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Challenge to scientists: does your ten-year-old code still run?

nature.com

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Re: Challenge to scientists: does your ten-year-old code still run?

#131

Post by atrettel »

hpcjoe wrote: post #86

Short answer: Yes, my 30 year old Fortran code runs (with a few minor edits between f77 and modern fortran), as did my ancient Perl codes. Watching the density functional theory based molecular dynamics zip along at ~2 seconds per time step on my 2 year old laptop, versus the roughly 6k seconds per time step on an old Sun machine back in 1991. I remember the same code getting down to 60 seconds per time step on my de…

> Whats been really awesome about that has been the fact that I've written some binary data files on big endian machines in the early 90s, and re-read them on the laptop (little endian) adding a single compiler switch.

I want to second the idea of just dumping your floating point data as binary. It's basically the CSV of HPC data. It doesn't require any libraries, which could break or change, and even if the endianness changes you can still read it decades later. I've been writing a computational fluid dynamics code recently and decided to only write binary output for those reasons. I'm not convinced of the long-term stability of other formats. I've seen colleagues struggle to read data in proprietary formats even a few years after creating it. Binary is just simple and avoids all of that. Anybody can read it if needed.

Re: Challenge to scientists: does your ten-year-old code still run?

#132

Post by Rochus »

hpcjoe wrote: post #86

Short answer: Yes, my 30 year old Fortran code runs (with a few minor edits between f77 and modern fortran), as did my ancient Perl codes. Watching the density functional theory based molecular dynamics zip along at ~2 seconds per time step on my 2 year old laptop, versus the roughly 6k seconds per time step on an old Sun machine back in 1991. I remember the same code getting down to 60 seconds per time step on my de…

Yes, I know a couple of Fortran 77 apps and libraries which were developed more than 25 years ago and which are still in use today.

My C++ Qt GUI application for NMR spectrum analysis (https://github.com/rochus-keller/CARA) runs since 20 years now with continuing high download and citation rates.

So obviously C++/Qt or Fortran 77 are very well suited to outlast time.

Re: Challenge to scientists: does your ten-year-old code still run?

#134

Post by searine »

Jabbles wrote: post #108
djaque wrote: post #98

Earlier quoted context omitted.

I am all for open science, but you understand that the links in your post are the exact worry people have when it comes to releasing code: people claiming that their non-software engineering grade code invalidates the results of their study. I'm an accelerator physicist and I wouldn't want my code to end up on acceleratorskeptics.com with people that don't understand the material making low effort critiques of minor…

I am interested to know the distinction between "production-ready" and "science-ready" code. I do not think "non-experts" should be able to use your code, but I do think an expert who was not involved in writing it should be.

>I am interested to know the distinction between "production-ready" and "science-ready" code.

In general, scientists don't care how long it takes or how many resources the code uses. It is not a big deal to run a script for an extra hour, or use up a node of supercomputer. Extravagent solutions or added packages to make the code run smoother or faster is only wasting time. It speed/elegance only really matters when you know the code is going to be distributed to the community.

Basically scientists only care if the result, is true. If the result it outputs is sensible, defensible, reliable, reproducible. It would be considered a dick move to criticism someones code, if the code was proven to produce the correct result.

Re: Challenge to scientists: does your ten-year-old code still run?

#135

Post by James_Henry »

ivanbakel wrote: post #125
djaque wrote: post #98

Earlier quoted context omitted.

I am all for open science, but you understand that the links in your post are the exact worry people have when it comes to releasing code: people claiming that their non-software engineering grade code invalidates the results of their study. I'm an accelerator physicist and I wouldn't want my code to end up on acceleratorskeptics.com with people that don't understand the material making low effort critiques of minor…

Doesn't it concern you that it would be possible for critics to look at your scientific software and find mistakes (some of which the OP mentioned are not "minor") so easily? Given that such software forms the very foundation of the results of such papers, why shouldn't it fall under scrutiny, even for "minor" points? If you are unable to produce good technical content, why are you qualified to declare what is or isn…

When you say OP, do you mean djsumdog? If so, what mistakes does he mention that aren't minor?

Re: Challenge to scientists: does your ten-year-old code still run?

