Mailman 3 March 2012 - yt-dev

2.4: Release and bug roundup
by Matthew Turk April 20, 2012

April 20, 2012

Hi all, A couple people have mentioned to me recently (in IRC and over email) that the stable branch is missing some fixes for FLASH and Enzo data. I'd like to start a discussion on wrapping up the dev cycle and moving for a 2.4 release. The showpoint of this release I believe will be improvements to volume rendering; more on that below. Here are the open, targeted bugs for 2.4: https://bitbucket.org/yt_analysis/yt/issues?status=new&status=open&mileston… These touch on a few major areas: * Minor improvements to reason and reason widgets: Adding vectors, layers (which should get postponed) a volume rendering widget (should get postponed) and a file open dialog (Nathan had been working a bit on that.) * FLASH updates to make it more user friendly: John Z and I had a brainstorming session after I spoke to some FLASH users last week, and I filled out tickets to try to address any remaining weak points. * Time Series updates: Nathan has made a few suggestions, and I'm going to implement them. I like where Time Series is going! * Volume rendering refactor (Sam, if you have a few minutes, could you give an update on what that includes and what it provides? This could be a great centerpiece of 2.4!) * Rockstar integration is incomplete and undocumented, but that may also be postponed. There are also a few bugs that need to be addressed: * MPI attributes now break pickling in some cases; I will address this * Ghost zone issues seem to be everywhere, as corner cases keep coming up. John W and I have spoken about this and we have an idea for how to fix it moving forward. * Quadproj scales poorly, but that'll be a bit of a tricky piece of work. Does anyone have any comments or ideas about these bugs, or want to tackle any of them? Are there any other concerns, or thoughts on this? How would aiming to release in a month from now sound? April 16 is a Monday, which would be a good day for a release. -Matt

2 3

Re: [yt-dev] Interacting with data in yt 3.0 (was Field units from code to code)
by Matthew Turk April 3, 2012

