yt-users January 2016

yt-users@python.org

19 participants
31 discussions

by david collins

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.

10 months, 3 weeks

Problem when run yt dev in parallel on Blue Waters

by Pengfei Chen

Hi all, I have trouble running yt in parallel on Blue Waters. I installed yt using miniconda, the version of yt is ~/miniconda/lib $yt version yt module located at: /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg The current version and changeset for the code is: --- Version = 3.3-dev Changeset = 90f900be7a36+ yt Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I tried to make the following simple output in parallel, I get: import yt yt.enable_parallelism() from yt.utilities.parallel_tools.parallel_analysis_interface import\ parallel_objects, communication_system comm = communication_system.communicators[-1] print comm.rank, comm.size 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 ... When I run a similar code but with yt-2.x also on Blue Waters, I get what I expect: 7 16 15 16 6 16 9 16 11 16 8 16 0 16 4 16 ... I'm confused about it. Could anyone give me some suggestions please? Thanks, Pengfei

4 years, 6 months

Covering Grid Dimensions: multiple refinement levels

by Carla Bernhardt

Dear YT Users, To better understand covering_grid (or smoothed_covering_grid), can someone explain what dimensions I should use when I have multiple levels of refinement? If I have 1 level of refinement from AMR data, the dimensions should be the same, I believe, but what if I have 2 or 3 levels of refinement? Should the fixed resolution region then have dimensions of dims*2^2 and dims*3^2 respectively? Here is one example from a tutorial <http://yt-project.org/doc/examining/low_level_inspection.html#examining-gri…> if that helps isolate my question: all_data_level_2 = ds.covering_grid(level=2, left_edge=[0,0.0,0.0], dims=ds.domain_dimensions * 2**2) Thanks in advance, Carla

4 years, 10 months

yt-3.2.1 installation error

by Muhammad Latif

Hi all, I'm getting the following error while installing yt-3.2.1 latest release. Any idea what is going on here? thanks in advance, cheers Latif Installing nose-1.3.6 Installing python-hglib-1.6 Installing sympy-0.7.6 Doing yt update, wiping local changes and updating to branch stable install_script.sh: line 1025: cd: /home/latif/YT/yt-x86_64/src/yt-hg/: No such file or directory Installing yt ******************************************** FAILURE REPORT: ******************************************** running install_data copying doc/man/isympy.1 -> /home/latif/YT/yt-x86_64/share/man/man1 running install_egg_info Writing /home/latif/YT/yt-x86_64/lib/python2.7/site-packages/sympy-0.7.6-py2.7.egg-info Collecting jinja2 Using cached Jinja2-2.8-py2.py3-none-any.whl Collecting MarkupSafe (from jinja2) Installing collected packages: MarkupSafe, jinja2 Successfully installed MarkupSafe-0.23 jinja2-2.8 /home/latif/YT/yt-x86_64/bin/python2.7: can't open file 'setup.py': [Errno 2] No such file or directory ******************************************** ******************************************** Failure. Check /home/latif/YT/yt-x86_64/yt_install.log. The last 10 lines are above.

4 years, 11 months

Pyx + Tex

by John Regan

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

5 years

EnzoDatasetInMemory not working in parallel

by Britton Smith

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

5 years

DM density profiles

by Junhwan Choi (최준환)

Hi yt user, I make a simple DM and gas density profile for my enzo simulation with following script: ====================== import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _radiuspc(field, data): return data[('radius')].in_units('pc') yt.add_field('radiuspc', function=_radiuspc, units="pc") Nbin= 100 rmax = 4000 index = 60 ds = yt.load("../DD%04d/DD%04d" % (index,index)) ds.index ad= ds.all_data() center = ds.find_max(("gas", "density"))[1] my_sphere = ds.sphere(center, rmax*units.pc) rmin = max([1.0e-4,2.0*ds.index.get_smallest_dx().in_units('pc')]) profile = yt.Profile1D(my_sphere, 'radiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field='cell_volume') profile.add_fields(('gas','density')) profile.add_fields(('gas','dark_matter_density')) profile.add_fields(('deposit','all_density')) plt.plot(np.log10(profile.x), np.log10(profile[('gas','density')]), label="('gas','density')", linestyle="-", color='g') plt.plot(np.log10(profile.x), np.log10(profile[('gas','dark_matter_density')]), label="('gas','dark_matter_density')", linestyle="-", color='r') plt.plot(np.log10(profile.x), np.log10(profile[('deposit','all_density')]), label="('deposit','all_density')", linestyle="-", color='b') plt.legend(loc=0,prop={'size':9}) plt.savefig('DMTest') ====================== The only particle in the simulation is the dark matter so that profile[('gas','dark_matter_density')] and profile[('deposit','all_density')] should be same. However, as shown in the attached figure, they are very different. I would like to ask a few questions regarding to this plot. 1) Why do profile[('gas','dark_matter_density')] and profile[('deposit','all_density')] show significant difference? 2) What limit the minimum r in profile[('deposit','all_density')]? 3) If I would like to make total density profile, what do I do? I think that profile[('deposit','all_density')] is more liable result. Can I add data[('gas','density')] and data[('deposit','all_density')], two different field types, in the derived field? Thank you in advance, Junhwan Choi _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

