Questions tagged [hpc]
High Performance Computing generally uses large arrays of computers connected in clusters or grids.
121
questions
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1answer
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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 ...
1
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2answers
204 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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0answers
36 views
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
96 views
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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0answers
17 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
54 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
...
0
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1answer
79 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 ...
3
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0answers
45 views
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 ...
0
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0answers
88 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 ...
4
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1answer
137 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 ...
1
vote
1answer
45 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 ($N/n = {\rm const}$). ...
3
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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 ...
2
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1answer
59 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 ...
7
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2answers
636 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 ...
1
vote
1answer
83 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 ...
1
vote
1answer
153 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
votes
1answer
94 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 ...
0
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2answers
216 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?
...
4
votes
2answers
234 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 ...
1
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1answer
218 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,
...
2
votes
0answers
510 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/...
0
votes
1answer
108 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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0answers
73 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 ...
0
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2answers
2k 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 ...
0
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1answer
413 views
Python implementation of Quadtree for trajectory analysis
I am working on a trajectory analysis project using python and its data science related libraries. I am planning to implement Quadtrees for for trajectory analysis, each trajectory has sequence of (x,...
4
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3answers
2k 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
305 views
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1answer
694 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. ...
6
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1answer
190 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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3answers
292 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:
$$(...
1
vote
1answer
366 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 ...
0
votes
2answers
284 views
Using two computers to run one parallelized program with intel fortran [closed]
I have two computers, both with 4-cores and I am running some heavy computational stuff in one of them using Intel Parallel Studio Cluster edition. I am coding in fortran and making extensive use of ...
2
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1answer
78 views
Need help understanding cluster process managers and MPI
I apologize if this is a relative simple question. I am very new to setting up a cluster computer and I am attempting to make heads and tails of the information.
I was reading on setting up a cluster ...
1
vote
2answers
653 views
How to determine MPI compatibility [closed]
I have recently acquired a server that I will be using for distributed simulations. However, I was wondering how do I determine which MPI version the server is compatible with?
The reason that I am ...
3
votes
1answer
246 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, ...
0
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1answer
65 views
Running a script that asks for user input from a pbs file
I am trying to run a pbs file which runs a script on a cluster. The script prompts for a user input. I wish to write this user input in my pbs file, what is a good way to do this?
3
votes
2answers
197 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 ...
3
votes
0answers
157 views
Beowulf Cluster For MD simulations
What would you recommend as an all-in-one cluster management software for a Beowulf cluster? We have about 7(most of them are 8 core machines and 1 is a 48 core machine) very good compute nodes in our ...
1
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2answers
492 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 ...
9
votes
2answers
182 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 ...
1
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1answer
105 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 ...
3
votes
1answer
400 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 ...
1
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2answers
219 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 ...
8
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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 ...
6
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2answers
1k views
Borrow computational power from machines around me
I'm a computational chemist working with little computational power and dealing with increasingly demanding chemical systems. My work machines are part of a big network (mixed with windows and linux) ...
3
votes
1answer
122 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 ...
1
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1answer
588 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?
5
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1answer
59 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 ...
1
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1answer
47 views
CPU Specification Within Each Node of a Cluster
In essence we can create a cluster based on a number of machines(e.g., Beouwulf style). Here the question is, do all the cluster nodes require the exact same cpu(s) specification (e.g., core, cache, ...
3
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1answer
1k views
Computer Build for Scientific Computing
I am currently a .NET software developer(SQL Server, ASP.NET, C#, MVC & Web Forms). In my spare time I'm researching different areas of environmental science. E.g.(Hydrology, Ecology, Atmospheric ...
