Mailman 3 March 2011 - yt-users

yt user survey 2011
by j s oishi 22 Mar '11

22 Mar '11

Hi All, We'd like some feedback on your use and your opinions about the future of yt. It's really short, and no questions are mandatory, so feel free to fill in as many or as few as you'd like. Please visit https://spreadsheets.google.com/viewform?formkey=dGlFazdOcUtFbHJLVU80a2NGM3… and answer away. The last user survey was really useful for us to help make yt-2.0 what it was. The future of yt is looking really bright, and we'd like to ensure it is as useful as we can make it. If you'd like to get involved at any point in the development process, feel free to email yt-dev, or any member of the dev team individually. Thanks, and we look forward to hearing from you! Jeff

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mpi4py
by gso＠physics.ucsd.edu 22 Mar '11

22 Mar '11

Hi all, I was trying to use a script that calls yt.func.only_on_root to write the results to an output file if my script is ran in parallel, when it gave me the following: Traceback (most recent call last): File "QuantityTotal.py", line 127, in <module> yt.funcs.only_on_root(flush, "frames/StarFormationRate.txt", "%12.12e %12.12e %12.12e %12.12i %12.12e %12.12i %12.12i %12.12i %12.12i\n" % (yr, TotEmis, redshift, num_sources, 0, Ion10, IonE3, IonE5, num_star)) NameError: name 'yt' is not defined I was wondering if either I messed up an import or something similar since this script was from an older version of yt... with #from yt.config import ytcfg #ytcfg["lagos","serialize"] = "False" commented out at the top. I also thought that maybe because I was using only 1 processor so I tried this on multiple processors on Triton after installing mpi4py by hand, instead I got: from mpi4py import MPI ImportError: No module named mpi4py Traceback (most recent call last): File "QuantityTotal.py", line 6, in <module> from yt.mods import * File "/home/gso/TritonYT/src/yt-hg/yt/mods.py", line 44, in <module> from yt.data_objects.api import \ File "/home/gso/TritonYT/src/yt-hg/yt/data_objects/api.py", line 34, in <module> from hierarchy import \ File "/home/gso/TritonYT/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/home/gso/TritonYT/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 47, in <module> I used the same directory for both my YT installation and mpi4py, so I shouldn't have to change anything for my environment variables such as where the /lib and /bin are (dev yt 2.1 works fine in serial), so I'm not sure what's going on now. Has anyone else encountered anything similar? Are they two different problems or one of the same? From G.S.

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Re: [yt-users] memory required estimate
by Stephen Skory 18 Mar '11

18 Mar '11

Geoffrey, > File "ContourFinding.pyx", line 92, in > yt.utilities.amr_utils.construct_boundary_relationships > (yt/utilities/amr$ > IndexError: Out of bounds on buffer access (axis 0) I've just pushed a fix for this problem, go ahead and update. I actually fixed this a few days ago in my own branch. However, I was waiting to merge with the mainline because there are very alpha/non-functional things I'm working on in my branch that I am not ready to merge yet. Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

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memory required estimate
by gso＠physics.ucsd.edu 18 Mar '11

18 Mar '11

Hi everyone, I have a simple memory question... I was running my script that uses extract_connected_set on a tiny 64 cube test data and it worked fine (using the install script with python2.7), but when I tried it on a big 1024 cube dataset I got the error at the end of the email on a triton pdaf node 8 core 64GB of memory (was using only 1 core, only used more core for their memory). I believe I may have underestimated the amount of memory I needed. If I have am extract connected set on a derived field using two different fields on a 1024 cube, the memory I need: 1024^3 (number of cells) 2+1 (number of fields) 8 (double precision) multiplying those numbers gave me ~25GB of memory which I had, am I missing some other factors? From G.S. First pass100% |||||||||||||||||||||||||||||||||||||||||||||||| Time: 01:30:35 Calculating joins 0% | | ETA: --:--:-- Traceback (most recent call last): File "create_bubble.py", line 55, in <module> new_region = dd.extract_connected_sets(field, num_levels, ion_min, ion_max)[1][0] File "/home/gso/TritonYT/src/yt-hg/yt/data_objects/data_containers.py", line 2330, in extract_connected_sets cached_fields) File "/home/gso/TritonYT/src/yt-hg/yt/analysis_modules/level_sets/contour_finder.py", line 303, in identify_cont$ boundary_tree = amr_utils.construct_boundary_relationships(fd) File "ContourFinding.pyx", line 92, in yt.utilities.amr_utils.construct_boundary_relationships (yt/utilities/amr$ IndexError: Out of bounds on buffer access (axis 0)