5 years

Can I specify the particle type when loading data?

by Bili Dong - Gmail

Hi yt users, I'm working with a particle dataset and I'm wondering if it is possible to only load a certain type of particle fields from the snapshot as my dataset? For example, there might be 'PartType0' and 'PartType1' in the snapshot, but I only want to load 'PartType0'. The reason I want to do this is that, to my understanding, the octree of the particle dataset is constructed adaptively according to the number of particles, including all types of particles in the dataset. But I want the octree constructed only according to the type of particles I'm interested in. Is it possible? Thanks, Bili

5 years

POLL: A New Default Colormap

by Matthew Turk

Hi folks, The current default colormap that yt uses is called "Algae," and it's been with us for a while. Recently some of us on the yt-dev mailing list (which is open to join!) have begun to look at alternate colormaps that have better characteristics, particularly from an accessibility perspective. If you have the time, it would be really, *really* helpful if you could take this anonymous, two question (only one of which is mandatory!) poll about which of the four candidates we've come up with you like the best. http://goo.gl/forms/D4qQqkPIMq Thanks very much! The poll will be open at least a week, and I'll report back the results here sometime after that. -Matt

5 years, 1 month

particle angular momentum profile error and accumulation profile

by Junhwan Choi (최준환)

Hi yt users, I try to make a particle angular momentum profile using the following script: ================================ import matplotlib as matplotlib matplotlib.use('Agg') import yt import yt.units as units import numpy as np import matplotlib.pyplot as plt def _radiuspc(field, data): return data[('radius')].in_units('pc') yt.add_field('radiuspc', function=_radiuspc, units="pc") index = 45 Nbin= 100 rmax = 3000 ds = yt.load("../DD%04d/DD%04d" % (index,index)) ds.index ad= ds.all_data() center = ds.find_max(("gas", "density"))[1] rmin = max([1.0e-3,2.0*ds.index.get_smallest_dx().in_units('pc')]) sphere = ds.sphere(center, rmax*units.pc) bulk_velocity = sphere.quantities['BulkVelocity']() sphere.set_field_parameter('bulk_velocity', bulk_velocity) profile = yt.Profile1D(sphere, 'radiuspc', Nbin, x_min=rmin, x_max=rmax, x_log=True, weight_field=None) profile.add_fields(('all', 'particle_angular_momentum_x')) profile.add_fields(('all', 'particle_angular_momentum_y')) profile.add_fields(('all', 'particle_angular_momentum_z')) PartAngularMomentum = np.sqrt(profile[('all', 'particle_angular_momentum_x')]**2 + profile[('all', 'particle_angular_momentum_y')]**2 + profile[('all', 'particle_angular_momentum_z')]**2) plt.plot(profile.x, PartAngularMomentum, label='Total',linestyle="-",color='r') plt.xlabel('r [pc]') plt.ylabel('pang') ====================================== And I got the following error: ……….. Traceback (most recent call last): File "pang.py", line 26, in <module> profile.add_fields(('all', 'particle_angular_momentum_x')) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 112, in add_fields self._bin_chunk(chunk, fields, temp_storage) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 425, in _bin_chunk rv = self._get_data(chunk, fields) File "/home/jhchoi/common/src/yt/yt/data_objects/profiles.py", line 240, in _get_data arr[:,i] = chunk[field][filter].in_units(units) File "/home/jhchoi/common/src/yt/yt/units/yt_array.py", line 1123, in __getitem__ ret = super(YTArray, self).__getitem__(item) IndexError: index 1322 is out of bounds for axis 1 with size 1322 I do not understand what the problem is? One more question: Is there any way to make accumulation density profile with yt.Profile1D(……)? Thank you in advance, Junhwan

5 years, 1 month

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