Mailman 3 February 2016 - yt-users

Compilation problem
by Mark Krumholz 24 Feb '16

24 Feb '16

Hi yt Users, I’m having a problem compiling the current development branch of yt on NASA pleiades, and I’m hoping that someone can suggest what could be going wrong. Here’s what I get when I try to compile: bridge4:yt mkrumhol$ /nasa/python/2.7.9/bin/python setup.py develop --prefix=/u/mkrumhol running develop running egg_info writing requirements to yt.egg-info/requires.txt writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching 'scripts/pr_backport.py' no previously-included directories found matching 'doc/source/reference/api/generated' no previously-included directories found matching 'doc/build' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext pyrexc yt/analysis_modules/photon_simulator/utils.pyx --> yt/analysis_modules/photon_simulator/utils.c /home3/mkrumhol/yt/yt/analysis_modules/photon_simulator/utils.pyx:6:17: Syntax error in C variable declaration building 'yt.analysis_modules.photon_simulator.utils' extension gcc -fno-strict-aliasing -O2 -Wno-error -pipe -DHAVE_DB_185_H -pthread -I/usr/include -I/nasa/pkgsrc/2014Q4/include/db4 -I/nasa/pkgsrc/2014Q4/include -DNDEBUG -O2 -Wno-error -pipe -DHAVE_DB_185_H -pthread -I/usr/include -I/nasa/pkgsrc/2014Q4/include/db4 -I/nasa/pkgsrc/2014Q4/include -fPIC -I/nasa/pkgsrc/2014Q4/include/python2.7 -I/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/numpy/core/include -c yt/analysis_modules/photon_simulator/utils.c -o build/temp.linux-x86_64-2.7/yt/analysis_modules/photon_simulator/utils.o gcc: yt/analysis_modules/photon_simulator/utils.c: No such file or directory gcc: no input files error: command 'gcc' failed with exit status 1 I’m using python 2.7.9 and cython 0.23.4. The problem only occurs with the development branch; the stable branch compiles fine. I’d appreciate any suggestions. Thanks. -- Mark Krumholz http://www.mso.anu.edu.au/~krumholz/