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Install Script Upgrade to Python 2.7 - fix for OS X 10.6 compilation
by Matthew Turk 17 Mar '11

17 Mar '11

Hi all (Especially Emilio and Peng), >From some detective work by Emilio, Peng, Stephen Skory and myself, it looks like an upgrade to Python 2.7 fixes the installation issues on OSX 10.6. I have updated the install_script.sh for the *unstable* branch to use Python 2.7, along with an update to Mercurial 1.8.1 and HDF5 1.8.6. This new version of the install script also brings with it the yt-supplemental repository, which is a clearing house for several related repositories, including the documentation, cookbook, and some other small scripts. This is located in $YT_DEST/src/yt-supplemental , and it is being documented on a "kickstart" webpage that will act as a shorter version of the orientation documentation. yt 2.1 will be released relatively soon, and with it the stable repository will also move to Python 2.7. To get the install script for the development branch: $ wget http://hg.enzotools.org/yt/raw/yt/doc/install_script.sh $ bash install_script.sh If you want to upgrade to Python 2.7 now, it's recommended that you remove your existing yt installation directory and re-run the install script, as Python 2.7 will need new packages installed. Please note that yt does not require Python 2.7; upgrading is strictly optional at this point; if you do decide to upgrade, the commands "python2.6" scattered throughout the documentation will need to be changed to either "python2.7" or the newly added alias, "pyyt", which will point at the current python installation. If you run into any issues, please let me know. Best, Matt

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hierarchy file for light cone simulation
by Britton Smith 15 Mar '11

15 Mar '11

Hi everyone, I'm trying to make some projections of the data from the Santa Fe Light Cone simulation, but it's getting hung trying to parse the hierarchy file. After looking around, I noticed that the one dataset that I had success with has a different format for the hierarchy file than the ones that aren't working. The ones that are working have hierarchy files that look like this: Grid = 1 GridRank = 3 GridDimension = 134 70 70 GridStartIndex = 3 3 3 GridEndIndex = 130 66 66 GridLeftEdge = 0 0 0 GridRightEdge = 0.25 0.125 0.125 Time = 101.45398694554 SubgridsAreStatic = 0 NumberOfBaryonFields = 7 FieldType = 0 1 2 4 5 6 22 BaryonFileName = /dsgpfs/projects/enzo/ux453739/GC512_L7_New/RD0009/RD0009.cpu0000 CourantSafetyNumber = 0.400000 PPMFlatteningParameter = 0 PPMDiffusionParameter = 0 PPMSteepeningParameter = 0 NumberOfParticles = 445435 ParticleFileName = /dsgpfs/projects/enzo/ux453739/GC512_L7_New/RD0009/RD0009.cpu0000 GravityBoundaryType = 0 Pointer: Grid[1]->NextGridThisLevel = 2 The ones that aren't working have formats like this: Grid = 1 GridRank = 3 GridDimension = 134 70 70 GridStartIndex = 3 3 3 GridEndIndex = 130 66 66 GridLeftEdge = 0 0 0 GridRightEdge = 0.25 0.125 0.125 Time = 128.98486432526 SubgridsAreStatic = 0 FileName = RD0012.cpu0000 GroupName = /Grid00000001 NumberOfBaryonFields = 7 FieldType = 0 1 2 4 5 6 22 CourantSafetyNumber = 0.400000 PPMFlatteningParameter = 0 PPMDiffusionParameter = 0 PPMSteepeningParameter = 0 NumberOfParticles = 408561 GravityBoundaryType = 0 Pointer: Grid[1]->NextGridThisLevel = 2 The first type seems to be the standard. Is there anything I can do to make this nonstandard hierarchy format work with YT? Thanks, Britton

