Questions tagged [hpc]
High Performance Computing generally uses large arrays of computers connected in clusters or grids.
127
questions
0
votes
1answer
29 views
MPI_Test not progressing MPI_Isend/MPI_Irecv requests
I am running a CFD simulation with a 200,000-vertex mesh. I've decomposed the mesh into 2 load-balanced sub-domains to test my parallel implementation. In the specific function that I am time-...
2
votes
0answers
44 views
Collaborative coding platform in the style of Google Colab
(I hope this question is fitting for this SE, I couldn't find very relevant tags)
I am looking for an online platform in the style of Google Colab with the following requirements:
possibility to run ...
3
votes
1answer
104 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 ...
1
vote
2answers
149 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 ...
2
votes
1answer
589 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 ...
0
votes
1answer
93 views
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 ...
1
vote
2answers
74 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 ...
0
votes
3answers
114 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 ...
1
vote
1answer
39 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 ...
1
vote
2answers
243 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 ...
1
vote
2answers
99 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 ...
1
vote
0answers
21 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/...
1
vote
1answer
137 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
votes
1answer
87 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 ...
4
votes
0answers
53 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
votes
0answers
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 ...
4
votes
1answer
148 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
56 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 ($N/n = {\rm const}$). ...
4
votes
0answers
59 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
votes
1answer
66 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
votes
2answers
743 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
106 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
162 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
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 ...
0
votes
2answers
244 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
314 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
vote
1answer
295 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,
...
0
votes
1answer
125 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,...
1
vote
0answers
101 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 ...
1
vote
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 ...
0
votes
1answer
449 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
votes
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, ...
0
votes
1answer
376 views
1
vote
1answer
902 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
votes
1answer
219 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 ...
0
votes
3answers
297 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
437 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
348 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
votes
1answer
85 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
1k 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
281 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
votes
1answer
79 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
203 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
166 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
vote
2answers
704 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 ...
10
votes
2answers
212 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
vote
1answer
111 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
626 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
vote
2answers
235 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
votes
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 ...
