Mailman 3 August 2012 - yt-users

xspec with yt python
by Eric Hallman 24 Aug '12

24 Aug '12

Hello, I know this is not a yt specific issue, however it involves an interaction of the yt installed python and XSPEC. Maybe some of you on this list have done an XSPEC install on Mac OS X (Lion in this case) and run into this. At link time during the build of XSPEC, it gives the following error: Undefined symbols for architecture x86_64: "_environ", referenced from: _initposix in libpython2.7.a(posixmodule.o) ld: symbol(s) not found for architecture x86_64 Originally on my Mac, XSPEC tried to build 32-bit, and failed with python linkages (since python is 64 bit in the yt install build). Once I went to 64-bit, this was the only remaining error. Does anyone have ideas? Thanks! Eric Hallman

2 1

Editing my own fork
by Carolyn Peruta 22 Aug '12

22 Aug '12

Hello all, I'm taking my first stab at editing my own fork of yt-dev and need some help. I'm trying to add several more species to the list in frontends/enzo/fields.py which act exactly like the fields already there. I've edited the code to add these new fields then ran "python setup.py develop" from the yt-hg directory. When I did this I never saw a message about compiling/building this edited file. When I load a data set it still treats my fields as 'unknown'. 1) Are there any other files I should be editing to add new species fields (akin to HII_Density)? 2) What is the proper way to build yt once I've made these changes? Thanks, Carolyn

2 2

How to fix "yt update"
by Matthew Turk 19 Aug '12

19 Aug '12

Hi all, Recently bitbucket has been having issues with DNS for custom domain names. If you have trouble running "yt update", you can fix this by editing the file: $YT_DEST/src/yt-hg/.hg/hgrc and replacing the line: default = http://hg.yt-project.org/yt/ with: default = https://bitbucket.org/yt_analysis/yt/ I've also uploaded a replacement .hgrc, if you want to swap it out: http://paste.yt-project.org/show/2653/ This should fix any issues you may have had with running "yt update" recently. We've changed over the domain name in the install script to avoid this coming up again. -Matt

1 0

Density/Column density along a ray
by Thomas Robitaille 19 Aug '12

19 Aug '12

Hi I'm still relatively new to yt, and I'm trying to figure out a way to extract the density along a ray joining two points. I've managed to make a plot using PlotCollection.add_ray, but I can't figure out how to get the actual data as a Numpy array. Also, I'd ultimately like to compute the cumulative column density along the ray, so I'd like to ensure that the sampling of distances along the ray is very fine to get an accurate column density. Is there a way to do this? Thanks for any help! Cheers, Tom

4 5

YT Installation Problem/Resolution
by Matt Malloy 15 Aug '12

15 Aug '12

Hello Everyone! I am extremely new to yt, and attempted to install it for the first time this morning. However, when doing so, I encountered a problem with the server which caused the installation to fail (I have attached the segment of the install log which shows the original errors). After contacting Sam Skillman, he kindly suggested altering the following lines in the install script to read https intead of http, which resolved everything: 554 YT_DIR="$PWD/yt-hg/" 555 ( ${HG_EXEC} --debug clone http://hg.yt-project.org/yt-supplemental/ 2>&1 ) 1>> ${LOG_FILE} 556 # Recently the hg server has had some issues with timeouts. In lieu of 557 # a new webserver, we are now moving to a three-stage process. 558 # First we clone the repo, but only up to r0. 559 ( ${HG_EXEC} --debug clone http://hg.yt-project.org/yt/ ./yt-hg 2>&1 ) 1>> ${LOG_FILE} 560 # Now we update to the branch we're interested in. 561 ( ${HG_EXEC} -R ${YT_DIR} up -C ${BRANCH} 2>&1 ) 1>> ${LOG_FILE} Just wanted to let you know in case others encounter this problem or if you wanted to change the install script. Thanks and have a good night! Matt Malloy

2 1

yt installation error
by Erik Rosolowsky 15 Aug '12

15 Aug '12

Hi all -- My student and I are both replicating the same error. I successfully built 2.4 on the same machine last week using the Automated Install script. If it helps, we are running SuSE Linux 11.4 and have no connection problems to the hg site. running install_egg_info Writing /UBC-O/erosolo/yt-x86_64/lib/python2.7/site-packages/mercurial-2.2.2-py2.7.egg-info using http://hg.yt-project.org/yt-supplemental/ sending capabilities command abort: HTTP Error 404: NOT FOUND using http://hg.yt-project.org/yt/ sending capabilities command abort: HTTP Error 404: NOT FOUND abort: repository /UBC-O/erosolo/yt-x86_64/src/yt-hg/ not found! /UBC-O/erosolo/yt-x86_64/bin/python2.7: can't open file '/UBC-O/erosolo/yt-x86_64/src/yt-hg//distribute_ e. -- Erik Rosolowsky Asst. Prof. of Physics and Astronomy University of British Columbia Okanagan 3333 University Way, Kelowna BC V1V 1V7 Canada (250) 807-9623 - erik.rosolowsky(a)ubc.ca > > Message: 3 > Date: Wed, 15 Aug 2012 10:47:27 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > > Hi Chao, > > Is this problem repeatable? > > Our source code host, bitbucket.org, has been going down for a minute or > two every once in a while, it's possible that you were unlucky and tried > to run the install script while bitbucket was having some downtime. > > Can the machine you're trying to install yt on connect to > hg.yt-project.org? You should be able to check by saying 'ping > hg.yt-project.org' from the command line. > > Cheers, > > Nathan > > On 8/15/12 10:43 AM, Chao Shi wrote: >> Hi all, >> >> I've been re-installing yt today but got a weird error output as below: >> >> * >> ******************************************** >> FAILURE REPORT: >> ******************************************** >> >> running install_egg_info >> Writing >> /home/cshi31/yt-x86_64/lib/python2.7/site-packages/mercurial-2.2.2-py2.7.egg-info >> using http://hg.yt-project.org/yt-supplemental/ >> sending capabilities command >> abort: HTTP Error 404: NOT FOUND >> using http://hg.yt-project.org/yt/ >> sending capabilities command >> abort: HTTP Error 404: NOT FOUND >> abort: repository /home/cshi31/yt-x86_64/src/yt-hg/ not found! >> /home/cshi31/yt-x86_64/bin/python2.7: can't open file >> '/home/cshi31/yt-x86_64/src/yt-hg//distribute_setup.py': [Errno 2] No >> such file or directory >> >> ******************************************** >> ******************************************** >> >> * >> >> >> It looks like the failure is due to the HTTP Error, but I can open the >> link in browser. >> Can anyone help me out here? >> >> Thanks, >> >> Chao >> >> >> _______________________________________________ >> 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 54, Issue 19 > ****************************************

