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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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Problems with High-Performance Computing and Stack Exchange Data Explorer. Any Advice? [closed]

I'm currently experiencing some challenges with my high-performance computing setup and a Stack Exchange product. As someone relatively new to managing both hardware and software in this capacity, I ...
Judy Watson's user avatar
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2 answers
75 views

Source for scalability challenge for number of finite element nodes per process

Context In distributed simulation of a finite element mesh with $N$ nodes and $P$ processes, a professor stated to me that "achieving good scaling for more than 25,000 finite element nodes per ...
Jared Frazier's user avatar
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Split RAM asked between nodes and different partitions

I'm using a Slurm-based HPC at my university to run memory-intensive software. I need to know if it's possible to distribute the required RAM across multiple nodes and partitions. My lab has exclusive ...
Zoranis's user avatar
8 votes
2 answers
215 views

How to find a computational bottleneck

I am a PhD student and my lab has developed a code to run simulations. It relies on external libraries and code my lab has written. I've run a strong scaling study which shows poor performance, see ...
nyaki's user avatar
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Approximately, at any given time, what proportion of the world's total HPC resources are dedicated towards inverting matrices?

I had heard in a lecture, perhaps 15 years ago, that the vast majority of the world's HPC resources were dedicated to solving linear systems by iterative methods. I seem to remember it was 90%. I can'...
djps's user avatar
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Problems on the algebraic theory of sparse matrices

I have finished testing basic large densely parallel matrix multiplication on 4 gpu's ,and have done work on TSLU and TSQR on cpu's based on mpi. I am going to continue working on the theory of ...
Haitao Xiao's user avatar
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236 views

Right blocked linear equation solver on Dense Algebra and Sparse Algebra

I have implemented 1D mesh parallel QR decomposition and LU decomposition,I would like to ask if a linear equation Ax=b,b is a large matrix and I need to shard b or Shard A,b at the same time. Is ...
Haitao Xiao's user avatar
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1 answer
101 views

row and column based distributed LU factorization

The LU parallel computation theories I've seen are based on $M\times N$ mesh computations, is there a theory for one dimensional device mesh LU parallel decomposition? For example, $A$ is a matrix. we ...
Haitao Xiao's user avatar
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1 answer
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Questions on the theory of distributed numerical algebraic computation

I'm trying to build a pure python distributed numerical algebra computation kernel based on GPU. but after I've learnt most of the software engineering, I realise that I'm seriously lacking in ...
Haitao Xiao's user avatar
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36 views

What is the fastest library for multiplying polynomials and multi-point evaluation over finite fields?

I am looking for a library (don't care about the programming language) that performs the following two tasks as quickly as possible: Compute the coefficients of the product of a set of degree 1 ...
Finn's user avatar
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OpenFOAM- write interval changed after restarting simulation

I am running a pimpleFoam simulation on a supercomputer. I have to submit it as a job which has an allocated time. The simulation I was running ran out of this allocated time. So then I restarted it ...
Bernhard Listing's user avatar
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How can I port bind an interactive transient PBS session to the head node and then port bind the head node to my local machine?

The short of it: How can I port bind an interactive transient PBS session to the head node and then port bind the head node to my local machine? So, a chain of port bind of three machines. More ...
Sudoh's user avatar
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2 answers
714 views

PhD in scientific computing to be a scientific programmer

Intro and disclaimer: this question concerns developing a career in Scientific Computing in industry, starting from an (applied) mathematics background, say an MSc. It definitely arises from my ...
Lilla's user avatar
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2 votes
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OpenMP Fortran array operations in target regions

I am asking this here for the possibility that someone here is familiar with OpenMP offloading. Is there some other way to parallelise Fortran array operations outside of unrolling the loops of the ...
Touko Puro's user avatar
1 vote
0 answers
42 views

Where to find datasets to research the optimal parameter search space for HPC systems? [closed]

I am a student researcher who is new to the HPC domain. I have recently taken a project where I am working on optimizing the parameter search space (both application level and hardware level ...
Abrar Hossain's user avatar
3 votes
1 answer
150 views

Profiling scientific computing codes on MacOS

I'm a PhD working in the mechanical engineering community. I constantly use open-source FEM libraries to solve my problems. Up to now I didn't really care about the performance of my codes, mainly ...
FEGirl's user avatar
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How do the current FEM opensource libraries compare?

