yt workshop 2012: A success!
by Matthew Turk
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
6 years, 11 months
Memory leaks and volume rendering
by John ZuHone
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
6 years, 11 months
support for particles in Orion
by j s oishi
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.
6 years, 11 months
error launching yt: __gnu_cxx::__concurrence_lock_error
by Jean-Claude Passy
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
6 years, 11 months
Problem with Orion data
by Andrew Myers
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
6 years, 12 months
Re: [yt-users] installing yt on mac OS bzlib issue
by David Riethmiller
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/
6 years, 12 months
Problem with bootstrap_dev
by Christopher Moody
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/001...
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.
6 years, 12 months
trouble with fisheye renderer
by Christine Simpson
Hey all,
I'm trying to use the fisheye renderer and am having some trouble. I've pasted the script and error here: http://pastebin.com/AUhSfsMS. I've already tried deleting the .harrays and .yt files and it didn't make a difference.
Christine
6 years, 12 months
Visualising new particle types
by Elizabeth Tasker
Hi,
I've added in some new particle types (I accidentally just typed
'peculiar' types... Freudian slip) to my last Enzo simulation and I'd
like to be able to visualise just those when I do a
p.modify["particles"]() .
Is that possible?
Elizabeth
6 years, 12 months
