# Questions tagged [hpc]

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

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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 ...
168 views

### 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'...
202 views

### 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 ...
234 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 ...
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 ...
288 views

### 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 ...
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 ...
49 views

### 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 ...
26 views

### 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 ...
681 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 ...
80 views

### 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 ...
1 vote
41 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 ...
149 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 ...
1 vote
153 views

### 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 ...
1 vote
271 views

### 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 &...
85 views

### 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 ...
36k 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 ...
83 views

### 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 ...
474 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 ...
1 vote
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 ...
590 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 ...
50k 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 ...
1k views

### 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 ...
214 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-...
58 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 ...
131 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 ...
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 ...
110 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
92 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 ...
199 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
2k views

### Flush output in Torque scheduler?

I'm trying the Torque scheduler. I have previous experience with the LSF scheduler, and I quite like being able to use 'bsub -I make -j 12' to compile a program really quickly, i.e. running an '...
21k 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 -xSSE4....
3k 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 ...
1 vote
112 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
438 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
106 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 ...
2k 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 ...
1 vote
28 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
419 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 ...
106 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 ...
221 views

### Removing non-determinism from molecular dynamics code

I've been looking through the other answers, and I haven't found a good answer yet. I'll describe the simulation I am running, and then the problems. The program simulates particles undergoing ...
57 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 ...
224 views

### Using computational libraries on a machine without root access

If you want to use a computational library on a high-performance computing center where you have no root access to install new software you can use header-only template libraries such as MTL4, Eigen3, ...
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 ...
382 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, ...
399 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 ...
22k 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<vector<double>> (using std) to form a matrix class for high performance scientific computing code? If the answer is no. ...
1 vote
97 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 ($N/n = {\rm const}$). ...