Mailman 3 November 2011 - yt-dev

QC for 2.3 release
by j s oishi Dec. 1, 2011

Dec. 1, 2011

Hi All, Per today's developer meeting, we decided on a 15 Dec 2011 release date for 2.3. The only remaining outstanding tickets concern documentation, and we want to ensure that the documentation undergoes some kind of quality control before the release. Unlike the code itself, which can (and will) be submitted to automated answer testing, the documentation will need to be tested by actual humans. We decided the best way to go about this would be to have a potential pull request acceptor first test the documentation by reading it and attempting to use the new feature before accepting. This shouldn't take too long, and should ideally be done using the acceptor's own data (to ensure that at least some modification of the script is taking place). If there are any questions or comments about this, let me know. If people not in the meeting this morning are satisfied with this, we'll just adopt it as we go to close the tickets sam has added here: https://bitbucket.org/yt_analysis/yt/issues?status=new&status=open&mileston… thanks, j

2 2

Contributing to the documentation
by Christopher Moody Nov. 24, 2011

Nov. 24, 2011

Hi folks, It's been a while now that I've been using the Sunrise exporter that Matt wrote a long time ago, and I've written up a bit of documentation (and troubleshooting) on how to actually go about using it. How do I post this to the yt documentation website? What section does it go in, analysis modules? Cookbook? Thanks! chris

3 2

hg clarification
by Geoffrey So Nov. 24, 2011

Nov. 24, 2011

Since I screwed up forking yt last time (wanted dev but got stable), I didn't want to repeat my mistake, so I need someone to check my findings. I went to http://yt-project.org/ and clicked on "Fork us on BitBucket!" and it brought me to BitBucket page with a name "yt" and a specific tip of 4ec73cabefb6 But it doesn't say anything about if it is the stable or dev branch. I then went and looked at the two install scripts available, and found that the variable $(BRANCH) is "stable" or "yt", so I am guessing after I forked on BitBucket, I need to do the following # update the local branch to dev branch named "yt" hg up -C yt # commit the change on local machine hg commit -m "" # push the change of branch up to the fork in BitBucket hg push to switch the yt I just forked from whatever branch it is in right now into the dev branch of yt named "yt" Is that correct? If that is the case, I think last time I did the fork but didn't switch branches, and it defaulted to the stable branch. From G.S.

2 1

Off-axis projections -- Discrepancies between homogenized volume vs KDtree methods
by Cameron Hummels Nov. 22, 2011

Nov. 22, 2011

Hello peeps (mostly Britton, Matt and Sam), I have recently been doing some off-axis projections in my cosmological runs (using the supercool new off_axis_projection helper function Matt wrote), and I've encountered some problems. I find different results when I do the off-axis projection using a homogenized volume versus when I do not use a homogenized volume (when it uses the default behavior for camera objects -- ie a KDtree). Of course, these two results should be identical, and they are when I use a normal field like "Density". However, I'm trying to use a derived field from some code Britton wrote, part of a package called ion_balance, which creates derived fields for different atomic ions. So when I compare the CIV Number Density from these two methods, I get very different results. Even when I do this on a normal vanilla yt field, like "Density", the KDtree method takes exceptionally longer than the homogenized volume method (I think this is because I'm only doing the HV for a small subsample of the overall volume). On the other hand, they both take about the same amount of time when my sample volume is the entire box volume. I've pastebinned a demonstration script which shows this discrepancy at: http://paste.yt-project.org/show/1953. If you don't have ion_balance, you can comment that import out, and comment the line for defining the field as "CIV_Cloudy_eq_NumberDensity", and run it to see the time discrepancy between the two methods. It should work on any sort of parameter file, not just the specific one I'm using. What I do is take an off-axis projection using each method, then divide the two images against each other to form a ratio image, and then output the average and stddev for this ratio. The average of the ratio is: 2e-8. I've changed the width of the off-axis projection and it has a minimal (but nonzero) change on the overall ratio between the two. So I'm not sure what to do. It appears that the CIV field is initiated in the same way that a normal field is, with the projection_conversion set to 'cm', just as it is for "Density". Any ideas on what could be making this difference? Any ideas on which is the value to trust? Cameron

4 4

Re: [yt-dev] Memory leak issue with ParallelHOP code
by Patel, Pragneshkumar B Nov. 22, 2011

