Mailman 3 April 2009 - yt-dev

Fw: X1024 jobs on Ranger
by Stephen Skory 30 Apr '09

30 Apr '09

I'm breaking Ranger... before I reply, do any of you have something intelligent to add that I can say? Because the .cpu files aren't spatially restricted, each thread of parallel HOP may have to access many of the .cpu files, which is how the MDS server gets pummeled. _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________ ----- Forwarded Message ---- > From: Tommy Minyard <minyard(a)tacc.utexas.edu> > To: "sskory(a)physics.ucsd.edu" <sskory(a)physics.ucsd.edu> > Sent: Thursday, April 30, 2009 12:54:49 PM > Subject: X1024 jobs on Ranger > > Hello Stephen, > > In our monitoring of Ranger, we've noticed that some of your recent jobs named > x1024 seem to be causing an abnormally high load on the /scratch filesystem > meta-data server (MDS). From our monitoring, it appears that the MDS load goes > way up when your job initially begins to run for up to the first 30 minutes to > hour, but then it drops back down to a more reasonable load after the job has > been running for a while. > > Do you have any idea what may be triggering such a high load from the > application you are running? It does not seem to cause any major problems or > generate errors, however, the filesystem access becomes much more sluggish when > the MDS load is so high. If you could give us a few more details that might > help explain the high load or point us to the source code for your application, > we want to check and confirm that the MDS is acting as it should. > > Thanks, > Tommy > > ____________________________________________________________________ > Tommy Minyard, Ph.D. - Assoc. Director (512) 232-6578 > Advanced Computing Systems Group (512) 475-9445 (fax) > Texas Advanced Computing Center http://www.tacc.utexas.edu > The University of Texas at Austin minyard(a)tacc.utexas.edu

2 3

1024^3 amr hop problem
by Stephen Skory 30 Apr '09

30 Apr '09

(I'd send this to -users, but since we're not emphasizing parallel hop just yet, I'll put it here.) I am trying to run hop on Ranger on a 1024^3 AMR dataset I got from Robert Harkness. I've been running it with a varying number of threads, always greater than 64. I'm pretty sure it's not a memory problem, I ssh-ed into the head node and ran 'top.' I think I'll try this on Kraken tomorrow, but for now, can any of you make heads or tails of the error message below: AttributeError: 'list' object has no attribute 'append' When can a list not have 'append' as an attribute? http://paste.enzotools.org/show/112/ I can sucessfully run parallel hop on L7 with this exact same install of yt. The script I'm running is dead simple: from yt.mods import * pf = load("DD0082") hop = HaloFinder(pf,padding=0.02) hop.write_out(filename="benchmark-hop.out") Britton, I know you've been doing some large-scale stuff lately. Have you run hop on something this large? Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

3 7

APLpy
by Matthew Turk 28 Apr '09

28 Apr '09

This is an interesting project which might end up coming in handy as a display-layer for FixedResolutionBuffers as we get closer to simulated observation output. http://permalink.gmane.org/gmane.comp.python.matplotlib.general/17300

1 0

L7 HOP center_of_mass problem
by Stephen Skory 27 Apr '09

27 Apr '09

Hi all, With the new setup, I'm getting negative values for the center_of_mass() for some of the haloes in L7 running parallel HOP. It's a small fraction of the total. I am not getting this effect on smaller datasets for this reason. Because L7 takes a while to run through HOP, I haven't been able to do much testing yet. I've only run this on Ranger. I'm going to try on Kraken soon, but I suspect I'll get the same thing. I also suspect I'd get the same problem with parallel FOF. I haven't tested this on a serial run on L7, because it takes a long time. I'd guess that it would work OK. I'll see if I can get that going, too. Matt, can you think of anything you changed when you did the HaloFinding switchover that would affect this? I'll see what I can figure out, but I just wanted to see if anyone (Matt in particular) had some ideas of where this is coming from before I jump headlong into this. Thanks! _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