April 3, 2012

In general, I agree with the idea Nathan put out. (Also, I think this is a fine time to have a bikeshed discussion. Many of the underlying assumptions about how yt works were laid out a long time ago.) But, I'm not entirely sure I understand how different it would be -- conceptually, yes, I see what you're getting at, that we'd have a set number of attributes. In what I was thinking of for the geometry refactor so far I'm trying to get rid of the "hierarchy" as existing for every data set, and instead relying on what amounts to an object-finder and io-coordinator, which I'm calling a geometry handler. It sounds like what you would like is: 1) Get rid of accessing parameters with an implicit __getitem__ on the parameter file (i.e., pf["SomethingThatOnlyExistsInOneCode"]). I'm +10 on this. 2) Move units into the .units object (I'm mostly with Casey on this, but I think it should be a part of the field_info object) 3) Have things like current_time, domain_dimensions and so on move into basic_info and make them dict objects. I think of those, I'm in favor of one and two, but somewhat opposed to #3. Right now we have these attributes mandated for subclasses of StaticOutput: refine_by dimensionality current_time domain_dimensions domain_left_edge domain_right_edge unique_identifier current_redshift cosmological_simulation omega_matter omega_lambda hubble_constant The only ones here that I think would be okay to move out of properties would be the cosmology items, and even those I'm -0 on moving. But, in general, the idea of moving from this two-stage system of parameter file (rather than dataset) and hierarchy (rather than an implicitly-handled geometry) is something I am in support of. The geometry is something that should nearly *always* be handled by the backend, rather than by the user. So having the library require pf.h.sphere(...) is less than ideal, since it's exposing something relatively unfortunate (that building a hundred thousand grid objects can take some time). The main ways that the static output is interacted with: * Parameter information specific to a simulation code * Properties that yt needs to know about * To get at the hierarchy * Input to plot collections The main ways that the hierarchy is interacted with: * Getting data objects * Finding max * Statistics about the simulation * Inspecting individual grids (much less common use case now that it was before) All of these use cases are still valid, but I think it's clear that accessing individual grids and accessing simulation-specific parameters are not "generic" functions. What a lot of this discussion has really brought up for me is that we're talking about *generic* functionality, not code-specific functionality, and we right now do not have the best enumeration of functionality and where it lies. With the geometry_refactor, I'd like to consolidate functionality into the main "dataset" object. The geometry can still provide access to the individual grids (of course) but data objects, finding max, getting stats about the simulation, etc, should all go into the main dataset object, and the geometry handler can simply be created on the fly if necessary. This brings up two points, though -- 1) Does our method of instantiating objects still hold up? i.e., ds.sphere(...) and so on? Or does our dataset object then become overcrowded? I would also like to move *all* plotting objects into whatever we end up deciding is the location data containers come from, which for instance could look like ds.plot("slice", "x") (for instance, although we can bikeshed that later), which would return a plot window. 2) Datasets and time series should behave, if not identically, at least consistently in their APIs. Moving to a completely ds-mediated mechanism for generating, accessing and inspecting data opens up the ability to then construct very nice and simply proxy objects. As an example, while something this is currently technically possible with the current Time Series API, it's a bit tricky: ts = TimeSeriesData.from_filenames(...) plot = ts.plot("slice", "x", (100.0, 'au')) ts.seek(dt = (100, 'years')) plot.save() ts.seek(dt = (10, 'years')) plot.save() (The time-slider, as Tom likes to call it ...) In general, this idea of moving toward more thoughtful dataset-construction, rather than the hokey parameter file + hierarchy construction brings with it a mindset shift which I'd like to spread to the time series, which can continue to be a focus. What do you think? -Matt On Thu, Mar 29, 2012 at 7:08 PM, Casey W. Stark <caseywstark(a)gmail.com> wrote: > +1 on datasets, although I would like to see the unit object(s) at the field > level. > > > On Thu, Mar 29, 2012 at 4:04 PM, Cameron Hummels > <chummels(a)astro.columbia.edu> wrote: >> >> +1 on datasets. >> >> >> On 3/29/12 6:58 PM, Nathan Goldbaum wrote: >>> >>> +1. I'd also be up to help out with the sprint. Doing a virtual sprint >>> using a google hangout might help mitigate some of the distance problems. >>> >>> While we're brining up Enzo-isms that we should get rid of, I think it >>> might be a good idea to make a conceptual shift in the basic python UI. >>> Instead referring to the interface between the user and the data as a >>> parameter file, I think instead we should be talking about datasets. One >>> would instantiate a dataset just like we do now with parameter files: >>> >>> ds = load(filename) >>> >>> A dataset would also have some universal attributes which would present >>> themselves to the user as a dict, e.g. ds.units, ds.parameters, >>> ds.basic_info (like current_time, timestep, filename, and simulation code), >>> and ds.hierarchy (not sure how that would interfere with the geometry >>> refactor). >>> >>> This may be a paintibg the bike shed discussion, but I think this shift >>> will help new users understand how to access their data. Thoughts? >>> >>> On Mar 29, 2012, at 3:40 PM, Matthew Turk<matthewturk(a)gmail.com> wrote: >>> >>>> Hi Nathan and Casey, >>>> >>>> I agree with what both of you have said. The Orion/Nyx units should >>>> be made to be consistent, but more importantly I think