Fwd: [yt_analysis/yt] Change time series objects to *not* instantiate pfs by default (pull request #143)
by Matthew Turk
Hi all,
A couple people (Nathan and Britton) have mentioned memory problems
with time series data because the StaticOutput objects sometimes hold
on to hierarchies. I've taken a pass at preventing this from
happening by keeping the static outputs from being instantiated until
requested, and allowing the references to be passed rather than
retained.
Anyway, it works for me and I've checked that the references go to
zero. If somebody else that was having memory issues could take a
gander that'd be great. Here's my sample script; if you run
before&after the numbers it prints out at the end should be
"something" and "0".
http://paste.yt-project.org/show/2302/
-Matt
---------- Forwarded message ----------
From: Matthew Turk <pullrequests-noreply(a)bitbucket.org>
Date: Sun, Apr 22, 2012 at 10:52 AM
Subject: [yt_analysis/yt] Change time series objects to *not*
instantiate pfs by default (pull request #143)
To: yt(a)enzotools.org
A new pull request has been opened by Matthew Turk.
MatthewTurk/yt has changes to be pulled into yt_analysis/yt.
https://bitbucket.org/yt_analysis/yt/pull-request/143/change-time-series-...
Title: Change time series objects to *not* instantiate pfs by default
This change, as described in the commit message, will prevent time
series data from initially instantiating any parameter file objects.
By keeping the references to pfs temporary, this will prevent
hierarchies from sticking around during the course of analysis, which
should improve overall memory usage.
Changes to be pulled:
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6 years, 11 months
Vector fields
by Matthew Turk
Hi all,
I got an email from someone identifying a problem in profiles. This
person was dealing with vector fields, which were giving bad results.
I wanted to open up discussion here, as I know Jeff and Sam and others
have thought about this. I'll contribute some thoughts after giving
the mic over to someone else.
In an ideal world, how should a vector field -- like angular momentum,
in particular -- be presented and dealt with in yt?
-Matt
6 years, 11 months
2.4: Release and bug roundup
by Matthew Turk
Hi all,
A couple people have mentioned to me recently (in IRC and over email)
that the stable branch is missing some fixes for FLASH and Enzo data.
I'd like to start a discussion on wrapping up the dev cycle and moving
for a 2.4 release. The showpoint of this release I believe will be
improvements to volume rendering; more on that below.
Here are the open, targeted bugs for 2.4:
https://bitbucket.org/yt_analysis/yt/issues?status=new&status=open&milest...
These touch on a few major areas:
* Minor improvements to reason and reason widgets: Adding vectors,
layers (which should get postponed) a volume rendering widget (should
get postponed) and a file open dialog (Nathan had been working a bit
on that.)
* FLASH updates to make it more user friendly: John Z and I had a
brainstorming session after I spoke to some FLASH users last week, and
I filled out tickets to try to address any remaining weak points.
* Time Series updates: Nathan has made a few suggestions, and I'm
going to implement them. I like where Time Series is going!
* Volume rendering refactor (Sam, if you have a few minutes, could
you give an update on what that includes and what it provides? This
could be a great centerpiece of 2.4!)
* Rockstar integration is incomplete and undocumented, but that may
also be postponed.
There are also a few bugs that need to be addressed:
* MPI attributes now break pickling in some cases; I will address this
* Ghost zone issues seem to be everywhere, as corner cases keep
coming up. John W and I have spoken about this and we have an idea
for how to fix it moving forward.
* Quadproj scales poorly, but that'll be a bit of a tricky piece of work.
Does anyone have any comments or ideas about these bugs, or want to
tackle any of them? Are there any other concerns, or thoughts on
this?
How would aiming to release in a month from now sound? April 16 is a
Monday, which would be a good day for a release.
-Matt
6 years, 11 months
Gridding Particles
by Christopher Moody
Hi everyone,
I just asked the IRC list this, but I guess no one was there. I'm trying to
grid a few million particles onto the yt grids, but checking if the left
and right edges of my particles are inside every cell is slow:
#find particles inside cell
idx = na.logical_and(na.all(le < pos,axis=1), na.all(re > pos,axis=1))
#assign them to a grid
...
#remove particles from future searches
pos = pos[~idx]
I start with the finest grids at the highest levels, and once the particles
are gridded they're removed -- so the list of particles is always
decreasing, and the coarsest mesh tends to have only a few particles. I'm
guessing that somewhere this has been done before - I'd rather not reinvent
the wheel. Has anyone used any relevant kdtree (or cython) code in the yt
utilities that can select a subvolume of particles quickly?