3 3

HOP/FoF problems
by Stephen Skory 27 Apr '09

27 Apr '09

Hi all, I've been trying to get the new HOP/FoF implementation to run on L7 and on Kraken. I have found a couple problems. The easy one is when trying to statically link both EnzoHop.a and EnzoFOF.a, it complains because they share the same kdtree naming structure. FoF should have its function names that conflict with HOP changed. I'll get around to changing this sometime. For now, I doubt anyone is using it. Alternatively, if they are identical enough, it may be good to use just one set of kdtree code for both. Thoughts? Second, halo_list.write_out() is obtaining the particle_velocity_* fields serially, because now those fields aren't read in in parallel before calling the halo finder. What is the best way to read that data in parallel too, but only when its needed? _______________________________________________________ sskory(a)physics.ucsd.edu o__ Stephen Skory http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student ________________________________(_)_\(_)_______________

2 3

HOP/FOF changes
by matthewturk＠gmail.com 27 Apr '09

27 Apr '09

This patch looks mostly alright to me -- thanks very much for getting rid of the temporary file, and I agree that the FOF code should have a suffix to distinguish it from HOP structures. Here are some very minor comments... http://codereview.appspot.com/52058/diff/1/2 File yt/lagos/HaloFinding.py (right): http://codereview.appspot.com/52058/diff/1/2#newcode175 Line 175: _fields = ["particle_position_%s" % ax for ax in 'xyz',"particle_velocity_%s" % ax for ax in 'xyz'] This line is too long, split it to the next one. http://codereview.appspot.com/52058/diff/1/2#newcode404 Line 404: self.data_source.get_data(["particle_velocity_%s" % ax for ax in 'xyz']) This is redundant with the line above; additionally, we don't need particle_velocity until the write_out. http://codereview.appspot.com/52058/diff/1/5 File yt/lagos/fof/kd.h (right): http://codereview.appspot.com/52058/diff/1/5#newcode38 Line 38: } KDFOFNFOF; I think this should be KDNFOF; maybe the search-n-replace was done out of order? http://codereview.appspot.com/52058

1 0

Release 1.5
by Matthew Turk 23 Apr '09

23 Apr '09

Hi guys, I'd like to take a moment to sketch out my proposal for releasing yt-1.5. We all run off trunk, but right now, 1.0 is the version included with Enzo. Furthermore, the documentation has not been substantially updated since 1.0, so almost all of the stuff we have been doing and working on for the past year (yes, *year*) has not been advertised or included. I'd like to compile some of the things that have happened, most of which have been visible in the ticket tracker, but not all. http://yt.enzotools.org/query?status=closed&group=resolution&milestone=1.5 There are a couple things that don't show up quite so visibly: * Fully parallel slices, projections, cutting planes, profiles, quantities (although scaling will be a target of 2.0) * Mostly parallel HOP (scaling is a major problem here) * FoF halo finding * Object storage and serialization * Major performance improvements to the clump finder (factor ~5) * Generalized domain sizes * Generalized field info containers (which need some work for 2.0) * Dark Matter-only simulations * 1D and 2D simulations * Better IO for HDF5 sets * Support for the Orion AMR code * Spherical re-gridding * Halo profiler (ticket 95 needs some love) * Light cone generator * Callback interface improved * Several new callbacks * New data objects -- ortho and non-ortho rays, limited ray-tracing * Fixed resolution buffers * Spectral integrator for CLOUDY data * Substantially better interactive interface * Performance improvements basically everywhere * Command-line interface to *many* common tasks * Isolated plot handling, independent of PlotCollections I'm pretty sure there's a lot more I'm forgetting -- but the improvements have been numerous. I think the biggest thing to emphasize here would be that yt works in parallel. Scaling is not ideal. That's going to be a task for a later date, I do believe, and for now I think it's important to push out the improvements -- frankly, I'm a little embarrassed people may be using yt-1.0 at this point, because so much work has gone on in the trunk to improve basically every aspect of the code. (And yes, our audience is small, by almost all metrics: but I think this particular set of improvements will help to increase it.) I think this release is much more compelling than the last, and I think we all have something to be proud of. We still have to finish up these tickets: http://yt.enzotools.org/report/12 Most or all of these are my repsonsibility; I'd like some help with #95, though. Additionally, if anybody wants to volunteer to look at (even if just attempting to replicate and getting proper tracebacks) #189, #191 and #197, I'd really appreciate it. #208 might get bumped to 2.0, since I'm the only one using fido anymore; I'd like to bring it back in some way some day, but right now it's not a priority. Now, for the meat of the remaining process: the documentation. This will be primarily my responsibility, but I will need help from other people. Specifically, I need someone to volunteer to read and edit what I write. Additionally, I would like to submit a request that sections of prose be written, in the style of a tutorial, by the people who really are the experts on different sections of the code. I've noticed a substantial uptick in feelings of ownership of various sections, and I'm really happy about that. I think we really need some semi-tutorial style sections written by the people who feel they know best certain sections of the code that are really valuable and useful. Here's my proposed set: * Halo finding: Stephen * Halo profiler: Britton * Clump finder: Britton * Light Cone Generator: Britton * Interactive Usage: Jeff Now, I know you are all very busy -- me too! -- so if this doesn't work for you, it's all good, just let me know. :) I'll handle all the format conversions and integration and so forth. The current documentation repo (has not been put in SVN, but will be once it's working better) is here: http://hg.enzotools.org/yt-doc/ . Furthermore, there's a page set up for comments on the existing documentation: http://yt.enzotools.org/wiki/Plans/DocEnhancements Please, if you have any complaints about existing documentation, making them there will ensure that while I go through the process of editing and rewriting, I will ensure they are taken into account. Additionally, while I am willing to take the burden of documentation, I would really love it if somebody else would help out. So, let me know if you are interested. Okay guys, thanks so much for trudging through this email. Any thoughts on any of this? Did I forget any big features? Anybody feel like helping with extra documentation? Anything else that needs to go in? We've all put a lot of work into this stuff, and I think we have a great chance of making a big splash with a new release. Thanks guys, and talk to you soon, -Matt