we should >>>> continue breaking away from Enzo-isms in the code. >>>> >>>> As it stands, all of the universal fields call underlying Enzo-named >>>> aliases -- Density, ThermalEnergy, etc etc. I hope we can have a 3.0 >>>> out within a calendar year, hopefully by the end of this year. (I've >>>> been pushing on the geometry refactor, although recently other efforts >>>> have been paying off which has decreased my output there.) I am much, >>>> much less doubtful than Casey is that we cannot do this; in fact, I'm >>>> completely in favor of this and I think it would be relatively >>>> straightforward to implement. >>>> >>>> In the existing system we have a mechanism for aliasing fields. What >>>> we can do is provide an additional translation system where we >>>> enumerate the fields that are available for items in UniversalFields, >>>> and then construct aliases to those. This would mean changing what is >>>> aliased in existing non-Enzo frontends, and adding aliases in Enzo. >>>> The style of name Casey proposes is what I woudl also agree with: >>>> underscores, lower cases, and erring on the side of verbosity. The >>>> fields off hand that we would need to do this for (in their current >>>> enzo-isms): >>>> >>>> x-velocity => velocity_x (same for y, z) >>>> Density => density >>>> TotalEnergy => ? >>>> GasEnergy => thermal_energy_specific (and thermal_energy_density) >>>> Temperature => temperature >>>> >>>> and so on. >>>> >>>> Once we have these aliases in place, an overall cleanup of >>>> UniversalFields should take place. One place we should clean up is >>>> ensuring that there are no conditionals; rather than conditionals >>>> inside the functions, we should place those conditionals inside the >>>> parameter file types. So for instance, if you have a field that is >>>> calculated differently depending on the parameter HydroMethod (in Enzo >>>> for instance) you simply set a validator on the field requiring the >>>> parameter be set to a particular value, and then only the field which >>>> satisfies that validator will be called when requested. >>>> >>>> So we've gotten rid of a bunch of enzo-isms in the parameter files; >>>> after fields, what else can we address? And, I'd be up for sprinting >>>> on this (which should take just a few hours) basically any time next >>>> week or after. I'd also be up for talking more about geometry >>>> refactoring, if anyone is interested, but it's not quite to the point >>>> that I think I am satisfied enough with the architecture to request >>>> input / contributions. Sometimes (especially with big architectural >>>> things like this) I think it's a shame we do all of our work >>>> virtually, as I think a lot of this would be easier to bang out in >>>> person for a couple hours. >>>> >>>> -Matt >>>> >>>> On Wed, Mar 28, 2012 at 6:14 PM, Casey W. Stark<caseywstark(a)gmail.com> >>>> wrote: >>>>> >>>>> Hi Nathan. >>>>> >>>>> I'm also worried about this and I agree that fields with the same name >>>>> should all be consistent. I would support some sort of cleanup of >>>>> frontend >>>>> fields, and I can get the Nyx fields in line and help with Enzo. >>>>> >>>>> I doubt we can do this, but I would prefer changing the field names as >>>>> part >>>>> of the removing enzo-isms and geometry handling refactoring pushes. For >>>>> instance, the field in Orion could be thermal_energy_density and the >>>>> field >>>>> in Enzo could be specific_thermal_energy. I also noticed this issue >>>>> when I >>>>> was using "Density" in Enzo (proper density in cgs) and "density" in >>>>> Nyx >>>>> (comoving density in cgs). >>>>> >>>>> Best, >>>>> Casey >>>>> >>>>> >>>>> On Wed, Mar 28, 2012 at 1:47 PM, Nathan Goldbaum<goldbaum(a)ucolick.org> >>>>> wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> On IRC today we noticed that Orion defines its ThermalEnergy field per >>>>>> unit volume but Enzo and FLASH define ThermalEnergy per unit mass. Is >>>>>> this >>>>>> a problem? Since yt defaults to the Enzo field names, should we try >>>>>> to make >>>>>> sure that all fields are defined using the same units as in Enzo? Is >>>>>> there >>>>>> a convention for how different codes should define derived fields that >>>>>> are >>>>>> aliased to Enzo fields? >>>>>> >>>>>> One problem for this particular example is that the Pressure field is >>>>>> defined in terms of ThermalEnergy in universal_fields.py so the units >>>>>> of >>>>>> ThermalEnergy become important if a user merely wants the gas pressure >>>>>> in >>>>>> the simulation. >>>>>> >>>>>> One possible solution for this issue would be the units overhaul we're >>>>>> planning. If all fields are associated with a unit object, we can >>>>>> simply >>>>>> query the units to ensure that units are taken care of correctly and >>>>>> code-to-code comparisons aren't sensitive to the units chosen for >>>>>> fields in >>>>>> the frontend. >>>>>> >>>>>> Personally, I think it would be best if we could make sure that all of >>>>>> the >>>>>> fields aliased to Enzo fields have the same units. >>>>>> >>>>>> Nathan Goldbaum >>>>>> Graduate Student >>>>>> Astronomy& Astrophysics, UCSC >>>>>> >>>>>> goldbaum(a)ucolick.org >>>>>> http://www.ucolick.org/~goldbaum >>>>>> >>>>>> _______________________________________________ >>>>>> yt-dev mailing list >>>>>> yt-dev(a)lists.spacepope.org >>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> yt-dev mailing list >>>>> yt-dev(a)lists.spacepope.org >>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>>> >>>> _______________________________________________ >>>> yt-dev mailing list >>>> yt-dev(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>>> >>>> !DSPAM:10175,4f74e5073356450621218! >>>> >>> _______________________________________________ >>> yt-dev mailing list >>> yt-dev(a)lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> _______________________________________________ >> yt-dev mailing list >> yt-dev(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org > > > > _______________________________________________ > yt-dev mailing list > yt-dev(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >