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Volume Rendering and Weighted Fields
by John ZuHone 14 Mar '11

14 Mar '11

Hi all, I have figured out how to do an off-axis projection using the camera interface, it was actually pretty straightforward. I'm primarily concerned with simulating X-ray images for clusters, and I would like to extend my process to projections of weighted quantities, say emission-weighted temperature (or "spectroscopic-like" temperature, which means weighting by dens*temp**(-alpha)). I imagine that I have to use MultiVariateTransferFunction for this... does anyone have a good example of how to do something like this? I've looked at the source code but the process is still not exactly transparent to me. Best, John ZuHone

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Re: [yt-users] Problem in simple volume rendering (yt-users Digest, Vol 36, Issue 18)
by Kuo-Chuan Pan 12 Mar '11

12 Mar '11

Dear Matt, Thank you very much for your quick reply. 1. The balck_center I found is back_center = [-0.28306926 -0.1132277 -0.39629696] 2. The physical size I used is from -8.2605e11 cm to 8.2605e11 cm (same for x,y,z directions) The domain is correctly printing when running my yt script yt INFO 2011-02-24 13:08:20,186 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11] yt INFO 2011-02-24 13:08:20,186 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11] 3. I set the width = 1 as used in the example code. (all value are the same as the example code, except center, c=[0.,0.,0.] and the datafile is the Flash output file) Thank you very much for your kindly assistance. Best, Kuo-Chuan I have got some warning from yt, but I think that may not relate to my problem. The whole output are listed as bellow: [kpan2@taranaki yt-scripts]$ ./ShowPlots.py yt WARNING 2011-02-24 13:21:00,791 Setting 1.0 in code units to be 1.0 cm yt WARNING 2011-02-24 13:21:00,793 No time units. Setting 1.0 = 1 second. yt INFO 2011-02-24 13:21:00,794 Parameters: current_time = 5635.73778789 yt ERROR 2011-02-24 13:21:00,794 Missing domain_dimensions in parameter file definition! yt INFO 2011-02-24 13:21:00,794 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11] yt INFO 2011-02-24 13:21:00,794 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11] yt INFO 2011-02-24 13:21:00,795 Parameters: cosmological_simulation = 0.0 yt WARNING 2011-02-24 13:21:00,795 Setting 1.0 in code units to be 1.0 cm yt WARNING 2011-02-24 13:21:00,795 No time units. Setting 1.0 = 1 second. Warning: invalid value encountered in sqrt Warning: invalid value encountered in sqrt Adding gaussian at -5.8560788466 with width 0.02 and colors (0.2867691866508944, 0.015686274509803921, 0.031372549019607843, 0.01) Adding gaussian at -4.32198464433 with width 0.02 and colors (0.23702881439314105, 0.20784313725490194, 0.41568627450980389, 0.025118864315095794) Adding gaussian at -2.78789044206 with width 0.02 and colors (0.40392156862745099, 0.40392156862745099, 0.80784313725490198, 0.063095734448019331) Adding gaussian at -1.25379623979 with width 0.02 and colors (0.59607843137254901, 0.59607843137254901, 0.59115561118064242, 0.15848931924611143) Adding gaussian at 0.280297962486 with width 0.02 and colors (0.792156862745098, 0.792156862745098, 0.21568627450980413, 0.39810717055349731) Adding gaussian at 1.81439216476 with width 0.02 and colors (0.98431372549019602, 0.98431372549019602, 0.94080651128375881, 1.0) THIS MANY GRIDS! 0| | ETA: --:--:-- Partitioning 100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 KC>>> back_center = [ 0.21693074 0.3867723 0.10370304] KC>>> bricks = [] KC>>> LE = [] Traceback (most recent call last): File "./ShowPlots.py", line 161, in <module> test.plotVR() File "./ShowPlots.py", line 126, in plotVR vp.ray_cast() File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 111, in ray_cast LE = na.array(LE) - self.back_center ValueError: shape mismatch: objects cannot be broadcast to a single shape Exception AttributeError: "'NoneType' object has no attribute 'chdir'" in <bound method ShowPlots.