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19 votes
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Should I rent computing resources, or buy my own computers

Ultimately, the answer to this question depends on the prices being charged for the services that you need. At some very low price, this would almost certainly be better than buying your own computer,...
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13 votes
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Why does sparse linear algebra have a low arithmetic intensity?

BLAS1-operations, BLAS2-operations, and sparse-operations share the same curse of low arithmetic intensity, that they perform $O(1)$ flops for each memory read (contrast this to a BLAS3-operation like ...
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12 votes

Should I rent computing resources, or buy my own computers

$6.60/core-month is less than a penny a core-hour. This is a good deal, and it's a better deal than you can get if you buy identical hardware yourself and pay your own power and sysadmin bill. If all ...
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10 votes

Communication overhead in supercomputing

A long standing favorite benchmark in high performance computing has been the HPLinpack benchmark, which measures the speed of a computer system in floating point operations per second while solving a ...
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9 votes

Direct Numerical Simulation of reacting flows

Like WolfgangBangerth, I strongly recommend that you reconsider your motivation (or your supervisor's motivation) for this goal. First, look at Center for Exascale Simulation of Combustion in ...
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9 votes
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Computer Build for Scientific Computing

Many of us in scientific computing simply have well-equipped laptops for regular software development tasks, some multicore workstations for smaller-scale testing, and access to clusters for larger ...
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8 votes
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Intel Knights Landing work loads vs NVIDIA GeForce

Like Brian said, the Xeon Phi cores are not at all comparable to the CUDA ones. The problem with the Phi is that it's somewhere between two horses. If you are doing highly parallel floating point ...
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  • 2,473
8 votes

Python implementation for Frechet Distance

I realize this question was asked a while ago, but I recently needed the Freschet distance as well. I couldn't find any implementations for Python, so I wrote my own based on the paper: "Computing ...
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7 votes
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Using computational libraries on a machine without root access

Almost everything you can build and install in your own space. With GNU autotools, you can do something like ./configure --prefix=/path/to/your/work/space ... and ...
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7 votes

Intel Knights Landing work loads vs NVIDIA GeForce

CUDA cores aren't at all comparable to the separate processor cores in the Xeon Phi coprocessors. The Phi coprocessor cores are full fledged processors that can have their own loops, branching, etc. ...
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7 votes
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A good, simple book/resource on Parallel Programming in C++ for scientific computing

One of the first things that you need to understand about parallel programming is the difference between shared memory multiprocessor computer systems and distributed memory clusters. A shared ...
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6 votes

Should I rent computing resources, or buy my own computers

Will you be using it all the time, for a long time? In general, the economics for this are simple - if you need a valuable resource for short intermittent bursts, it will generally be cheaper to rent ...
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6 votes
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Many processors reading a single HDF5 file

It will not scale! Use the parallel HDF5 functionality to read it in parallel with a relatively small number of readers, or do what your colleague suggests. There will be tradeoffs with both methods, ...
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6 votes

Borrow computational power from machines around me

You could install BOINC on those machines. When the computers become idle, the BOINC screensaver/client requests tasks from a server and computes them. See more information about it here. This is ...
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6 votes

Communication overhead in supercomputing

The honest answer is that we don't know. The answer depends heavily on what is actually being run and what code the user has written. As Brian Borchers points out, there's a big difference between two ...
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6 votes

How to simulate over 1 billion particles?

A first step, if you "have never been up in computing", is to read the literature and see what others are doing and have done. The second step is that you will likely learn that what you want to do ...
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6 votes
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Can Julia be used to create a large-scale CFD software like OpenFOAM?

I think the question is just too subjective to answer. In the end, there are excellent C++ libraries for nearly everything that has to do with the solution of PDEs, whereas they are largely missing in ...
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5 votes

Additional cost associated with quad (or higher) precision

It depends on how quad precision is implemented. If you want to implement it as "traditional" floating point numbers with sign, mantissa, and exponent (the latter two just having more than the normal ...
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5 votes
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Borrow computational power from machines around me

You can use HTCondor that is designed exactly to "steal" cpu cycles from remote machines. It may be a little difficult to setup but I think this may be the best approach.
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5 votes

HPC : should I compile on the head node or on a compute node?

Let me supply a belated answer from the POV of a cluster user and a cluster administrator. A well-designed cluster will, in general, be as homogeneous as possible, with login-nodes being generally a ...
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  • 341
5 votes

Leveraging scipy for matrix free finite elements

I would say that the implementation + verification + unit testing would take you more than just 3 weeks. Although, if you are planning to invest that time, you might add that capabilities to ...
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5 votes
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Where can an undergraduate go to find cores on a budget?

You need funding, you need a better algorithm, a better implementation, or you need to change your problem. To get funding, you need to work with your adviser. This could be about using grant money or ...
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5 votes

Why does sparse linear algebra have a low arithmetic intensity?

This really depends on the operations you are including in your question. If you took the sparse equivalent of any level 1 BLAS or level 2 BLAS algorithm, then yes they are memory bound (not compute ...
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5 votes
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How much space store a matrix of numbers?

If you consider a 4 by 4 matrix of integers, it will be stored in memory as a unique array of integers. Since each integer is 4 bytes ( 32 bits) (sometimes not, but it's not important here) then you ...
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  • 540
4 votes

Fast way to compute all eigenvalues of a dense Hermitian matrix

SLEPc is a library designed for the solution of large sparse eigenvalue problems, while your matrix is dense. The algorithms used by SLEPc are based on matrix-vector multiplication, and the ...
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4 votes

C++ vs Fortran for HPC

Sorry for digging up an old thread but it seems that even in 2015, Fortran is being used a lot. I just came across this (alternate link) list which basically is a list of 13 codes approved by DOE's ...
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  • 1,779
4 votes

Is it a good idea to use vector<vector<double>> to form a matrix class for high performance scientific computing code?

I don't recommend it, but not because of performance issues. It will be a little less performant than a traditional matrix, which are usually allocated as a big chunk of contiguous data that is ...
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4 votes
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Automated software optimization and tuning

You could just write an edit, compile, run loop in shell or Python that does it directly in the .h file if you think hard-coding this value is likely to give the compiler an advantage. If the runs are ...
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  • 10.8k
4 votes

Direct Numerical Simulation of reacting flows

What you suggest is a multi-year research program. Don't even think about doing this yourself, you will not within several years achieve anything that comes close to the current research. Rather, ...
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4 votes

Is there a way to ensure that PBS array jobs will be run in order?

If you need a guarantee, submit element zero as a separate job and make 1-9 dependent on its completion.
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