yt-users January 2012

yt-users@python.org

20 participants
16 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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problem with fields that use ghost zones
by Britton Smith 29 May '12

29 May '12

Hi everyone, I'm having a problem using fields that use ghost zones. The following simple script: http://paste.yt-project.org/show/2010/ gives this error: http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/ I am working from the tip, but I get the same behavior from yt/2.3. In yt/2.2, everything is working. I am working now to narrow that range down a bit, but does anyone have an idea? Britton

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yt workshop 2012: A success!
by Matthew Turk 31 Jan '12

31 Jan '12

Hi all, The yt workshop last week in Chicago ( http://yt-project.org/workshop2012/ ) was an enormous success. On behalf of the organizing and technical committees, I'd like to specifically thank the FLASH Center, particularly Don Lamb, Mila Kuntu, Carrie Eder, for their hospitality; the venue was outstanding and their hospitality touching. Additionally, we're very grateful to the Adler Planetarium's Doug Roberts and Mark SubbaRao for hosting us on Wednesday evening -- seeing the planetarium show as well as volume renderings made by yt users up on the dome was so much fun. The yt workshop was supported by NSF Grant 1214147. Thanks to everyone who attended -- your energy and excitement helped make it a success. Thanks also to the organizing and technical committees: Britton Smith, John ZuHone, Brian O'Shea, Jeff Oishi, Stephen Skory, Sam Skillman, and Cameron Hummels. All talks have been recorded, and you can clone a unified repository of talk slides and worked examples: hg clone https://bitbucket.org/yt_analysis/workshop2012/ A few photos have been put up online, too: http://goo.gl/g02uP As I am able to edit and upload talks, they'll appear on the yt youtube channel as well as on the yt homepage: http://www.youtube.com/ytanalysis Thanks again, and wow, what a week! Matt

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Memory leaks and volume rendering
by John ZuHone 29 Jan '12

29 Jan '12

Hi all, I'm volume rendering a ~1 GB dataset on an 8 CPU machine with 32 GB of RAM. I keep using up the memory on the machine with the following script, which creates a time series object and runs through the pfs to create each image. Is there other memory I should be freeing up at each iteration in the loop? http://paste.yt-project.org/show/2137/ Best, John

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support for particles in Orion
by j s oishi 27 Jan '12

27 Jan '12

Hi All, I'm quite pleased to announce that Orion's StarParticles are now supported by yt, thanks to Andrew Myers. It would be great if any Orion users could test them. You can find this in the unstable repository, at https://bitbucket.org/yt_analysis/yt Thanks, Andrew! j ps--the wiki has been updated to reflect the now full support for orion.

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error launching yt: __gnu_cxx::__concurrence_lock_error
by Jean-Claude Passy 26 Jan '12

26 Jan '12

Hi all, I am encountering a weird error when trying to execute yt-unstable on my MacBook Pro (10.6.8): ---------------------------------------------------------------- [13:26:06] Obiwan:$ iyt terminate called after throwing an instance of '__gnu_cxx::__concurrence_lock_error' what(): __gnu_cxx::__concurrence_lock_error Abort trap ---------------------------------------------------------------- I re-installed everything successfully but the error is still there. Any help will be much appreciated! Thanks a lot, JC

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Problem with Orion data
by Andrew Myers 25 Jan '12

25 Jan '12

Hello All, It looks like there is a problem with the current stable version of yt that comes up when creating a PlotCollection using Orion datasets. See the script here <http://paste.yt-project.org/show/t02maMs6OShv1uGJbOLu/> and the traceback here. <http://paste.yt-project.org/show/zAgcYyrKH2vmv4ZaQJQ5/> I think the fix is that there needs to be the line self.field_info = pf.field_info somewhere in the constructor for OrionHierarchy (around line 120 of yt/frontends/orion/data_structures.py). It looks like a line like this used to be here, but was removed during some code cleanup. If the other Orion users are anything like me, they haven't updated yt in a while and thus haven't noticed the problem. Glancing at the Nyx, Maestro, and Castro frontends, those look like they might suffer from the same issue, but I don't have any of their data to confirm or deny this. -Andrew Myers

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Re: [yt-users] installing yt on mac OS bzlib issue
by David Riethmiller 25 Jan '12

