[Yt-dev] Parallelism, or, how I learned to stop worrying and love open source development

[Matthew Turk]

Hi all,

I'm going to top post, which I guess I do more than I ought to anyway,
because I'm going to try to address a number of issues that have been
brought up.  I've spent some of the day thinking about this issue, and
what it says about yt as a community and about my level of involvement
in various areas.

So, I'll touch on those at the end, but first I'll hit back on the
issue of parallelism and how to address it.

= Parallelism =

I think what is becoming clear is that the step from serial to
parallel, in terms of user experience, should be more well-handled
than it currently is.  As it stands, the section in the manual that
covers parallelism basically says, "These things work, go ahead and
give it a go!"  This is my fault, and it's not really sufficient.
More detail has to be given, and rather than a whitelist of actions
that are parallel safe we need to also include a *blacklist*.

The second step we need to take is provide examples of how to submit a
parallel job -- how much it requires in terms of resources and so on.
Unfortunately, it's not entirely clear to me the best way to organize
the documentation, and I don't even really know where this would go.
Stephen did a really rad job of doing this in the halo finding paper,
and he's done an excellent job with his work on the halo finder as a
whole.  (It's just that last 5% toward the user experience, I think.
:)  My own work on the parallel projections should be better
documented and the UX there should be improved as well.

The third is to keep an eye on memory usage.  Memory profiling is
difficult, but it's something we have tried before and that I believe
needs to be re-examined.  Specifically, it seems that both projections
and the parallel halo finder suffer from this problem.  As a note,
next week I will be spending some time swapping out the old projection
method for the new quad-tree method.  This should improve both speed
and memory usage.

Okay, on to the larger problems that I think this relates to.

= Bugs =

First off, we need a mechanism for handling and bugs.  I don't want to
use the word "triage" here, but it is becoming clear that we need a
mechanism.  Currently, we have a Trac site that really doesn't get
used at all.  I've explored a couple mechanisms for encouraging bug
reports.

 * I can enable OpenID login -- this means using something like your
GoogleName to log in and report a bug.
 * I've already replicated the .htpasswd between mercurial and the
Trac site, so anyone who has a report there can log in to the Trac
site.
 * yt could register a default excepthook that encourages the user to
report a bug.  I'm leery of this because I'm not sure I want to muck
about with Python internals that much, but it could be done nicely, I
think.

Overall, though, what really needs to happen is some kind of *buy-in*
on the part of the user -- which in this case is anyone who has had
trouble with yt.  I have pulled back from yt-users, and I'm really
happy that everyone else has stepped up.  But I'm worried that as time
goes on, people will pick up knowledge in ways that aren't indexable
by search engines and then this knowledge keeps getting re-learned.

Public reporting of bugs, particularly as it could relate to
improvements in documentation, is essential.  But this can't happen if
it's just driven by one or two people.  And if no one else is
motivated to encourage this, then perhaps that's just where we'll
stay.  I can't force buy-in, I can only encourage people to see the
benefits to reporting bugs, sharing experiences, and all of that.  We
need to have people to read and handle bugs, and then people to whom
they apply.  I really would like for this not always to be me.

Anyway, if you have an hg account, you can login:

http://yt.enzotools.org/login/

and then report a bug:

http://yt.enzotools.org/newticket

It helps if you paste the traceback with --paste on the command line
of your script.

= Fixing Bugs =

We've had great success with people taking ownership of different bugs
on the mailing list and fixing them.  This is a huge success story,
and I thank all the developers that have made this happen.  But I
think it's important that we continue to develop this sense of
ownership through the Trac site.

= Major Enhancements =

Adding on major enhancements is unfortunately an open problem.  For
instance, I would really like to see the parallelism framework
essentially rewritten to be more modular and to take advantage of
nested MPI communicators.  I have a sketch of how this would go, and
I've even written some code.  But, I'm not employed to work on yt.  I
mostly develop it either as it suits my research interests (and I am
operating under the working assumption that this is true for everyone
else) or as I find it something fun to do in the evenings.  I want it
to be used, and to be useful, and I believe that my stewardship of the
project up to this point supports this conclusion.

I *truly* do believe in cross-code simulation analysis, sharing
facilities with other users, and reproducible research.  But I am
reaching the limits of what I, alone, can do.  So far we've had some
pretty major contributions from a number of developers, but I think
it's important that we communicate to the community that this is still
a volunteer project.