Thanks ahead of time!
chris
6 years, 11 months
Fwd: [yt_analysis/yt] Adding IPython notebook dependencies (on-by-default) to the install script. (pull request #137)
by Matthew Turk
Hi all,
I thought this pull request might be of interest to the list, and we
could discuss it here, rather than in the PR itself.
The IPython notebook is awesome. I love Reason, and I'm super proud
of the work we have done on it, but the clunkiest part of Reason is
the cell-evaluation (and, it's also the part of it that we spent the
least time on.) I think it would be worthwhile to discuss and
consider moving forward with de-emphasizing our own notebook solution,
embed IPython inside Reason, and then re-focus on providing awesome
widgets. I am still reading through the API for the IPython
notebook's engine interface, but I believe this could be accomplished
by:
1) Spinning up an SSL-enabled, passworded IPython engine when reason is started
2) Construct actual RPC interfaces for the existing (and new) widgets,
with payload delivery systems
3) Embed the IPython notebook as another widget
Anyway, if you want to test it out, pull the new install script, run
it, and then start the notebook with:
ipython notebook
There are some pretty awesome things in there. Fernando Perez and I
discussed this on a G+ post of his (
https://plus.google.com/105051551851350439748/posts/gd9fDgpV8iY ) and
I'd particularly draw your attention to the blog post he cited by
Titus Brown ( http://ivory.idyll.org/blog/apr-12/replication-i.html ;
I believe his office is just down the hall from where we held the Enzo
workshop last Spring!) and the possibilities therein.
Even if down the road we don't find a way to marry Reason widgets with
the IPython notebook in a seamless way, I'm still issuing this PR
because I would like to make it easier to get up and running with the
notebook. Note that they have a detailed discussion of the security
implications ( http://ipython.org/ipython-doc/rel-0.12/interactive/htmlnotebook.html#sec...
), which become very important on shared user systems, which I think
make up the majority of yt installations.
Thoughts on this?
-Matt
---------- Forwarded message ----------
From: Matthew Turk <pullrequests-noreply(a)bitbucket.org>
Date: Wed, Apr 4, 2012 at 3:31 PM
Subject: [yt_analysis/yt] Adding IPython notebook dependencies
(on-by-default) to the install script. (pull request #137)
To: yt(a)enzotools.org
A new pull request has been opened by Matthew Turk.
MatthewTurk/yt has changes to be pulled into yt_analysis/yt.
https://bitbucket.org/yt_analysis/yt/pull-request/137/adding-ipython-note...
Title: Adding IPython notebook dependencies (on-by-default) to the
install script.
The IPython notebook requires 0MQ, Tornado and pyzmq. This change
adds those dependencies.
Changes to be pulled:
--
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You are receiving this either because you are the participating
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6 years, 11 months
Fwd: SciPy 2012 - The Eleventh Annual Conference on Scientific Computing with Python
by Matthew Turk
---------- Forwarded message ----------
From: Warren Weckesser <warren.weckesser(a)enthought.com>
Date: Wed, Apr 4, 2012 at 5:30 PM
Subject: [pydata] SciPy 2012 - The Eleventh Annual Conference on
Scientific Computing with Python
To: SciPy Users List <scipy-user(a)scipy.org>,
scikit-learn-general(a)lists.sourceforge.net, SciPy Developers List
<scipy-dev(a)scipy.org>, IPython Development list
<ipython-dev(a)scipy.org>, enthought-dev(a)enthought.com,
epd-users(a)enthought.com, Discussion of Numerical Python
<numpy-discussion(a)scipy.org>, pystatsmodels(a)googlegroups.com,
pydata(a)googlegroups.com
SciPy 2012, the eleventh annual Conference on Scientific Computing
with Python, will be held July 16–21, 2012, in Austin, Texas.
At this conference, novel scientific applications and libraries
related to data acquisition, analysis, dissemination and visualization
using Python are presented. Attended by leading figures from both
academia and industry, it is an excellent opportunity to experience
the cutting edge of scientific software development.
The conference is preceded by two days of tutorials, during which
community experts provide training on several scientific Python
packages. Following the main conference will be two days of coding
sprints.
We invite you to give a talk or present a poster at SciPy 2012.
The list of topics that are appropriate for the conference includes
(but is not limited to):
new Python libraries for science and engineering;
applications of Python in solving scientific or computational problems;
high performance, parallel and GPU computing with Python;
use of Python in science education.
