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

[Brian O'Shea]

Hi all,

Captain Paininthebutt chiming in here.  I wasn't up all night reading Matt's
email, but the owner of the local Starbucks franchise got a pretty
substantial addition to their kid's college fund, if you get my meaning.

I agree strongly with Matt's point that the level of parallelism of various
functions would be useful for the end user (case in point: we were startled
to learn that we're probably wasting our time doing slices in parallel).  A
small table of function vs. parallelism would be great:  "scales
embarrassingly well", "scales somewhat - use carefully", "should be used in
serial", and "must be used in serial" would be useful.  This is probably an
oversimplification, but some footnotes would help:  "If you want to do a
projection through a very large simulation, use fixed resolution buffers."
A similar estimate of memory usage for problems would be very handy, at
least for the largest calculations.  Furthermore, a couple of example batch
scripts would go a long way - a Kraken batch script for Parallel HOP made
its way to Brian Crosby and I, and we found that very informative.

I also think that Matt and Britton have made some very important points
regarding bugs and the yt-users list.  My student and I have not really
helped this - I tend to go right to the person who I suspect can help us
most effectively, rather than through yt-users.  There are various reasons
for that, but it's not what is best for the community, and we'll go through
yt-users as much as possible in the future, even if discussions get taken
off-list.  If this is done, making a practice of posting a recap to the list
after a bug is solved would be useful, since Matt assures me that the lists
are archived.

Regarding expectations vs. obligations, I think that it is appropriate for
developers to fix bugs in features they create, and to give users some idea
of the resources that those features require.  On the other side of the
coin, non-developer users (like myself) are obligated to give feedback on
features: what's useful?  what's not?  what appears to be broken?  My
observation has been that a few of the yt features could become vastly more
useful to people other than their developer if a few widgets were added.
This is generally not trivial, but is far easier for the original developer
than for somebody who is new to yt and python in general, and a given yt
feature in particular.  Documentation and examples are also key - I
personally have found the cookbook to be invaluable!

I very much like the idea of a "wish list", particularly if other
users/developers can comment on what wished-for features would be useful to
them, and the level of difficulty in implementing the feature.  This would
also facilitate coordination between yt community members - if I need to
design a kitchen-sink-cleaning module for yt, and so does Britton, it's
probably better for the two of us to work together than to separately
implement our tools.  Also, it's much more likely that the resulting product
will be generally usable.

Matt and Britton both mentioned something that I've been thinking about for
the last couple of days - nobody gets paid to develop yt.  I really do think
this could change, if we wanted it to - the NSF does occasionally give out
money for code development, often as part of a larger science grant, and I'd
be happy to start writing this into my proposals.  Of course, this would
require somebody with deep familiarity with yt to commit to working on
specific parts of yt for an extended period of time, but depending on the
circumstances might be good for all parties concerned, including the larger
yt community.

Anyway, that's my $0.02 of coffee-fueled ramblings.

--Brian

On Fri, Aug 20, 2010 at 3:04 PM, Britton Smith <brittonsmith at gmail.com>wrote:

> Hi everyone,
>
> I would like to chime in on some of the issues Matt has raised.  These are
> very important things to think about, which is why I stayed up all night to
> read the whole email.
>
> I will mostly stay out of the parallelism issue, but I'll only add that I
> have been doing projections of 1024^3 unigrid data on kraken with 64 cores.
> They have gone fine for me, taking roughly 10 seconds or so each.  I also
> think an explicit list of actions that do not run in parallel is a really
> good idea.
>
> On the bugs issue, it is not clear to me how a new user can tell the
> difference between a bug and simply doing something wrong.  Either way, I
> think that the users list is succeeding in getting people's issues solved,
> provided that the issues make it there.  I think we really need to encourage
> all users to be taking all potential issues through the list first, even if
> the resolution eventually takes place off-list.  Even if the feature author
> is doing all of the talking, this makes any new knowledge public, and allows
> other people to help out if they can.  Most people already do this, but I
> would suggest again that we ask that any requests for help we receive
> directly be resent to the user list.
>
> On the community, there clearly needs to be a balance between what users
> expect to get from the code and what the developers are obligated to
> provide.  With exceptions, a vast majority of those contributing code are
> not doing so in their spare time.  Much of this code is related to their own
> work, but a nonzero amount is stuff that simply needs to get done.  Users of
> the code need to recognize this.  However, at the same time, we as
> developers need to hold ourselves to some standards, namely, if we say the
> code does something, it better do it.  Clearly, there are situations where
> we can not deliver on this, at least not right away.  In general though, we
> need to be clear about what the code will and will not do, and see that our
> statements are and remain true.
>
> I think we should consider setting up a wish list, where users can submit
> ideas for features that they would like see added to the code.  This should
> be viewable by everyone.  I think this might help people stay conscious of
> the fact that if they want something, that means someone has to physically
> go and do it for them.  Maybe this will even give people the notion that
> they can do it on their own.
>
> Britton
>
>
> On Thu, Aug 19, 2010 at 11:54 PM, Matthew Turk <matthewturk at gmail.com>wrote:
>
>> 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/ <http://physics.ucsd.edu/%7Esskory/>_.>/ _Graduate Student
>> > ________________________________(_)_\(_)_______________
>> >
>> > _______________________________________________
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