3 3

Pyx + Tex
by John Regan 24 Feb '16

24 Feb '16

Hi All, I recently moved to working on a new machine and I've run into problems with eps_writer and pyx and tex. It seems pyx and tex are not talking to one another. I know pyx can sometimes have an iffy relationship with tex but does anyone know how to make them like each other? This is the output I get. yt : [INFO ] 2015-11-25 14:51:23,198 xlim = 0.456408 0.541884 yt : [INFO ] 2015-11-25 14:51:23,198 ylim = 0.482775 0.568251 yt : [INFO ] 2015-11-25 14:51:23,200 Making a fixed resolution buffer of (('gas', 'H_number_density')) 800 by 800 Create Multiplot.... yt : [WARNING ] 2015-11-25 14:51:24,085 No field specified. Choosing first field (('gas', 'H2_fraction')) yt : [WARNING ] 2015-11-25 14:51:24,955 No field specified. Choosing first field (('gas', 'H_number_density')) still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. We try to finish the dvi due to an unhandled tex error still waiting for tex after 5 (of 60) seconds... still waiting for tex after 10 (of 60) seconds... still waiting for tex after 15 (of 60) seconds... still waiting for tex after 20 (of 60) seconds... still waiting for tex after 25 (of 60) seconds... still waiting for tex after 30 (of 60) seconds... still waiting for tex after 35 (of 60) seconds... still waiting for tex after 40 (of 60) seconds... still waiting for tex after 45 (of 60) seconds... still waiting for tex after 50 (of 60) seconds... still waiting for tex after 55 (of 60) seconds... the timeout of 60 seconds expired and tex did not respond. Traceback (most recent call last): File "OnAxisMultiPlot_TimeSeries.py", line 173, in <module> figsize=(8,4), shrink_cb=1.8) File "/cosma/home/jregan/YT/yt-x86_64/src/yt-hg/yt/visualization/eps_writer.py", line 1164, in multiplot bbox = (100.0 * d.canvas.bbox().left().t, File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 156, in bbox obbox += cmd.bbox() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 181, in bbox self.finish() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 311, in finish self.doaxes() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 588, in doaxes self.dolayout() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 572, in dolayout self.doaxiscreate(axisname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/graph.py", line 248, in doaxiscreate self.axes[axisname].create() File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 586, in create self.canvas = self.axis.create(self.data, self.positioner, self.graphtexrunner, self.errorname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 245, in create return _regularaxis._create(self, data, positioner, graphtexrunner, self.parter, self.rater, errorname) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 146, in _create return layout(data) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/axis.py", line 141, in layout self.painter.paint(canvas, data, self, positioner) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 258, in paint _title.paint(self, canvas, data, axis, axispos) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/graph/axis/painter.py", line 109, in paint title = canvas.layer("title").text_pt(x, y, axis.title, titleattrs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/canvas.py", line 334, in text_pt return self.insert(self.texrunner.text_pt(x, y, atext, *args)) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1223, in text_pt return self.text(x * unit.t_pt, y * unit.t_pt, expr, *args, **kwargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 1201, in text raise e pyx.text.TexResultError: TeX didn't respond as expected within the timeout period (60 seconds). The expression passed to TeX was: \scrollmode \raiseerror% \def\PyX{P\kern-.3em\lower.5ex\hbox{Y}\kern-.18em X}% \gdef\PyXBoxHAlign{0}% \newbox\PyXBox% \newbox\PyXBoxHAligned% \newdimen\PyXDimenHAlignLT% \newdimen\PyXDimenHAlignRT% \gdef\PyXFlushHAlign{0}% \def\PyXragged{% \leftskip=0pt plus \PyXFlushHAlign fil% \rightskip=0pt plus 1fil% \advance\rightskip0pt plus -\PyXFlushHAlign fil% \parfillskip=0pt% \pretolerance=9999% \tolerance=9999% \parindent=0pt% \hyphenpenalty=9999% \exhyphenpenalty=9999}% \newbox\PyXBoxVBox% \newdimen\PyXDimenVBox% \newbox\PyXBoxVAlign% \newdimen\PyXDimenVAlign% \newdimen\PyXDimenVShift% \long\def\ProcessPyXBox#1#2{% \setbox\PyXBox=\hbox{{#1}}% \PyXDimenHAlignLT=\PyXBoxHAlign\wd\PyXBox% \PyXDimenHAlignRT=\wd\PyXBox% \advance\PyXDimenHAlignRT by -\PyXDimenHAlignLT% \gdef\PyXBoxHAlign{0}% \immediate\write16{PyXBox:page=#2,lt=\the\PyXDimenHAlignLT,rt=\the\PyXDimenHAlignRT,ht=\the\ht\PyXBox,dp=\the\dp\PyXBox:}% \setbox\PyXBoxHAligned=\hbox{\kern-\PyXDimenHAlignLT\box\PyXBox}% \ht\PyXBoxHAligned0pt% {\count0=80\count1=121\count2=88\count3=#2\shipout\box\PyXBoxHAligned}}% \def\PyXInput#1{\immediate\write16{PyXInputMarker:executeid=#1:}}% \def\PyXMarker#1{\hskip0pt\special{PyX:marker #1}}%% \PyXInput{1}% After parsing the return message from TeX, the following was left: This is TeX, Version 3.14159265 (TeX Live 2015) (preloaded format=tex) Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Full Error in sys.exitfunc: Traceback (most recent call last): File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/site-packages/pyx/text.py", line 744, in _cleantmp texrunner.expectqueue.put_nowait(None) # do not expect any output anymore File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 148, in put_nowait return self.put(item, False) File "/cosma/home/jregan/YT/yt-x86_64/lib/python2.7/Queue.py", line 123, in put raise Full Queue.Full The call I make is: multi = eps.multiplot(NCOLS, NROWS, projections, bare_axes=True,cb_labels=colorbar_label, figsize=(8,4), shrink_cb=1.8) Cheers, John

3 4

EnzoDatasetInMemory not working in parallel
by Britton Smith 24 Feb '16

24 Feb '16

Hi all, I've recently been trying to use yt's inline analysis functionality with Enzo and am having some difficultly getting it to work in parallel. I am using the development tip of yt. In serial, everything works fine, but in parallel, I get the following error: http://paste.yt-project.org/show/5694/ It seems that the issue is that yt is not correctly identifying which grids are available on a given processory for the EnzoDatasetInMemory object. Does anyone have an idea of how to fix this? Has anyone else seen this? For reference, my user_script is just this: import yt from yt.frontends.enzo.api import EnzoDatasetInMemory def main(): ds = EnzoDatasetInMemory() ad = ds.all_data() print ad.quantities.total_quantity("cell_mass") Thanks for any help, Britton

3 9

working with general hdf5 data from galaxy simulations
by D Mick 24 Feb '16

24 Feb '16

Hello all, yt has some of the greatest plotting capabilities, and I greatly enjoy working with yt! Recently I have begun to work with hdf5 data from a large scale galaxy simulation (illustris) and I was wondering how I can work with the data, is there a general munging procedure for getting it into the correct yt format? When I try to plot import yt ds = yt.load("Groups_hdf5_plt_cnt_0150") yt.SlicePlot(ds, 'x', "density", width = (800.0, 'kpc')).save() yt.SlicePlot(ds, 'y', "density", width = (800.0, 'kpc')).save() yt.SlicePlot(ds, 'z', "density", width = (800.0, 'kpc')).save() I get the following error: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/yt/frontends/gadget_fof/data_structures.pyc in _parse_parameter_file(self) * 151* self.periodicity = (True, True, True) * 152* self.current_redshift = hvals["Redshift"] --> 153 self.omega_lambda = hvals["OmegaLambda"] * 154* self.omega_matter = hvals["Omega0"] * 155* self.hubble_constant = hvals["HubbleParam"] KeyError: 'OmegaLambda' I am guessing this is because the field entries do not match up. Any help is much appreciated! Dan

