All Questions
Tagged with cluster-computing or hpc
149 questions
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How to setup Slurm to encourage efficient HPC use?
I'm currently setting up Slurm to use across researchers, and I want to fix the problem of inefficient allocation. I need advice on configuring Slurm better to encourage this.
Here's my summary of ...
- 2,799
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93
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How much HPC time goes on different basic operations like matrix multiplication, linear programming, sorting etc.?
I'm teaching a course on parallel computing, and have been trying to find a breakdown of how much high performance computing time is spent on different basic building-block operations, but haven't ...
- 11
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2
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94
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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 ...
- 265
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50
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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 ...
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8
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2
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262
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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 ...
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1
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170
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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'...
- 31
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1
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212
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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 ...
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238
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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 ...
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1
answer
105
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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 ...
0
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1
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297
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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 ...
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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 ...
- 101
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2
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838
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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 ...
- 259
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91
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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 ...
- 131
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43
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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 ...
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1
answer
155
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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 ...
- 435
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181
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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 ...
- 506
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1
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340
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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 &...
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92
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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 ...
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89
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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 ...
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2
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513
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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 ...
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1
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2k
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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 ...
- 2,851
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1
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2k
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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 ...
- 527
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1
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240
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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-...
- 233
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62
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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 ...
- 443
3
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1
answer
138
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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 ...
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2
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3
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641
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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 ...
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4
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1
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2k
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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 ...
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1
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113
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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 ...
- 103
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2
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95
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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 ...
- 125
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3
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203
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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 ...
- 109
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1
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121
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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 ...
- 139
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2
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459
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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 ...
- 117
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2
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108
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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 ...
- 2,236
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29
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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/...
- 121
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1
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446
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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
...
- 121
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1
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112
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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 ...
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4
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59
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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 ...
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93
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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 ...
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4
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1
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533
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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 ...
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1
answer
102
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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 ($N/n = {\rm const}$). ...
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4
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0
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78
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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 ...
- 508
2
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1
answer
81
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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 ...
8
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2
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1k
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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 ...
- 108
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345
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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 ...
- 113
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1
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182
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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 ...
user27075
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112
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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 ...
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2
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281
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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?
...
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4
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2
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599
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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 ...
- 672
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1
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1k
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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,
...
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1
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203
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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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