Specialized Tracks
Two specialized tracks run in parallel to the main conference:
High Performance Computing with Python
Whether your algorithm is distributed, threaded, memory intensive or
latency bound, Python is making headway into the problem. We are
looking for performance driven designs and applications in Python.
Candidates include the use of Python within a parallel application,
new architectures, and ways of making traditional applications execute
more efficiently.
Visualization
They say a picture is worth a thousand words--we’re interested in
both! Python provides numerous visualization tools that allow
scientists to show off their work, and we want to know about any new
tools and techniques out there. Come show off your latest graphics,
whether it’s an old library with a slick new feature, a new library
out to challenge the status quo, or simply a beautiful result.
Domain-specific Mini-symposia
Mini-symposia on the following topics are also being organized:
Computational bioinformatics
Meteorology and climatology
Astronomy and astrophysics
Geophysics
Talks, papers and posters
We invite you to take part by submitting a talk or poster abstract.
Instructions are on the conference website:
http://conference.scipy.org/scipy2012/talks.php
Selected talks are included as papers in the peer-reviewed conference
proceedings, to be published online.
Tutorials
Tutorials will be given July 16–17. We invite instructors to submit
proposals for half-day tutorials on topics relevant to scientific
computing with Python. See
http://conference.scipy.org/scipy2012/tutorials.php
for information about submitting a tutorial proposal. To encourage
tutorials of the highest quality, the instructor (or team of
instructors) is given a $1,000 stipend for each half day tutorial.
Student/Community Scholarships
We anticipate providing funding for students and for active members of
the SciPy community who otherwise might not be able to attend the
conference. See
http://conference.scipy.org/scipy2012/student.php
for scholarship application guidelines.
Be a Sponsor
The SciPy conference could not run without the generous support of the
institutions and corporations who share our enthusiasm for Python as a
tool for science. Please consider sponsoring SciPy 2012. For more
information, see
http://conference.scipy.org/scipy2012/sponsor/index.php
Important dates:
Monday, April 30: Talk abstracts and tutorial proposals due.
Monday, May 7: Accepted tutorials announced.
Monday, May 13: Accepted talks announced.
Monday, June 18: Early registration ends. (Price increases after this date.)
Sunday, July 8: Online registration ends.
Monday-Tuesday, July 16 - 17: Tutorials
Wednesday-Thursday, July 18 - July 19: Conference
Friday-Saturday, July 20 - July 21: Sprints
We look forward to seeing you all in Austin this year!
The SciPy 2012 Team
http://conference.scipy.org/scipy2012/organizers.php
6 years, 11 months
Re: [yt-dev] Interacting with data in yt 3.0 (was Field units from code to code)
by Matthew Turk
In general, I agree with the idea Nathan put out. (Also, I think this
is a fine time to have a bikeshed discussion. Many of the underlying
assumptions about how yt works were laid out a long time ago.) But,
I'm not entirely sure I understand how different it would be --
conceptually, yes, I see what you're getting at, that we'd have a set
number of attributes. In what I was thinking of for the geometry
refactor so far I'm trying to get rid of the "hierarchy" as existing
for every data set, and instead relying on what amounts to an
object-finder and io-coordinator, which I'm calling a geometry
handler. It sounds like what you would like is:
1) Get rid of accessing parameters with an implicit __getitem__ on the
parameter file (i.e., pf["SomethingThatOnlyExistsInOneCode"]). I'm
+10 on this.
2) Move units into the .units object (I'm mostly with Casey on this,
but I think it should be a part of the field_info object)
3) Have things like current_time, domain_dimensions and so on move
into basic_info and make them dict objects.
I think of those, I'm in favor of one and two, but somewhat opposed to
#3. Right now we have these attributes mandated for subclasses of
StaticOutput:
refine_by
dimensionality
current_time
domain_dimensions
domain_left_edge
domain_right_edge
unique_identifier
current_redshift
cosmological_simulation
omega_matter
omega_lambda
hubble_constant
The only ones here that I think would be okay to move out of
properties would be the cosmology items, and even those I'm -0 on
moving.
But, in general, the idea of moving from this two-stage system of
parameter file (rather than dataset) and hierarchy (rather than an
implicitly-handled geometry) is something I am in support of. The
geometry is something that should nearly *always* be handled by the
backend, rather than by the user. So having the library require
pf.h.sphere(...) is less than ideal, since it's exposing something
relatively unfortunate (that building a hundred thousand grid objects
can take some time).