5 12

Install script issue
by Andrew Myers April 3, 2012

April 3, 2012

Hello yt developers, I don't know if this is a "bug," exactly, but I noticed an issue when doing a clean install of yt today involving the h5py install. Namely, it looks like if you have an non-empty CFLAGS environment variable (which can happen without your knowledge if you load certain module files in a supercomputing environment, for example), the h5py build will proceed without getting the "-fno-strict-aliasing" flag and the resulting module will not work. You can get around this either by 1) clobbering CFLAGS, or 2) adding "-fno-strict-aliasing" to it and re-running the script. It seems like the install script should either detect this and work around it, or else warn you that the h5py build has gone of the rails after the installation, because the tracebacks you get from trying to use the whacked-out h5py module are not very illuminating. I would do this myself, but I'm not sure my shell scripting skills are up to the task. Thanks, Andrew

2 4

Field units from code to code
by Nathan Goldbaum March 30, 2012

March 30, 2012

Hi all, On IRC today we noticed that Orion defines its ThermalEnergy field per unit volume but Enzo and FLASH define ThermalEnergy per unit mass. Is this a problem? Since yt defaults to the Enzo field names, should we try to make sure that all fields are defined using the same units as in Enzo? Is there a convention for how different codes should define derived fields that are aliased to Enzo fields? One problem for this particular example is that the Pressure field is defined in terms of ThermalEnergy in universal_fields.py so the units of ThermalEnergy become important if a user merely wants the gas pressure in the simulation. One possible solution for this issue would be the units overhaul we're planning. If all fields are associated with a unit object, we can simply query the units to ensure that units are taken care of correctly and code-to-code comparisons aren't sensitive to the units chosen for fields in the frontend. Personally, I think it would be best if we could make sure that all of the fields aliased to Enzo fields have the same units. Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

5 7

yt in Macports
by Erica Rosenblum March 26, 2012

March 26, 2012

Hi all, I tried using macports to install yt and ran into a couple of issues. First, there was a conflict because I had hdf5 installed to use flash and yt required hdf5-18. Secondly, after uninstalling hdf5 to see what would happen, I received these errors: Error: Checksum (md5) mismatch for yt-2.2.tar.gz Error: Checksum (sha1) mismatch for yt-2.2.tar.gz Error: Checksum (rmd160) mismatch for yt-2.2.tar.gz Error: Target org.macports.checksum returned: Unable to verify file checksums Error: Status 1 encountered during processing. Any ideas? Thanks! Erica

4 4

(Fun!) Call for testing: Alpha version of the yt data hub
by Matthew Turk March 24, 2012

March 24, 2012

Hi all, This cycle I applied to Amazon Research, and last week I received notice that the grant was accepted (woo hoo!) Using the AWS credits, I've been able to deploy an alpha version of a "data hub" on Amazon EC2. It's nearly fully backed by S3, SimpleDB and EC2 (only user authentication is stored on the instance, which I'd like to change eventually.) The idea behind this is to make an easy way to share *data*, not just images, scripts, and so on. It's not designed to be robust for many years (like a proper archiving solution would be) and it's not designed to be fully generic, but rather it's designed ... as a pastebin for data. You construct a widget, a representation of a data object, and then you can shove it up there and display the data through the widget. Right now it contains widgets for: * 3D Vertices, displayed with WebGL * Variable mesh maps (i.e., the mapserver) * Image collections * Parameter files There are a number of places where it's not yet finished: the vertices and image collections haven't been wrapped into yt proper but as it stands, yt can upload both parameter files and variable mesh (slices, projections) really easily. The Data Hub has been deployed here: https://data.yt-project.org/ and some example scripts are here: https://bitbucket.org/MatthewTurk/yt.hub_examples/ You might get errors about the certificate, which is self-signed, or about loading non-secure content (the XTK source for the 3D models), and you'll *probably* be able to crash the view or get a "Server incorrectly configured" error. It's still pretty early! But I'd like to request that you try hammering on this, try uploading data, and I would really appreciate any help with design, coding, new widgets, etc. The source is at http://bitbucket.org/MatthewTurk/yt.hub/ . As you'll find, it's still a bit hacked together, but I am interested in continuing to refine it, make it look better and nicer, and to ensure that it's maintainable. (If you are interested in this, fork away!) Any feedback would be *greatly* appreciated. I'm pretty excited about using this for collaboration and data sharing! Down the road I could see adding on more functionality like synchronized views, annotations (halos, points of interest, etc), 3D volumes (for phase plots) and on and on and on. In fact, this could be a way to share results with collaborators from a running simulation. Better than feedback, though, would be if you tried it out -- and uploaded some data! -Matt PS The variable mesh maps should work on phones and tablets. :)

2 1

missing objects using parallel_objects()
by Geoffrey So March 23, 2012

March 23, 2012

Hi everyone, I am trying to improve the efficiency of my analysis script which calculates attributes of haloes, after watching the workshop video on YT parallelism I was motivated to give parallel_objects a try. I am basically trying to calculate, then output some properties of each haloes found by parallel HOP. It turns out that even if I just output the (DM particles) mass of each halo, I am missing halo(s). It doesn't matter if I run this in serial or parallel, I end up missing the same amount of haloes if I use parallel_objects() like: haloes = LoadHaloes(pf, HaloListname) for sto, halo in parallel_objects(haloes, num_procs, storage = my_storage): to iterate over the haloes, and the problem goes away if I just switch to: for halo in haloes: I noticed this when I tried it on an 800 cube dataset with around 50k haloes, I only get 4k haloes in return, I then tried to narrow things down, and it ruled out the way I am calculating the attributes, because I can just output the mass from halo.total_mass() that was basically read in from the .h5 file and I'd end up missing halo using the parallel_objects. For 128 cube dataset with 85 haloes, I'd end up missing 3 and get 82 back, and for 64 cube dataset with 22 haloes, I'd get back 21 haloes. Has anyone else encountered this behavior or can confirm it? From G.S.