3 18

Radius Calculation
by Matthew Turk 20 Apr '09

20 Apr '09

Hi guys, I've been exploring the idea of changing radius to be correct for periodic boxes. Right now it is incorrect; each component (x,y,z) should not have a distance greater than 0.5 * domain_size. The easiest way to do this would be: rx = min( abs( x - center_x ), abs( x - center_x - domain_x) ) I think the best way to do this is to set up a NumPy ufunc http://docs.scipy.org/doc/numpy/user/c-info.beyond-basics.html#creating-a-n… that accepts three arrays, along with the center and the domain width, and then returns the radius. What do you all think? Alternatively, I'm thinking maybe just a regular function that gets the arrays and returns one would be better; the ufunc machinery is a bit complicated and I might get confused. Once I come up with it, will somebody be able to look over my work? -Matt

2 6

hop improvements
by Matthew Turk 20 Apr '09

20 Apr '09

Hi guys, Britton and I worked on some improvements to hop today. Specifically, changing the means of accessing attributes from *copying* to *in-place* access. This should cut down on the memory substantially, but I believe there are still places that it could be improved. Specifically, I think a consolidation of the tags & iHop attributes could improve things. I've placed the patch at paste #97, and you additionally need: http://yt.enzotools.org/files/hop_numpy.h If y'all get a chance to look at it, see if it cuts down on memory usage at all, that'd be awesome. We're currently running a bunch of tests. If it works out, we're moving to this over the old method. -Matt

3 20

source keyword for slices
by Matthew Turk 20 Apr '09

20 Apr '09

Hi everyone, Do any of you now, or have you in the past, used the 'source' keyword as supplied to creation of a slice? I have successfully finished the parallelization of both cutting planes and slices, but to do the slices I had to (or chose to, really) move from a 2d domain decomp to a standard grid iterator; this means I got rid of source=. For 2.0, all the data objects will implement the correct protocol, so source will come back, but for 1.5 I'd like to put out a working parallel slice & cutting plane pair. But, I don't want to cut off anybody's legs. Thanks! -Matt

1 0

yt-dev April 2009