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Questions tagged [hpc]

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

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gsl-config: command not found HPC cluster [on hold]

I am trying to install the gsl libraries in a HPC cluster, so I don't have root access. I am following the instructions here. The problem is that when I type ...
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0answers
48 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
54 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
502 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
66 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
141 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 ...
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1answer
119 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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1answer
90 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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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, ...
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1answer
200 views

Decrease execution time using openMP

I have this method which computes the Fibonacci function: ...
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1answer
333 views

Strong scalability plot, HPC

I have to create a strong scalability plot, which measures the execution time for a numberOfThreads =1,2,4,8,16 with size=1024. ...
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1answer
182 views

Working with large mesh files

I am working on some medium to large scale finite element codes. By using established and available tools I am able to have an algorithm that scales well up to about 10,000 cores. Investigating ...
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2answers
181 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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2answers
163 views

Communication overhead in supercomputing

I am looking for credible references stating how much resources supercomputers spend on coordinating versus doing actual task-related work. Resources could be available processing power but even Watts ...
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1answer
97 views

Comparison of US HPC Resources

I was wondering if anyone knows about the differences between the large HPC resources available to US researchers. I am currently using a startup allocation (through the NSF GRFP) on XSEDE but was ...
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1answer
214 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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2answers
197 views

Programming language for HPC [closed]

I'm planning on building a program that will carry out HPC. I'm aware that C/C++ is significantly better than Python in terms of the speed of computation. However, I'm not yet proficient in C/C++, so ...
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2answers
1k views

Intel Knights Landing work loads vs NVIDIA GeForce

There are lot of articles being written about how the newly launched Intel Xeon Phi will steal the HPC\Super Computer market share from the competitors. Intel Knights is equipped with 72 cores and 4 ...
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1answer
109 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
497 views

Is there a single C++ IDE packed with necessary scientific libraries for computing purpose?

I am basically looking for a good open source C++ IDE with scientific and visualization libraries built in. Can any one suggest few projects?
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1answer
56 views

Is there a way to ensure that PBS array jobs will be run in order?

I run many PBS scripts that take advantage of the job array structure for similar jobs (e.g. 12345[0] through 12345[9]). With the way that the code is written, job [0] needs to run first, and then any ...
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2answers
159 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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1answer
133 views

Performance based on the Roofline model

To somewhat follow up on the question asked here, I have been told that the Roofline model is one way of assessing the performance of any scientific code. Basically I compute the Arithmetic Intensity (...
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2answers
282 views

Direct Numerical Simulation of reacting flows

I need to write a DNS code for simulating reacting flows in turbulent conditions. The code has to be highly scalable, because the computational cost of simulations is expected very large. My idea is ...
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2answers
322 views

Planning to build a HPC [closed]

I start a study the best way to mount a HPC. On my datacenter i have to initial tests 3 servers whit this settings. DELL PowerEdge R720 2 x Intel Xeon E5-2680v2 2.8GHz 10 x 16GB RDIMM XenServer 6.5 ...
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1answer
101 views

Shared memory parallel computing solutions compared

As of 2015, what shared memory parallel computing solutions are available? What are the advantages and disadvantages of each for various use cases arising in high performance scientific computing? I ...
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1answer
105 views

Additional cost associated with quad (or higher) precision

In going from double precision to quad (or higher) precision, roughly how much of a performance hit is taken on various architectures and frameworks. Do floating point operations take twice as much ...
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1answer
252 views

CUDA Fortran: Multi GPU Programming and memory allocation

I am writing a program that is supposed to use multiple GPUs on a single node using CUDA Fortran. Although I've looked through the Portland Group CUDA Fortran Reference, I am still unclear about how ...
3
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1answer
860 views

