Mailman 3 March 2012 - yt-dev

Re: [yt-dev] profiles on non-prgio sets
by Matthew Turk March 16, 2012

March 16, 2012

Hi Dave, Are you running in parallel? Which fields are you profiling? Do they have lots of dependencies, or require ghost zones? Is yt using lazy_reader? Does your data have many grids? Matt On Mar 14, 2012 12:37 AM, "david collins" <antpuncher(a)gmail.com> wrote: > I should add that this was done on 64 cores-- in serial it works fine, > just slow. > > On Tue, Mar 13, 2012 at 9:35 PM, david collins <antpuncher(a)gmail.com> > wrote: > > Hi, all-- > > > > I have an old dataset that I'm trying to make profiles on. It's a > > 512^3 root grid, but was written with ParallelRootGridIO off. I find > > that it's using strange amounts of memory, more than 12 Gb. Is this a > > known problem with a straight forward work-around? > > > > d. > > > > -- > > Sent from my computer. > > > > -- > Sent from my computer. > _______________________________________________ > yt-dev mailing list > yt-dev(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >

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seg fault on projections
by Stephen Skory March 15, 2012

March 15, 2012

Hi all, I'm getting seg faults on a simple projection: pc = PlotCollection(pf) pc.add_projection("Density", 0) <seg fault> I used 'hg bisect' and tracked it down to this changeset: https://bitbucket.org/yt_analysis/yt/changeset/306232c75c58 If I replace yt/data_objects/static_output.py with the parent version bbb5aeca876f, the seg fault goes away. I see the seg fault, and the fix, on both Mac and Linux. Does anyone else see this issue? Thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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Projection issues
by david collins March 15, 2012

March 15, 2012

Hi again-- I have another odd issue, again stemming from with this vintage dataset. It's a 512^3 root with 4 levels, and a refinement by 4. When the parallel analysis gave me problems yesterday, I tried re-griding the data by restarting and forcing parallel root grid io on (including a removal of the rebuild hierarchy call to ensure the grids stay the same, and returning before any hydro is done.) The odd bit is now projections look different. Attached are two images, sphere_serial is through the old serial root grid run, sphere_parallel is through the output with parallel root grid io. Centered on the max, 0.02 in radius, Density projection. Projections were made using proj = pf.h.proj(ax,field,center=center,source=sphere) You can see that less structure seems to be captured in the parallel dataset. I've done two checks to make sure that it's not a glitch in the re-griding. First is the actual data-- the grids are in a different order from parallel to serial, but once that's taken into account all the data in subgrids is identical (at least in density, the field in question). Additionally the new tiles match the corresponding positions in the old tile. So the data itself is fine. The other test I did was to regrid, but leaving serial root grid io on-- new serial set is identical (except again for grid order) to the old, and the projections match. Differences also show up in profiles. Again, not a major problem, but it's pretty counter-intuitive, so I was wondering if anyone had run into this. d. -- Sent from my computer.

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profiles on non-prgio sets
by david collins March 14, 2012

March 14, 2012

Hi, all-- I have an old dataset that I'm trying to make profiles on. It's a 512^3 root grid, but was written with ParallelRootGridIO off. I find that it's using strange amounts of memory, more than 12 Gb. Is this a known problem with a straight forward work-around? d. -- Sent from my computer.

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EPS writer
by Geoffrey So March 13, 2012

March 13, 2012

Hi, I guess this question mainly goes to John Wise, I currently have two columns of data I am plotting with matplotlib calls, but if I save them as EPS the file size is ~1.5 MB instead of png as ~35KB, is there a simple way to save them as EPS format, with PNG graph but LaTeX text for the axis in YT? During your latest YT workshop talk, you showed how we can create EPS images using PlotCollection png phase graph with LaTeX text, which is exactly what I wanted to do for my publication to bring down the image file size... Except my graphs were created from 2 columns of data (derived using YT but plotted with matplotlib) and not the PlotCollection engine. Can the png be inserted to PlotCollection to take advantage of the EPS writer? Other suggestions, comments are welcomed (such as not even bother worrying about the file size, or this is beyond the scope of YT). From G.S. PS. I've tried using the cmap=gray in the imshow call, and that cuts the file size down to 0.5MB, but colored plots are so much nicer!

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Clumps, parallel
by david collins March 13, 2012

March 13, 2012

Hi, All-- What's the current state of the art with regard to parallel clump finding? Out of curiosity, I did a clumpfind blocked into octant, and I found super-linear scaling (non-scientific, my 512^3 wouldn't finish in 24 hours, but each octant ran in 30 minutes). Now I have these clumps, and I'd like to sew them together. So I have a couple questions: 1.) What's the easiest way to join two extracted sets? I figure I can take these 8 sets and sew them together pretty easy ex-post-facto. If there's a tool that does new_joined_thing = yt.join( clump1.data, clump2.data) then writing the machinery to sort out which clumps hit which faces is pretty easy, as is sewing together the various joined things into a clump hierarchy. 2.) Is there anything about the countour finder that would not block decompose like this? 3.) Has anyone made any progress on things like this? d. -- Sent from my computer.

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Support for FLASH particle files
by Nathan Goldbaum March 8, 2012

March 8, 2012

Hello all, I'm trying to add support for FLASH particle files. However, my particle files are nonstandard and so my particle reader may not work with the default particle types that come with FLASH. I'm curious if anyone would like to share a more vanilla particle file dataset so I can test my yt modifications. Thanks very much, Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

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trying out reason
by Geoffrey So March 6, 2012

March 6, 2012

Hi yt-dev, I was giving reason a spin, and everything went smoothly, I was able to launch reason on Nautilus and Lens, and I tried it out with Safari 5.1.1, Firefox 7.0.1, and Chrome 17.0.963.65 installed under OS X 10.7.2. I didn't want to bogged down the login nodes if I want to do a projection of an 800 cube Enzo data, so dd=pf.h.all_data() was as far as I got with the 800 cube. I get channel 3: open failed: connect failed: Connection refused When I tried it on an interactive node and using a browser trying to connect to the compute node. Is reason only limited to the login nodes due to supercomputer security with the compute nodes? From G.S.

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