__del__ of <__main__.ShowPlots instance at 0x17bb3200>> ignored PS. (the lines with "KC>>>" are my debug outputs ) On Feb 24, 2011, at 1:11 PM, yt-users-request(a)lists.spacepope.org wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Problem in simple volume rendering (Kuo-Chuan Pan) > 2. Re: Problem in simple volume rendering (Matthew Turk) > 3. Forthon and yt installation problems. (Andrew Davis) > 4. Re: Forthon and yt installation problems. (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Feb 2011 04:12:18 -0600 > From: Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Problem in simple volume rendering > Message-ID: <7301A4B8-2601-4AFB-960D-D6CAC55F6D29(a)astro.illinois.edu> > Content-Type: text/plain; charset=us-ascii > > Dear Sir/Madam, > > I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering. > I followed the cookbook in: > > http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_renderi… > > However I got an error message: > > File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast > LE = na.array(LE) - self.back_center > ValueError: shape mismatch: objects cannot be broadcast to a single shape > > I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct. > I guess there are some problems when setting self.bricks. > > If anyone has any suggestions, I would be very happy to hear. > Thank you. > > Best regards, > Kuo-Chuan > > ------------------------------ > > Message: 2 > Date: Thu, 24 Feb 2011 07:49:45 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Cc: Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> > Subject: Re: [yt-users] Problem in simple volume rendering > Message-ID: > <AANLkTi=MeytZo=-7ENNgHs7KTeGmemtrT32CYUGYpep1(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Kuo-Chuan, > > Sorry to hear it didn't work for you! Do you think you could help us > out with a bit more information, and then we'll see if we can get it > working for you? > > * What is the exact value of back_center that you find? > * What is the physical size of your domain? > * What is the width you supplied to the volume_rendering object? > > It might also be easier if you could try it with the "Camera" > interface as described here: > > http://yt.enzotools.org/doc/visualizing/volume_rendering.html#volume-render… > > That should allow for a bit more flexibility in describing the scene, > and may help us narrow down the error. > > Best wishes, > > Matt > > On Thu, Feb 24, 2011 at 5:12 AM, Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> wrote: >> Dear Sir/Madam, >> >> I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering. >> I followed the cookbook in: >> >> ? ?http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rendering.py >> >> However I got an error message: >> >> ?File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast >> ? ?LE = na.array(LE) - self.back_center >> ValueError: shape mismatch: objects cannot be broadcast to a single shape >> >> I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct. >> I guess there are some problems when setting self.bricks. >> >> If anyone has any suggestions, I would be very happy to hear. >> Thank you. >> >> Best regards, >> Kuo-Chuan >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > ------------------------------ > > Message: 3 > Date: Thu, 24 Feb 2011 11:44:37 -0500 > From: Andrew Davis <andrew.davis(a)yale.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Forthon and yt installation problems. > Message-ID: <20110224114437.djff25pj404cc8sg(a)www.mail.yale.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi folks, > > I'm updating my yt to the latest version, and so I'm just starting from scratch > in installing everything on a local cluster. I am running into errors, however > with the install script (line 479). When running the script, I get the > following output regarding Forthon: > > Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4') > Doing yt update, wiping local changes and updating to branch stable > Installing yt > install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory > Failure. Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log. > > I haven't been able to find any directory called yt/utilities, which is probably > why it can't find it. > At the end of the yt_install.log file, I see the following error, which doesn't > seem to be related to the install error at first glance: > > abort: data/doc/install_script.sh.i@908327e16660: no match found! > /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno > 2] No such file or directory > > Any thoughts? > > Thanks, > andrew > > > ************************************************************* > ** Andrew J. Davis andrew.davis(a)yale.edu ** > ** Dept. of Astronomy 203-432-5119 ** > ** Yale University www.astro.yale.edu/adavis ** > ************************************************************* > > > > > > ------------------------------ > > Message: 4 > Date: Thu, 24 Feb 2011 11:51:38 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Forthon and yt installation problems. > Message-ID: > <AANLkTinvoEfjmRD1n80kk4=Ppmab9M3rGWdViwY_ta3z(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Andrew, > > Sorry about the problem -- this looks like an issue with our hg > server; I don't believe it's directly with Forthon. There's something > up with the webserver, so you should be able to do this: > > cd /home/ajd53/YT_NEW/yt-x86_64/src > rm -rf yt-hg > /home/ajd53/YT_NEW/yt-x86_64/bin/hg clone --pull --uncompressed > http://hg.enzotools.org/yt ./yt-hg > > and that *should* get you the full set of yt, and then re-run the > install script with no modifications. Please let me know if that > doesn't work. > > -Matt > > PS The webserver for serving hg has been an issue for a while now, and > I'm embarrassed by the problem. I had hoped to move us to a different > host several weeks ago, but we've been trying to get the username > "yt." I think I need to give up that particular goal and settle for > something different. I'll have an update on this soon. > > On Thu, Feb 24, 2011 at 11:44 AM, Andrew Davis <andrew.davis(a)yale.edu> wrote: >> Hi folks, >> >> I'm updating my yt to the latest version, and so I'm just starting from scratch >> in installing everything on a local cluster. ?I am running into errors, however >> with the install script (line 479). ?When running the script, I get the >> following output regarding Forthon: >> >> Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4') >> Doing yt update, wiping local changes and updating to branch stable >> Installing yt >> install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory >> Failure. ?Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log. >> >> I haven't been able to find any directory called yt/utilities, which is probably >> why it can't find it. >> At the end of the yt_install.log file, I see the following error, which doesn't >> seem to be related to the install error at first glance: >> >> abort: data/doc/install_script.sh.i@908327e16660: no match found! >> /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno >> 2] No such file or directory >> >> Any thoughts? >> >> Thanks, >> andrew >> >> >> ************************************************************* >> ** ?Andrew J. Davis ? ? ? ? ? ? andrew.davis(a)yale.edu ? ? ?** >> ** ?Dept. of Astronomy ? ? ? ? ?203-432-5119 ? ? ? ? ? ? ? ** >> ** ?Yale University ? ? ? ? ? ? www.astro.yale.edu/adavis ?** >> ************************************************************* >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > ------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > End of yt-users Digest, Vol 36, Issue 18 > ****************************************

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install problems
by Peng Oh 12 Mar '11

12 Mar '11

Hello, I just tried installing YT on my machine (Mac OS X 10.6.6) and ran into some problems. I attach my install log. Any help would be much appreciated. Thanks! Peng

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yt2.0 on OS X
by Emilio Romano-Diaz 11 Mar '11

11 Mar '11

Hi there, I'm trying to install yt-2.0 on my Intel MacBook3.1, OS X 10.6.6. I downloaded the script from the web site and tried the automated installation (I just added the enzo installation flag). I checked I have installed and running the gcc & g++ 4.2 compilers. However, the compilation crashes because it cannot find a module named _locale: File "/Users/millos/visualization/yt/yt-2.0/lib/python2.6/site-packages/mercurial/demandimport.py", line 85, in _demandimport return _origimport(name, globals, locals, fromlist) ImportError: No module named _locale /Users/millos/visualization/yt/yt-2.0/bin/python2.6: can't open file '/Users/millos/visualization/yt/yt-2.0/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory I looked for some info the installation doc but I didn't find anything. Perhaps I skipped some steps/info. I included at the end the full log-file. Could somebody help me with this issue? Thank you very much in advance. E

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