We don't have a team of dedicated software developers, we have a
handful of scientists who are working to both further their own
research interests while providing the best user experience possible
for an advanced analysis code.  And, to be perfectly frank, I think
we're doing a pretty darn good job on both of those fronts.  Many
people now use yt on a daily basis to analyze simulation outputs from
several different codes.  We've got advanced analysis and viz
functionality, thanks to *you* developers, that has been published a
dozen papers, been shown at the Adler Planetarium, taken home the
third place at the SciDAC visualization "Oscars," and even (ever so
briefly) been on the Discovery channel.

But, still, we have to keep our eye on the prize.  And if the prize
the other developers have *their* eye on isn't the prize *you* have
your eye on, unfortunately some responsibility will fall back on to
your shoulders.  I honestly wish I could spend more time helping
others use yt, developing yt, and building it to be the tool I really
wish it would be.  Don't think that I don't see all the warts and
problems that you all see -- I do.  In the docs, the source code, the
functionality, the user experience ... I see the warts too.

But even though developing yt is fun, I'm still developing it because
I'm a scientist who wants to ask questions of his data.

= Building Community =

We've done a good job of this, but it's becoming clear that there's a disjoint:

 * We're doing a mediocre job of shepherding users into being
contributing developers.  I'd like to help fix this by writing up more
suggestions on how to develop and share your changes.  yt will
stagnate if we don't continue to churn the developer list.
 * We need to articulate the vision for yt, and I'm not sure my vision
is the one anyone else has.

I'd love to hear suggestions about this aspect.

= Documentation =

Any help anyone can give with documentation would be great.
Organization, notes, suggestions, anything.  Report it as a bug.
Commit changes.  Email the list.

==

Anyway, that's basically what I've been thinking about, and what I
wanted to say.  I think we have an opportunity with yt to build a real
community of collaboration and sharing of resources.  And we've done a
great job with that so far.  But it still has to be something of a
jumpstart approach -- jumpstarting development and then encouraging
others to pick up the torch and run with it.  Grass roots,
science-driven development is kind of the name of the game here.

And when there *are* problems, I'm sure that lots of people are eager
to jump at helping you fix them.  But we have to hear about 'em before
we can.  :)

Thanks,

Matt

On Thu, Aug 19, 2010 at 1:12 PM, Stephen Skory <stephenskory at yahoo.com> wrote:
> Hi Brian & Eric,
>
>>As you know (since we discussed it off-list), I'm the reason for this being
>>mentioned to you.  I had some pretty horrible problems with the various
>>incarnations of HOP in yt being excruciatingly slow and consuming huge amounts
>>of memory for a 1024^3 unigrid dataset, to the point where my grad student and I
>>
>>ended up just using P-GroupFinder, the standalone halo finder that comes with
>>week-of-code enzo.  Note that when I say "excruciatingly slow" and "consuming
>>huge amounts of memory", I mean that when we used 256 nodes on Ranger, with 2
>>cores/node (so 512 cores total) for the 1024^3 dataset, it still ran Ranger out
>
>>of memory, or, alternately, didn't finish in 24 hours.
>
> A few notes in response:
>
> - Recently I ran a 2048^3 dataset on 264 cores that took about 2 hours which
> averaged about 8.5GB per task with a peak task of 10 GB. Your job is 1/8 the
> size and should have run, and I don't know why it didn't.
>
> - If I wasn't trying to graduate I would have had more time to assist when your
> student (Brian) asked me for help. I'm sorry so much of your time was wasted.
>
> - My tool as a public tool is not any good unless other people can use it too.
> Clearly I need to do some work on that.
>
> - It *does* use much more memory than it needs to, you are right. I know where
> the problems are, and whoo-boy they are there, but they are not easy to fix.
>
> - Speed could be better, but some of this has to do with how HOP itself works.
> For example, it needs to run the kD tree twice, unlike FOF which needs to only
> once. The final group building step is a "global" operation, so that's slow as
> well. On 128^3 particles, (normal) HOP takes about 75 seconds, and FOF about 25.
> The C HOP and FOF in yt both use the same kD tree, same data I/O methods, so
> that's a fair ratio of the increased workload.
>
>
>  _______________________________________________________
> sskory at physics.ucsd.edu           o__  Stephen Skory
> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
> ________________________________(_)_\(_)_______________
>
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