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

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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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32 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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dynamically chose PBS queues during job submission

I run a lot of small computing jobs in remote cluster where job submission is managed by PBS. Normally in a PBS (bash) script I specify the queue that I would like to submit the job through the ...
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209 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 ...
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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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101 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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96 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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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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202 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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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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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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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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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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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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2k 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 ...
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391 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 ...
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1answer
219 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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158 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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133 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
676 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 ...
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277 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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730 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> to form a matrix class for high performance scientific computing code? If the answer is no. Why? Thanks
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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 ...
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559 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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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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485 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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125 views

Anyone knows references summarizing the history of supercomputing?

Anyone knows references summarizing the history and ideas behind supercomputing including mentioning of developments in parallel programming languages, applications, startup companies (some was ...
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What is the best high performance computing platform for engineering simulations?

What is the best platform for high performance computing (HPC)? Windows is long gone, I think. So only Unix and Linux stand the chance. What platform will strongly back my interest on computational ...
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When is building a cluster in the cloud cheaper than building one in my lab for MD simulations?

An Amazon EC2 compute cluster costs about \$800-\$1000 (depending on duty cycle) per physical CPU core over the course of 3 years. In our last round of hardware acquisition, my lab picked up 48 cores ...
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Exit_status=15 , what does it mean? [closed]

I have a job which stops unexpectedly with Exit_status=15. What is the most probable error ?
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618 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 ...
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Online resources for reviewing graphics cards for GPGPU

Can anyone recommend a site that maintains up-to-date reviews of graphics cards for GPGPU use? Most benchmarks focus on gaming performance, whereas I am interested in the performance of scientific ...
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435 views

Parallel computing programming paradigms/models not based on a master/slave concept?

Do anyone know if there exist any widely used parallel computing programming paradigms/models not based on a master/slave concept?
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profiling CFD codes 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, the ...
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Will MPI continue to be a popular basis writing scalable massively parallel solvers on future many-core CPUs? [duplicate]

Possible Duplicate: What programming paradigms should I be investing in if I want my code to run on petascale machines in the future? Having entered the multi-core era (som already refers ...
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External hardware resources for running long and computationally intensive simulations

I've written code for an obstructed random walker simulation and I want to run long simulations (6 hours or more on my computer). I don't want to run this simulation on my computer because I will want ...
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How much should scientific software be optimized?

For applications requiring significant computational resources, high performance can be a critical factor when it comes to delivering scientific results or achieving "break-throughs" in reasonable ...
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156 views

Red(-Green)-Refinement vs. Newest-Vertex-Bisection

What are the "Pros and Cons" for these two methods of mesh-refinement? Both seem to be the prevalent methods. I can naturally imagine that global red refinement is comparatively easy to implement and ...
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477 views

Shape regularity in higher dimensions

In Finite Element theory, and other methods in scientific computing for PDEs, one uses meshes which fulfill several regularity criteria, many of them being equivalent. It is of interest to have ...
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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 ...
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338 views

What are the current obstacles to reaching exascale computing?

I have heard that one of the current goals in scientific computing is to surpass the exascale level by 2018 or so... After having passed the petascale a few years ago, one would think that the ...
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State of the Mac OS in Scientific Computing and HPC

Back towards the dawn of OS X, there seemed to be a great deal of hubbub, at least in the Mac world (I was nowhere near scientific computing at the time) about the Mac OS as a platform for scientific ...
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What does the priority of a PBS job really mean?

The qsub command which submits PBS jobs has a -p option that allows you to set the priority. From the man page: Defines the ...
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2k views

Future of OpenCL?

The OpenCL programming paradigm promises to be a royalty free opens standard for heterogenous computing. Should we invest our time in developing software based on OpenCL? Pros/cons?
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286 views

(How) do you take into account memory fragmentation?

I use an example from finite element theory, but anybody who maintains a large datastructure and successively extends it will find something similar. Suppose I have an unstructured mesh of points and ...
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C++ vs Fortran for HPC

In my computational science PhD program, we are working almost exclusively in C++ and Fortran. It seems like some professors prefer one over the other. I am wondering which one is 'better' or if one ...
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How should I study creating and programming HPC systems?

I'm in a field that doesn't necessarily do a great deal of HPC work, and when it does encounter it, it's often the result of researchers from other fields exploring new applications to their methods ...
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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 ...
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1k views

What programming paradigms should I be investing in if I want my code to run on petascale machines in the future?

It's pretty clear from a survey of the top500 that the industry is trending towards an exponential increase in processing cores. The largest supercomputers all use MPI for communication between ...
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310 views

Benchmarking performance in CFD: how to compare machines and codes?

Informally in our lab, we have developed 2 metrics to compare CFD solvers over the range of machines we have access to. One is called COMP, which stands for COde Machine Performance. This single ...