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Introduction to High-Performance Scientific Computing

pages.tacc.utexas.edu

11–20 of 55 posts

Re: Introduction to High-Performance Scientific Computing

#11

At Nerdalize we're building a cloud that's specifally build for high performance scientific compute: http://www.nerdalize.com/cloud/

I never got into high performance scientific computing, but I believe the stuff that was done in my department at university was all MPI based and required very high interconnect speeds (like with Infiniband). It looks like your offering is much more standard, what's the thinking there, or am I just wrong/out of date?

Re: Introduction to High-Performance Scientific Computing

#12
This site is going down the drain. More and more like Slashdot and others. I'll only post useless comments any more, anything else is a waste of effort. The only way to achieve change is to make things WORSE. New mission: I'll slowly help lower the quality of this "discussion" with two many angry know-nothing teenagers even more.

Re: Introduction to High-Performance Scientific Computing

#13

This site is going down the drain. More and more like Slashdot and others. I'll only post useless comments any more, anything else is a waste of effort. The only way to achieve change is to make things WORSE. New mission: I'll slowly help lower the quality of this "discussion" with two many angry know-nothing teenagers even more.

With an attitude like that, are you surprised? How about trying to bring it back up or offer some constructive criticism? Alternatively, you can just leave ...

Re: Introduction to High-Performance Scientific Computing

#14
post #8

Looks like a good collection of important topics. The tutorials feel a bit 2005 to me. GNUplot and svn? In my scientific universe it's all matplotlib and git these days. Maybe I'm unique.

Gnuplot is still used quite a lot in my area. You need to work more to make something aesthetically pleasing, but it's generally a better fit to plotting large amounts of data coming from another code. I've also been quite badly burnt by Matplotlib scripts no longer producing the same plot with changes in the library. Gnuplot version 5+ is nicer to use and has some pretty powerful features. This blog has been a good…

The nice thing about Ggnuplot is that it's extremely easy to connect it with anything, since it's basically its own language. Python has made a lot of inroads into the scientifc computing field but it's by no means the only one. This is a field where twenty year-old Fortran libraries are still relevant.

SVN also has the important advantage of being relatively easy to pick up by someone who's not a programmer. It would not be my first choice for a version control system now that we have Mercurial and git (frankly, it wasn't not even back when our only affordable alternatives were CVS and RCS), but it's very easy to teach it.

Re: Introduction to High-Performance Scientific Computing

#15
post #9
post #6

Earlier quoted context omitted.

You might want to run a spell check on that page, I just saw "comprimise" in the most prominent sentence. Also, white text on sky background with white patches (sun, clouds) has unreadable portions.

Thanks for the comment, we fixed the typo. Any ideas on the content of the website are also very welcome.

This MBP model is a little bit dated and the photo is blurry: http://www.nerdalize.com/wp-content/uploads/2016/06/mockup-e...

Re: Introduction to High-Performance Scientific Computing

#16

At Nerdalize we're building a cloud that's specifally build for high performance scientific compute: http://www.nerdalize.com/cloud/

I love that you work on computational heating. Have you thought about open sourcing your heater design like back-blaze does with their storage pods? I tried really hard to get fiber but Ziggo 300 is the best one can do here sadly, so I build my own heating rigs that run folding@home 24/7. But I'd guess I'm not the only one interested in heating their home with science, so maybe you could gather a crowd of computational heating enthusiast and diy around you and learn from one another!

Re: Introduction to High-Performance Scientific Computing

#17

At Nerdalize we're building a cloud that's specifally build for high performance scientific compute: http://www.nerdalize.com/cloud/

I never got into high performance scientific computing, but I believe the stuff that was done in my department at university was all MPI based and required very high interconnect speeds (like with Infiniband). It looks like your offering is much more standard, what's the thinking there, or am I just wrong/out of date?

It depends heavily on the kind of work. If you have a large scale simulation that needs to be partitioned like a weather system you are IO bound and need as thick interconnects as possible. However there are some problems which are very hard computationally but not very large. Basically everything in NP and exp is a good candidate. There you can distribute the same problem to a bazillion systems with a different starting configuration and let them run until one of them obtains a solution.

If you look at the BOINC project those are basically all problems of this kind. Folding proteins like folding@home does for example. The description of a protein is fairly small, a couple megabyte max. However it takes a long time to simulate the behaviour, since chemistry is a messy probabilistic process with lots of back and forth. Nature does this on trillions of proteins at the same time within nanoseconds, and while we cannot reasonably increase the simulation speed of an individual protein, we can at least simulate as many proteins at once as possible.

Re: Introduction to High-Performance Scientific Computing

#19

Looks like a good collection of important topics. The tutorials feel a bit 2005 to me. GNUplot and svn? In my scientific universe it's all matplotlib and git these days. Maybe I'm unique.

It really depends on the size and the age of the code you're working with. We, for instance, use a code package that was born in 2005 (and continuously developed since), so it lives in SVN. For all the heavy-duty scientific visualization, we use VisIt [1], because the size and dimensionality of the data require a special-purpose visualization package.

To me, "gnuplot or matplotlib" is a little beside the point - if we're using one of those it's for something quick 'n dirty, or for a relatively simple plot of summary data.

[1] https://wci.llnl.gov/simulation/computer-codes/visit

Re: Introduction to High-Performance Scientific Computing

#20

Looks like a good collection of important topics. The tutorials feel a bit 2005 to me. GNUplot and svn? In my scientific universe it's all matplotlib and git these days. Maybe I'm unique.

1. Do you know how much time it takes to keep a 600 page book up to the minute? 2. But yeah. I'm going to roll the tutorials into a volume of their own.
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