3 7

merger tree
by Stephen Skory March 23, 2012

March 23, 2012

Hi all, after chatting with Britton on IRC a few days ago, I pushed some changes that keeps the SQLite I/O on the root task only. Previously only the O was on the root task, but all tasks did the I. This change was done to hopefully A) speed things up with fewer tasks reading off disk and B) reduce memory usage with fopen()s and such. In my limited testing I saw a small increase in speed on 26 data dumps (something like 3m50s to 3m35s) excluding/precomputing the halo finding step. But this was on a machine with a good disk and there was no chance of running out of memory. The point of this email is as follows. After Britton had his problems, I re-acquainted myself with the merger tree code, and I realized there is a bit of a problem with the way it works. In brief, in order to reduce the amount of SQLite interaction on disk, which is slow, the results of the merger tree (namely the halo->halo relationships) are not written to disk until the very end. It's kept in memory up that point. This means that if the merger tree process is killed before the information is saved to disk, everything is lost. As I see it, there are a couple solutions to this. 1. When the halo relationships are saved, what actually happens is the existing halo database is read in, and a new one is written out, and in the process the just computed halo relationships are inserted into the new database. This is done because SELECT (on old) and then INSERT (on new) is magnitudes times faster than UPDATE (on old) on databases. I could change things such that this process is done after every new set of halo relationships is found between pairs of data dumps. Then, if the merger tree is killed prior to completion, not all work is lost. 2. Add a TTL parameter to MergerTree(). When the runtime of the merger tree approaches this number, it will stop what it's doing, and write out what it has so far. In both cases, restarts would just check to see what work has been done already, and continue on from there. For those of you who care, which do you think is a better solution? #1 is a bit less work for a user, but #2 is likely faster by some disk-dependent amount. -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

2 2

Question regarding changeset 71c2bfaa3b5f in yt on ghostzone calculations
by Cameron Hummels March 23, 2012

March 23, 2012

Hey everyone (but specifically John Wise), I just pulled to the newest version of yt, and I got significantly different behavior from some old scripts of mine which use yt than I did prior to the pull. I bisected the changesets to the one making the big difference for me, and it was your commit: 71c2bfaa3b5f from late January. Specifically, I'm doing some off axis projections which use the volume rendering interface and ghost zones. I homogenize my volume, then take a snapshot of the interior. When I do this with my old code, it takes about 20 seconds to partition and homogenize the volume, but now it takes over 10 minutes to partition the volume (I actually kill it at 10 minutes), and it uses so much memory that all of my other programs grind to a halt on a relatively big memory machine. I was wondering if you (or anyone else on the list) encountered any problems in volume rendering with ghost zones since this changeset (i.e. the last two months), or if you can think of any obvious reasons why there would be such a slow down? I know you're out of town right now, but I figured I'd send this to the list anyway to see if anyone else had experienced slowdowns. Thanks for the help! Cameron

2 1

embarrassingly parallel analysis
by Geoffrey So March 17, 2012

March 17, 2012

Hi all, I was trying out pobj_demo.py from the workshop to see if I can parallelize my halo analysis script, but I ran into the problem where I see: >mpirun -n 2 python pobj_demo.py --parallel gives a warning at the end yt : [WARNING ] 2012-03-16 16:25:05,445 parallel_objects() is being used when parallel_capable is false. The loop is not being run in parallel. This may not be what was expected. I've done a yt instinfo -u and got the latest tip: 052fac826701 (yt) tip but the problem persists. I've tried printing inside the parallel loops for sto, sp in parallel_objects(spheres, num_procs, storage = my_storage): print ytcfg.getint("yt", "__global_parallel_rank") sto.result = sp.quantities['TotalQuantity']('CellMass') sto.result_id = '%4e %4e %4e' % (sp.center[0], sp.center[1],sp.center[2]) and I always get "0", but 20 of them, so I'm guessing that confirms the loop isn't running in parallel, and just runs the 10 spheres serially on 2 processors, so I get double the results. Am I doing something wrong or missed something? From G.S.

2 3