3 2

How to make a projection plot of a desirable thickness?
by Reju Sam John 22 Feb '16

22 Feb '16

Hi, I would like to make a projection of a field along 'z' axis centered at [0.5, 0.5, 0.5] with a thickness of 10Mpc (5 Mpc to +z dir and 5 Mpc to -z dir). How to select the above-mentioned region from the whole simulation volume? I am using YT Legacy 2.x. Thank you. -- Reju Sam John

2 1

Google summer of code ideas for yt
by Nathan Goldbaum 19 Feb '16

19 Feb '16

Hi all, This year yt is applying with the OpenAstronomy organization to participate in Google Summer of Code. The ideas we've put forward are here (scroll down the page a bit): http://openastronomy.org/gsoc/gsoc2016/ideas.html#yt If you know any students (undergrad, grad) who might be interested in getting paid by Google to work on yt over the summer, please forward them this message. I'm happy to answer questions about this here or off list. -Nathan

1 0

Problem making Plots
by Yuxiao Dai 19 Feb '16

19 Feb '16

Hi all, I tried to get some plots using a python code but got this error message. ======================= Traceback (most recent call last): File "ytplots_BMag_plot_dai.py", line 58, in <module> *pcb.save('plots/Bullet_BMag_'+str(i))* File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 173, in save override=override, force_save=force_save)) File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 112, in save_image only_on_root(canvas.print_figure, fn) File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/funcs.py", line 368, in only_on_root return func(*args,**kwargs) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/backend_bases.py", line 2220, in print_figure **kwargs) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/backends/backend_agg.py", line 510, in print_png filename_or_obj = open(filename_or_obj, 'wb') IOError: [Errno 2] No such file or directory: 'plots/Bullet_BMag_0_Profile1D_0_RadiusMpc_BMag.png' ======================= I'm using yt Version = 2.6.1 Changeset = c994959ed3be ======================= I would very much appreciate it if anyone could help me on this. Thank you very much. Regards, Yuxiao

2 1

Add to list
by Azton I Wells 18 Feb '16

18 Feb '16

Can I please be added to the users list? Thanks, Azton

2 1

yt-2.x installation problem on Mac 10.11
by Pengfei Chen 17 Feb '16

17 Feb '16

Hi all, I'm trying to install yt-2.x on my Mac 10.11. I could use get_yt.sh to install yt-2.x. But I need to add "--enable-shared" while installing python, so that I could use inline python later on with yt. Is there a way that I could modify get_yt.sh to add the option "--enable-shared" while installing python? I also tried to install yt-2.x with install_script.sh, but I got the following error: Installing Python. This may take a while, but don't worry. yt loves you. ******************************************** FAILURE REPORT: ******************************************** -d /Users/madcpf/Documents/shared_yt2/lib/python2.7 -f \ -x 'bad_coding|badsyntax|site-packages|lib2to3/tests/data' \ /Users/madcpf/Documents/shared_yt2/lib/python2.7 Traceback (most recent call last): File "/Users/madcpf/Documents/shared_yt2/lib/python2.7/compileall.py", line 16, in <module> import struct File "/Users/madcpf/Documents/shared_yt2/lib/python2.7/struct.py", line 1, in <module> from _struct import * ImportError: No module named _struct make: *** [libinstall] Error 1 ******************************************** ******************************************** Failure. Check /Users/madcpf/Documents/shared_yt2/yt_install.log. The last 10 lines are above. Could someone please give me some suggestions about this? Thanks, Pengfei

1 0

yt install on mac 10.11.2
by Azton Wells 16 Feb '16

16 Feb '16

Hello all, I am trying to install yt on Mac 10.11.2. My most current efforts use ³yt² branch, and I am trying to install from the install_script.sh. We have modified the python installation section of the script from: ./configure --prefix=${DEST_DIR}/ ${PYCONF_ARGS} To: ./configure CPPFLAGS=-I/usr/local/opt/openssl/include --enable-shared --prefix=${DEST_DIR}/ ${PYCONF_ARGS} I have also added : export LD_LIBRARY_PATH=/usr/local/opt/openssl/lib:$LD_LIBRARY_PATH I have used: Brew install openssl Brew link force openssl My installation fails with: ******************************************** FAILURE REPORT: ******************************************** checking size of int... 0 checking size of long... 0 checking size of void *... 0 checking size of short... 0 checking size of float... 0 checking size of double... 0 checking size of fpos_t... 0 checking size of size_t... configure: error: in `/Users/Azton/Research/yt/src/Python-2.7.9': configure: error: cannot compute sizeof (size_t) See `config.log' for more details Using the get_yt.sh script that uses miniconda works, but I don¹t know if the ³conda install python² command will include ³--enable-shared² My question is two part: Does anyone have an idea for using the install_script.sh? (2) Failing using the install_script, would using the get_yt.sh install python with enable-shared? Thanks for any help, Azton

1 0