Nov. 22, 2011

________________________________ From: Patel, Pragneshkumar B Sent: Thursday, November 17, 2011 12:18 PM To: Britton Smith Cc: Geoffrey So; s(a)skory.us Subject: RE: [yt-dev] Memory leak issue with ParallelHOP code Hi Britton, I have subscribed to both yt-users and yt-dev. It may possible my requests are pending. As far as dataset is concern, Geoffrey can give you better explanation about it. Dataset contains 0-64 regions. I tried to run ParallelHOP with all regions but because of memory issue, I could not able to complete all in once. Then I ran it with only 0-3 regions to debug code "parallel_hop_interface.py". Please also find attached script. Let me know, if you have more questions. Thanks Pragnesh ________________________________ From: Britton Smith [brittonsmith(a)gmail.com] Sent: Thursday, November 17, 2011 12:00 PM To: yt-dev(a)lists.spacepope.org Cc: Patel, Pragneshkumar B Subject: Re: [yt-dev] Memory leak issue with ParallelHOP code Hi again Pragnesh, I mistakenly asked you to post this to the enzo-users mailing when I meant to say that you should post this to the yt-users mailing list. Sorry about that, not enough coffee this morning. Britton On Thu, Nov 17, 2011 at 8:56 AM, Britton Smith <brittonsmith(a)gmail.com<mailto:brittonsmith@gmail.com>> wrote: Hi Pragnesh, You need to provide us with some more information. What do you mean when you say you ran for 0-3 regions? What kind of dataset are you trying to analyze? How big is it? Can you also please post the script you are using for this? Finally, could you please sign up for the enzo-users mailing list and post this there? You've posted this to the development list, which isn't the best forum for this question. Also, if you're not on the list you won't receive any of the responses to your post. Britton On Thu, Nov 17, 2011 at 7:29 AM, Patel, Pragneshkumar B <pragnesh(a)utk.edu<mailto:pragnesh@utk.edu>> wrote: Hi Stephen, I found memory leak issue, when I ran Parallel_HOP code. It may not be in python itself but may be in packages(e.g. kdtree etc..), which we call from"parallel_hop_interface.py". Please find attach file, in which you see memory keep increase in every region (I ran program with 32 processes for 0-3 regions.) I like to get your comments/suggestions to solve this issue. I am trying to find more about it using Valgrind. I will let you know. Thanks Pragnesh _______________________________________________ yt-dev mailing list yt-dev(a)lists.spacepope.org<mailto:yt-dev@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org

4 9

PR 34
by Stephen Skory Nov. 18, 2011

Nov. 18, 2011

Hi all, can I get an up/down/suggestions vote on pull request 34? It's just one line, it's been there for three days, and I think it's useful. The only thing I might see as a better alternative is for Clump to inherit from AMR3DData, but that is a bigger change, and not necessarily better. Thanks! https://bitbucket.org/yt_analysis/yt/pull-request/34/quantities-for-clumps -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

3 3

Adding tracer particles
by david collins Nov. 18, 2011

Nov. 18, 2011

Hi, all-- I'm interested in adding a flock of tracer particles to an existing simulation. Has anyone done such a thing? If not I can drop what I come up with onto yt-hub, if anyone else is interested. d. -- Sent from my computer.

3 3

Memory leak issue with ParallelHOP code
by Patel, Pragneshkumar B Nov. 17, 2011

Nov. 17, 2011

Hi Stephen, I found memory leak issue, when I ran Parallel_HOP code. It may not be in python itself but may be in packages(e.g. kdtree etc..), which we call from"parallel_hop_interface.py". Please find attach file, in which you see memory keep increase in every region (I ran program with 32 processes for 0-3 regions.) I like to get your comments/suggestions to solve this issue. I am trying to find more about it using Valgrind. I will let you know. Thanks Pragnesh

2 2

confusion about tickets
by j s oishi Nov. 16, 2011

Nov. 16, 2011

Hi all, I just accepted yt-doc PR #7, https://bitbucket.org/yt_analysis/yt-doc/pull-request/7/parallel-docs-impro… which solves some of the parallel documentation, but not all of it, as is my understanding. Sam, you were going to document multilevel parallelism before we close issue #330 (https://bitbucket.org/yt_analysis/yt/issue/330/multilevel-parallelism), right? However, does this completely close issue #247 (https://bitbucket.org/yt_analysis/yt/issue/247/estimates-of-resources-for-p… If so, I'll close that ticket forthwith. thanks, j

2 2

yt devel documentation
by Geoffrey So Nov. 16, 2011

Nov. 16, 2011

Hi all, Catching up on some missed emails, I realized that to be able to implement a feature I'm still missing the documentation (and fixing my fork from stable to devel). I was looking on the site under developer's guide, and I didn't see any references as to how to edit the documentation. I found a README asking us to go to the repo http://hg.yt-project.org/yt-doc/ I was wondering how one should go about editing, then submitting changes to the doc? Do we do the same with YT: -fork yt-doc -edit yt-doc -commit to local repo -submit pull request From G.S. --be learning how to use Sphinx in the mean time

2 2