#136

Post by RandoHolmes »

djaque wrote: post #105
BeetleB wrote: post #87

Earlier quoted context omitted.

> their job is not coding To me, that's like a theoretical physicist saying "My job is not to do mathematics" when asked for a derivation of a formula he put in the paper. Or an experimental physicist saying "My job is not mechanical engineering" when asked for details of their lab equipment (almost all of which is typically custom built for the experiment).

The point is that as a scientist your code is a tool to get the job done and not the product. I can't spend 48 hours writing unit tests for my library (even though I want to) if it's not going to give me results. It's literally not my job and is not an efficient use of my time

> I can't spend 48 hours writing unit tests for my library

No one is insisting on top quality code, but there has to be an acceptance that code can be flawed and that needs to be tested for.

Re: Challenge to scientists: does your ten-year-old code still run?

#137

Post by rscho »

djsumdog wrote: post #13

This article brings up scientific code from 10 years ago, but how about code from .. right now? Scientists really need to publish their code artifacts, and we can no longer just say "Well they're scientists or mathematicians" and allow that as an excuse for terrible code with no testing specs. Take this for example: https://github.com/mrc-ide/covid-sim/blob/e8f7864ad150f40022... This was used by the Imperial College…

> If journals really care about the reproducibility crisis

All is well and good then, because journals absolutely don't care about science. They care about money and prestige. From personal experience, I'd say this intersects with the interests of most high-ranking academics. So the only unhappy people are idealistic youngsters and science "users".

Let's get back to non-profit journals.

Re: Challenge to scientists: does your ten-year-old code still run?

#138

Post by gowld »

James_Henry wrote: post #135
ivanbakel wrote: post #125

Earlier quoted context omitted.

Doesn't it concern you that it would be possible for critics to look at your scientific software and find mistakes (some of which the OP mentioned are not "minor") so easily? Given that such software forms the very foundation of the results of such papers, why shouldn't it fall under scrutiny, even for "minor" points? If you are unable to produce good technical content, why are you qualified to declare what is or isn…

When you say OP, do you mean djsumdog? If so, what mistakes does he mention that aren't minor?

How is it possible to know the difference between minor and major, if the mistakes are kept secret?

If we're supposed to accept scientific results on faith, why bother with science at all?

Re: Challenge to scientists: does your ten-year-old code still run?

#139

Post by prionassembly »

djsumdog wrote: post #13

This article brings up scientific code from 10 years ago, but how about code from .. right now? Scientists really need to publish their code artifacts, and we can no longer just say "Well they're scientists or mathematicians" and allow that as an excuse for terrible code with no testing specs. Take this for example: https://github.com/mrc-ide/covid-sim/blob/e8f7864ad150f40022... This was used by the Imperial College…

Institutions need to provide scientists and mathematicians with coders. It's a bit insane to expect them to be software engineers as well.

Re: Challenge to scientists: does your ten-year-old code still run?

#140

Post by neuromantik8086 »

jnxx wrote: post #78

Very related to this, see also Hinsens blog post: http://blog.khinsen.net/posts/2017/11/16/a-plea-for-stabilit... I think that GNU Guix is extremely well-suited to improve this situation. Also, one could think this is an academic problem, in the sense of am otherwise unimportant niche problem. It really isn't, it is just like in many other topics that academics get confronted first with this issue. I am sure that in…

Guix is one of several solutions that has been touted as a solution. Another one that is quite popular in HPC circles is Spack (https://spack.readthedocs.io/en/latest/).

At my institute, we actually tried out Spack for a little bit, but consistently felt like it was implemented more as a research project rather than something that was production-level and maintainable. In large part, this was due to the dependency resolver, which attempts to tackle some very interesting CS problems I gather (although this is a bit above me at the moment; these problems are discussed in detail at https://extremecomputingtraining.anl.gov//files/2018/08/ATPE...), but which produces radically different dependency graphs when invoked with the same command across different versions of Spack.

I've since come to regard Spack as the kind of package manager that science deserves, with conda being the more pragmatic / maintainable package manager that we get instead . Spack/Guix/nix are the best solution in theory, but they come with a host of other problems that made them less desirable.

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