25 Jan '12

Hi all - Did the archived solution below work for you? I'm trying to install and having exactly the same issue, and this doesn't seem to solve my problem. I'm running OSX 10.5, and my default version of gcc is 4.0.1: % gcc -v Using built-in specs. Target: i686-apple-darwin9 Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable-checking -enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/lib --build=i686-apple-darwin9 --with-arch=apple --with-tune=generic --host=i686-apple-darwin9 --target=i686-apple-darwin9 Thread model: posix gcc version 4.0.1 (Apple Inc. build 5465) I've installed gcc-4.2, but it won't take the "-shared" flag. % gcc-4.2 -v Using built-in specs. Target: i686-apple-darwin9 Configured with: ../gcc-4.2.4/configure --prefix=/sw --prefix=/sw/lib/gcc4.2 --mandir=/sw/share/man --infodir=/sw/share/info --enable-languages=c,c++,fortran,objc,java --with-arch=nocona --with-tune=generic --host=i686-apple-darwin9 --with-gmp=/sw --with-libiconv-prefix=/sw --with-system-zlib --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --disable-libjava-multilib Thread model: posix gcc version 4.2.4 Using either gcc-4.0.1 or gcc-4.2, I still get a compilation error that it couldn't find main: % make -f Makefile-libbz2_so CFLAGS=-fPIC LDFLAGS=-fPIC PREFIX=/Users/rieth/yt_analysis gcc -shared -Wl,-install_name -Wl,libbz2.so.1.0 -o libbz2.so.1.0.4 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o Undefined symbols: "_main", referenced from: start in crt1.10.5.o ld: symbol(s) not found collect2: ld returned 1 exit status make: *** [all] Error 1 I'm sure I'm doing something really stupid, but I can't figure out what it is. Can anyone help? (Also, sorry for the cut-and-paste; I couldn't figure out how to reply directly to the archived post.) Thanks, Dave -------------------------------------------------------------------- Matthew Turk wrote: Hi JC, Are you setting CC and CXX to gcc-4.2 and g++-4.2, as the note in the install script mentions you might have to? I believe that it's getting the OSX gcc, which would use the "-bundle" argument, but it should instead be getting the old-school gcc-4.2, which accepts "-shared". -Matt On Wed, May 18, 2011 at 3:03 PM, Jean-Claude Passy<jcpassy at gmail.com <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> wrote: >/ Hi all, />/ />/ I am able to install yt on my Mac if I turn off the Bzlib option. When it is />/ turned on, the installation fails the following way: />/ />/ ----------------------------------------------------------------------------------------------------------------------------- />/ echo ".so man1/bzgrep.1"> />/ /Users/jean-claudepassy/Work/yt-i386/man/man1/bzegrep.1 echo ".so />/ man1/bzgrep.1"> /Users/jean-claudepassy/Work/yt-i386/man/man1/bzfgrep.1 />/ echo ".so man1/bzmore.1"> />/ /Users/jean-claudepassy/Work/yt-i386/man/man1/bzless.1 echo ".so />/ man1/bzdiff.1"> /Users/jean-claudepassy/Work/yt-i386/man/man1/bzcmp.1 gcc />/ -shared -Wl,-install_name -Wl,libbz2.so.1.0 -o libbz2.so.1.0.4 blocksort.o />/ huffman.o crct\ able.o randtable.o compress.o decompress.o bzlib.o Undefined />/ symbols: "_main", referenced from: start in crt1.10.5.o ld: />/ symbol(s) not found collect2: ld returned 1 exit status make: *** [all] />/ Error 1 />/ ----------------------------------------------------------------------------------------------------------------------------- />/ />/ Does anyone have an idea how to fix this ? />/ />/ Thanks a lot, />/ />/ JC />/ />/ _______________________________________________ />/ yt-users mailing list />/ yt-users at lists.spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> />/ http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org />/ /> -- ------------------------------------------------- David A. Riethmiller Ph.D. Candidate, Astrophysical Institute Ohio University Clippinger Labs 338 http://www.phy.ohiou.edu/~rieth/

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Problem with bootstrap_dev
by Christopher Moody 25 Jan '12

25 Jan '12

Hi all, I'm having a problem similar to what Sam ran into using bootstrap_dev, found here: http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2011-June/00167… Even with a pretty pristine yt install, neither pip nor easy_install successfully install the lxml pacakge. Thanks! chris error log: creating build/temp.linux-x86_64-2.7/src/lxml gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/zdata/cemoody/code/yt-chasm/include/python2.7 -c src/lxml/lxml.etree.c -o build/temp.linux-x86_64-2.7/src/lxml/lxml.etree.o -w In file included from src/lxml/lxml.etree.c:239:0: src/lxml/etree_defs.h:9:31: fatal error: libxml/xmlversion.h: No such file or directory compilation terminated. error: command 'gcc' failed with exit status 1 ---------------------------------------- Command /zdata/cemoody/code/yt-chasm/bin/python2.7 -c "import setuptools;__file__='/zdata/cemoody/code/yt-chasm/build/lxml/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --single-version-externally-managed --record /tmp/pip-r32BZP-record/install-record.txt failed with error code 1 Storing complete log in /home/cemoody/.pip/pip.log Unable to install lxml. Please report this bug to yt-users.

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yt-users January 2012