Almost all FEM libraries are good enough, but I want to start with a FEM package and stick to it for some time. Instead of trying all of them, or going with what everyone else is using, I want to ...
CuteCompute's user avatar
1 vote
1 answer
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How does a blocking MPI all to all synchronization work?

I was trying to understand more in detail how a blocking MPI all to all really work. Of course, the actual all to all traffic is pretty straightforward, what I can't understand is how it is able to &...
Tommy95's user avatar
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where to use multiprocessing in multi-loop program

I am running a program that uses [a lot of] looping to perform a type of bootstrap analysis. The computational step - PCA - can take a long time (60+) seconds, which means that collectively this ...
Brian Barry's user avatar
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Is today's enterprise computing sytem architecture with CPU, GPU and DPU is still Von Neumann architecture?

The current enterprise server rack has, in most cases, more than 1 CPU socket per board and a bunch of graphics card together with a data processing unit on a single board in a node. Several such ...
eigenvalue's user avatar
0 votes
2 answers
484 views

Passing in user inputs with mpirun

I am building a quantum circuit simulator using mpi4py. The simulator takes user inputs to build the initial system and quantum gates the system passes through. I can get the code to work if I do not ...
Orphea12's user avatar
1 vote
1 answer
2k views

What is the use of arrayfun if a for loop is faster?

This may not be so much of a scientific computing question but more of a MATLAB question, if that is the case, please feel free to close or migrate the question. Root-finding problems are commonly ...
Abdullah Ali Sivas's user avatar
0 votes
1 answer
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How much space store a matrix of numbers?

When we work in numerical analysis, when the matrix is too big the computer runs out of memory (i guess it's ram memory). But how much space does a matrix of numbers (integer, single, double) use? I ...
yemino's user avatar
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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-...
niran90's user avatar
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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 ...
bela83's user avatar
  • 443
3 votes
1 answer
134 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 ...
Thijs Steel's user avatar
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2 votes
3 answers
596 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 ...
Debasish Das's user avatar
4 votes
1 answer
2k 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 ...
IamNotaMathematician's user avatar
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1 answer
111 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 ...
user206904's user avatar
1 vote
2 answers
94 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 ...
lelorrain7's user avatar
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3 answers
201 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 ...
Thermodynamix's user avatar
1 vote
1 answer
113 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 ...
John Snow's user avatar
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1 vote
2 answers
444 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 ...
Stdugnd4ikbd's user avatar
1 vote
2 answers
107 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 ...
GoHokies's user avatar
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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/...
user3488903's user avatar
1 vote
1 answer
429 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 ...
user3488903's user avatar
0 votes
1 answer
107 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 ...
tenichols's user avatar
4 votes
0 answers
58 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 ...
Anton Menshov's user avatar
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0 answers
92 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 ...
Monika's user avatar
  • 109
4 votes
1 answer
408 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 ...
Leeloo's user avatar
  • 143
1 vote
1 answer
98 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 ($N/n = {\rm const}$). ...
Alex's user avatar
  • 111
4 votes
0 answers
73 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 ...
Dmitry Kabanov's user avatar
2 votes
1 answer
81 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 ...
Ciro Santilli OurBigBook.com's user avatar
8 votes
2 answers
1k 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 ...
Sam Hatfield's user avatar
1 vote
1 answer
312 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 ...
Abhishek Verma's user avatar
1 vote
1 answer
175 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 ...
user avatar
0 votes
1 answer
109 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 ...
András Aszódi's user avatar
0 votes
2 answers
281 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? ...
dexterdev's user avatar
4 votes
2 answers
561 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 ...
user3482876's user avatar
1 vote
1 answer
1k 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, ...
EssentialAnonymity's user avatar