Fast way to compute all eigenvalues of a dense Hermitian matrix

I am finding the eigenvalues of dense NxN Hermitian matrix which is calculated from a density operator in quantum physics. All the eigenvalues are needed as I need to calculate the sum of the absolute ...
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1answer
59 views

eigenvalue of small symmetric matrices

If I am to solve a symmetric eigenvalue system $A=QDQ^T$, where $A\in\mathcal{R}^{n\times n}$ and $n$ is small (in the range 4 - 64); I want all the eigenvectors and eigenvalues; There are two major ...
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2answers
998 views

Many processors reading a single HDF5 file

I'm working on a code that we eventually plan to scale up to 10's or 100's of thousands of processors (using MPI). I have a single HDF5 file (mesh nodes and connectivity, etc) that needs to be read ...
3
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2answers
94 views

Automated software optimization and tuning

I'm writing code that uses a lot of graph operations; many higher-level algorithms iterate over all the graph edges and do some processing on them. There's an iterator method that returns a batch of ...
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4answers
173 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 ...
4
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1answer
450 views

Increasing thread number degrades performance

I have a problem with parallelization and the brownian dynamics (molecular dynamics) code that I am using. We have our own home-grown framework at the university, and recently we've made the change ...
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1answer
14k views

CUDA vs OpenCL as of late 2013

How do CUDA and OpenCL compare to each other as of late 2013 from a programmer's perspective? My group is thinking about trying to make use of GPU computing. Would we be limiting ourself ...
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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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2answers
1k views

HPC: Intel QPI versus AMD with HyperTransport

I am looking into upgrading to a High Performance Computing work-station to do mostly computational fluid dynamics computations and some fundamental numerics. The CFD software that is available does ...
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3answers
147 views

Can anyone recommend a pipeline dependency (“make”) tool for SGE jobs?

I am looking for a tool to specify pipelines of arbitrary multiple jobs with dependencies for the Sun Grid Engine. I can wire things together myself but I am hoping for something more declarative and ...
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5answers
1k views

Finding the correct Molecular Dynamics library

I just started working on some Biophysics research, and I was looking around for a good MD library to use. There is one right now at the university set up in C, with openMC parallelization, but the ...
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3answers
21k views

Difference between Nodes and CPUs when running software on a cluster?

I'm looking into moving some computations of mine to a data center to get more computation power. In the context of this process, I am getting confused by the differentiation of a computation node and ...
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1answer
142 views

Get job script directory with SGE

With the Sun Grid Engine, how can I get the directory where the job script is located, within the job script? I need this so I can start the script with ...
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4answers
9k views

Do currently available GPUs support double precision floating point arithmetic?

I have run the molecular dynamics (MD) code GROMACS on a Ubuntu Linux cluster consisting of nodes containing 24 Intel Xeon CPUs. My particular point of interest turns out to be somewhat sensitive to ...
17
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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/...
2
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1answer
611 views

Multi-node jobs with Sun Grid Engine without MPI

I am trying to figure out how to write a proper job file for the Sun Grid Engine so I can run a parallel computation using Mathematica on multiple nodes. Unfortunately almost all tutorials on the ...
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1answer
226 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. ...
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3answers
151 views

Offline (visualisation) rendering in scientific computing

I need to simulate the movement of a large number of agents. The processes that govern the agents' movement are complex and so the entire process requires parallelisation. The output from this ...
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4answers
3k views

Best hardware solution for microsecond Molecular Dynamics

We would like to reach Molecular Dynamics simulation of proteins with around 20000 atoms in explicit water with trajectories of around 1 microsecond each. We are looking at different options for ...
10
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2answers
377 views

Task-based shared-memory parallel libraries in Scientific Computing

In recent years, several libraries/software projects have appeared that offer some form or another of general-purpose data-driven shared-memory parallelism. The main idea is that instead of writing ...
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4answers
6k 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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3answers
244 views

How to efficiently structure simulation data in memory for cells with varying degrees of freedom?

For a discontinuous Galerkin-based simulation I need to store cell-based simulation data in memory. Since the order of the polynomial approximation $N_p$ may vary between cells, I wonder what the most ...