2 2

yt installation failure
by Chao Shi 15 Aug '12

15 Aug '12

Hi all, I've been re-installing yt today but got a weird error output as below: * ******************************************** FAILURE REPORT: ******************************************** running install_egg_info Writing /home/cshi31/yt-x86_64/lib/python2.7/site-packages/mercurial-2.2.2-py2.7.egg-info using http://hg.yt-project.org/yt-supplemental/ sending capabilities command abort: HTTP Error 404: NOT FOUND using http://hg.yt-project.org/yt/ sending capabilities command abort: HTTP Error 404: NOT FOUND abort: repository /home/cshi31/yt-x86_64/src/yt-hg/ not found! /home/cshi31/yt-x86_64/bin/python2.7: can't open file '/home/cshi31/yt-x86_64/src/yt-hg//distribute_setup.py': [Errno 2] No such file or directory ******************************************** ******************************************** * It looks like the failure is due to the HTTP Error, but I can open the link in browser. Can anyone help me out here? Thanks, Chao

2 1

Fwd: [asd-python-users] Fwd: [AstroPy] Astropy Project Coordination Meeting registration now available
by John ZuHone 15 Aug '12

15 Aug '12

Hi all, A workshop at STScI that may be of some interest... John ZuHone Laboratory for High-Energy Astrophysics NASA/Goddard Space Flight Center 8800 Greenbelt Rd., Code 662 Greenbelt, MD 20771 (w) 301-286-2531 (m) 773-758-0172 jzuhone(a)gmail.com john.zuhone(a)nasa.gov Begin forwarded message: > From: "Perkins, Jeremy S. (GSFC-661.0)[UNIVERSITY OF MARYLAND BALTIMORE COUNTY]" <jeremy.s.perkins(a)nasa.gov> > Date: August 15, 2012 9:01:49 AM EDT > To: "asd-python-users(a)lists.nasa.gov" <asd-python-users(a)lists.nasa.gov> > Subject: [asd-python-users] Fwd: [AstroPy] Astropy Project Coordination Meeting registration now available > > See Below. > > Begin forwarded message: > >> From: Perry Greenfield <perry(a)stsci.edu> >> Date: August 14, 2012 10:14:06 AM EDT >> To: "astropy-dev(a)googlegroups.com" <astropy-dev(a)googlegroups.com>, astropy <astropy(a)scipy.org> >> Subject: [AstroPy] Astropy Project Coordination Meeting registration now available >> >> >> We have set up a registration page for the Astropy Project >> Coordination meeting to be held at STScI October 9-10 (with the 11th >> as a sprint day). The registration site is: >> >> http://www.stsci.edu/institute/conference/astropy >> >> There is no registration charge. There are a limited number of rooms >> being held until September 1st at the nearby Colonnade hotel that is >> within easy walking distance of STScI. >> >> If you are planning on attending, please register as soon as you can >> confirm your attendance so that we can plan accordingly. We will be >> setting up a wiki site to go into more detail about what we will cover >> during the meeting. >> >> _______________________________________________ >> AstroPy mailing list >> AstroPy(a)scipy.org >> http://mail.scipy.org/mailman/listinfo/astropy >

1 0

axis ticks problem in ProjectionPlot function
by Ji Suoqing 13 Aug '12

13 Aug '12

Hi all, I've found a small problem in ProjectionPlot function: in FLASH4 data, I've already set the domain to be, say: xmin=0.0 xmax=1.0 ymin=0.0 ymax=1.0 But when I use ProjectionPlot to plot the figure, the axis ticks become -0.5<x<0.5, -0.5<y<0.5; while in VisIt, the axis ticks are right. Also, in YT if I print out: pf.domain_left_edge & pf.domain_right_edge the domain is correct: 0<x<1, 0<y<1. I've found this in 2d cylindrical case, where x represents for r direction, and y for z direction. I'm not sure whether in cartesian coordinate the same problem exists or not. Best wishes, Suoqing

4 9

clump finder
by Latif 13 Aug '12

13 Aug '12

Hi Guys, I tried to run clump finder using the sample script available on web and just changed the minimum value of the density. Running on single cpu took too much time. So, it tried to run it in parallel. Yt did not divide the task among cpus properly and just executed the same process on all cpus. In this way, it consumed all the memory available on the machine (128 GB ). Am i doing some thing stupid or there is a problem with yt clump finder? mpirun -np 48 ./clumpfind.py --parallel Thanks in advance! Latif

2 1