
263 views

Leveraging scipy for matrix free finite elements

This will be a very general question. I have a 3D finite element code in Python which I would like to extend to handle "large" problems (~10^8 unknowns in the global system). Right now I am using the ...
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3answers
2k views

Log-log parallel scaling/efficiency plots

A lot of my own work revolves around making algorithms scale better, and one of the preferred ways of showing parallel scaling and/or parallel efficiency is to plot the performance of an algorithm/...
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3answers
294 views

Full segmentation of a linear space using a clustering algorithm

Once again, I am not entirely sure how to describe what I am looking for, hence I have a hard time finding answers using Google or any other literal search method. Let's say I have a time series: $$(...
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2answers
198 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 ...
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0answers
57 views

How to implement register blocking for 3D finite-difference stencil computations

I am in need to optimize the performance of the 3D solver that integrates a system of equations for seismic wave propagation. Unsurprisingly, the function that implements the finite-difference stencil ...
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1answer
387 views

Pool two computers for MATLAB parfor without MDCS

I have two identical computers, both with 4 dual cores and MATLAB installed on them. They are connected to the same network. Is there anyway I can run a parforloop using the computation power of both ...
3
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1answer
495 views

HPC : should I compile on the head node or on a compute node?

I have a CFD code that I want to run on an HPC cluster. Of course, before it can be run, it first needs to be compiled. What is the best option between compiling on the head node and compiling on one ...
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1answer
2k views

Masters in HPC (High Performance Computing)

Is there a master degree in HPC (High Performance Computing) in US? I am asking this question because in my early research I found no direct mentioning of HPC instead invidual courese in parallel ...
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4answers
8k views

Profiling CFD code with Callgrind

I'm using Valgrind + Callgrind to profile a solver I have written. As the Valgrind user manual states, I've compiled my code with the debugging options for the compiler: "Without debugging info, ...
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5answers
267 views

Computational science contests. Why arent there any?

I was wondering why there are no online or offline computational science contests? At least I couldn't find much by googling. I mean, like a topcoder for computational sciences. I assume one reason is ...
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2answers
235 views

Is there any scalable machine learning tool like molecular dynamics software NAMD?

I work in Molecular dynamics of biomolecules. I am familiar with the software NAMD. We use NAMD in our CPU cluster with the aid of mpirun. Without GPUs can I implement large scale deep learning? ...
2
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1answer
60 views

What is the minimum raw FLOPS that supercomputers need to be included in the Green500 list?

The Green500 List lists the top 500 most energy efficient supercomputers. My question is, what is the minimum FLOPS that computers need to be considered for the Green500 list? Do they just take the ...
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2answers
545 views

How does MPI differentiate between two computers?

I am starting to dabble in MPI. I am fairly new to this area and I am currently reading the MPI standard. I would like to write my first MPI program, a simple hello world program, on a cluster that ...
7
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2answers
688 views

Why does sparse linear algebra have a low arithmetic intensity?

I often see the terms "low arithmetic intensity" and "memory-bound" associated with sparse matrix operations. However, my intuition is that a sparse matrix operation should be less memory-bound, if ...
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1answer
85 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 ...
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1answer
158 views

Where can an undergraduate go to find cores on a budget?

I've may have reached a point in my neural network research that I cannot continue without significant financial investment. I am using neuroevolution to evolve a network on the EMNIST data set. It ...
0
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1answer
495 views

FFT parallel processing in MPI

I am working now in Beowulf Cluster and parallel processing, I want code for Fast Fourier transfer functions written in any language, e.g., C/C++. Without using FFTW library based on message passing ...
3
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1answer
125 views

Suggestions for an out-of-core sparse solver

I have a sparse $2\times10^5$ by $2\times10^5$ matrix with $3.2\times10^9$ non-zero elements. I want a sparse solver with out-of-core functionality. I have attempted to use Intel's ...
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1answer
122 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,...
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1answer
95 views

Free access to Xeon Phi clusters

Apologies if this is not the right forum to ask, but there has been a somewhat related question here. I am working on a piece of software (nonlinear constrained optimisation, coded in C++11 and ...
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2answers
3k views

Python implementation for Frechet Distance

I am working on a trajectory analysis project using python and its data science related libraries. I am planning to implement Frechet Distance algorithm for trajectory analysis, each trajectory has ...
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4answers
1k views

What is a robust, iterative solver for large 3-d linear-elastic problems?

I'm diving into the fascinating world of finite element analysis and would like to solve a large thermo-mechanical problem (only thermal $\rightarrow$ mechanical, no feedback). For the mechanical ...
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1answer
240 views

Requesting less than a node with SLURM

I am curious if it is possible to request less than a node using SLURM. For example, if I use the commands, ...
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0answers
86 views

Implementing Frechet Distance on pandas data frame [duplicate]

I am working on a trajectory analysis project using python and its data science related libraries. I am planning to implement Frechet Distance algorithm for trajectory analysis, each trajectory has ...