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

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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 ...
17
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1answer
837 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
170 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
358 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
76 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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4answers
246 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 ...
4
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3answers
920 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 ...
2
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1answer
42 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 ...
10
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3answers
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 ...
9
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3answers
330 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 ...
2
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1answer
195 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 ...
10
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1answer
155 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. ...
4
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3answers
131 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
579 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
266 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
666 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
4
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3answers
180 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 ...
9
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2answers
519 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 ...
14
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5answers
1k 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 ...
7
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3answers
413 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 ...
8
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1answer
119 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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3answers
1k views

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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5answers
1k views

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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1answer
132 views

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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2answers
578 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 ...
7
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1answer
213 views

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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4answers
424 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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3answers
3k views

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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5answers
259 views

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 ...
7
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5answers
225 views

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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5answers
404 views

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 ...
7
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1answer
143 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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2answers
441 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 ...
2
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1answer
76 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 ...
3
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3answers
332 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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5answers
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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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2answers
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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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6answers
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?
7
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4answers
276 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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11answers
8k views

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 ...
14
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3answers
413 views

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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3answers
5k 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 ...
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7answers
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 ...
3
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1answer
291 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 ...
5
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3answers
166 views

Prolonging PBS job

It is quite painful to discover that a few-day long job is going to be prematurely killed due to an error in setting walltime limit for it. Is there a way to change it for a running PBS job?
13
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3answers
239 views

Desktop software with HPC resources for back end number crunching

Our workgroup produces a desktop application that simulates building energy performance. It is a .NET application and when the user is running a lot of simulations, they can be quite time consuming. ...