The main ways that the static output is interacted with:
* Parameter information specific to a simulation code
* Properties that yt needs to know about
* To get at the hierarchy
* Input to plot collections
The main ways that the hierarchy is interacted with:
* Getting data objects
* Finding max
* Statistics about the simulation
* Inspecting individual grids (much less common use case now that it was before)
All of these use cases are still valid, but I think it's clear that
accessing individual grids and accessing simulation-specific
parameters are not "generic" functions. What a lot of this discussion
has really brought up for me is that we're talking about *generic*
functionality, not code-specific functionality, and we right now do
not have the best enumeration of functionality and where it lies.
With the geometry_refactor, I'd like to consolidate functionality into
the main "dataset" object. The geometry can still provide access to
the individual grids (of course) but data objects, finding max,
getting stats about the simulation, etc, should all go into the main
dataset object, and the geometry handler can simply be created on the
fly if necessary.
This brings up two points, though --
1) Does our method of instantiating objects still hold up? i.e.,
ds.sphere(...) and so on? Or does our dataset object then become
overcrowded? I would also like to move *all* plotting objects into
whatever we end up deciding is the location data containers come from,
which for instance could look like ds.plot("slice", "x") (for
instance, although we can bikeshed that later), which would return a
plot window.
2) Datasets and time series should behave, if not identically, at
least consistently in their APIs. Moving to a completely ds-mediated
mechanism for generating, accessing and inspecting data opens up the
ability to then construct very nice and simply proxy objects. As an
example, while something this is currently technically possible with
the current Time Series API, it's a bit tricky:
ts = TimeSeriesData.from_filenames(...)
plot = ts.plot("slice", "x", (100.0, 'au'))
ts.seek(dt = (100, 'years'))
plot.save()
ts.seek(dt = (10, 'years'))
plot.save()
(The time-slider, as Tom likes to call it ...)
In general, this idea of moving toward more thoughtful
dataset-construction, rather than the hokey parameter file + hierarchy
construction brings with it a mindset shift which I'd like to spread
to the time series, which can continue to be a focus.
What do you think?
-Matt
On Thu, Mar 29, 2012 at 7:08 PM, Casey W. Stark <caseywstark(a)gmail.com> wrote:
> +1 on datasets, although I would like to see the unit object(s) at the field
> level.
>
>
> On Thu, Mar 29, 2012 at 4:04 PM, Cameron Hummels
> <chummels(a)astro.columbia.edu> wrote:
>>
>> +1 on datasets.
>>
>>
>> On 3/29/12 6:58 PM, Nathan Goldbaum wrote:
>>>
>>> +1. I'd also be up to help out with the sprint. Doing a virtual sprint
>>> using a google hangout might help mitigate some of the distance problems.
>>>
>>> While we're brining up Enzo-isms that we should get rid of, I think it
>>> might be a good idea to make a conceptual shift in the basic python UI.
>>> Instead referring to the interface between the user and the data as a
>>> parameter file, I think instead we should be talking about datasets. One
>>> would instantiate a dataset just like we do now with parameter files:
>>>
>>> ds = load(filename)
>>>
>>> A dataset would also have some universal attributes which would present
>>> themselves to the user as a dict, e.g. ds.units, ds.parameters,
>>> ds.basic_info (like current_time, timestep, filename, and simulation code),
>>> and ds.hierarchy (not sure how that would interfere with the geometry
>>> refactor).
>>>
>>> This may be a paintibg the bike shed discussion, but I think this shift
>>> will help new users understand how to access their data. Thoughts?
>>>
>>> On Mar 29, 2012, at 3:40 PM, Matthew Turk<matthewturk(a)gmail.com> wrote:
>>>
>>>> Hi Nathan and Casey,
>>>>
>>>> I agree with what both of you have said. The Orion/Nyx units should
>>>> be made to be consistent, but more importantly I think we should
>>>> continue breaking away from Enzo-isms in the code.
>>>>
>>>> As it stands, all of the universal fields call underlying Enzo-named
>>>> aliases -- Density, ThermalEnergy, etc etc. I hope we can have a 3.0
>>>> out within a calendar year, hopefully by the end of this year. (I've
>>>> been pushing on the geometry refactor, although recently other efforts
>>>> have been paying off which has decreased my output there.) I am much,
>>>> much less doubtful than Casey is that we cannot do this; in fact, I'm
>>>> completely in favor of this and I think it would be relatively
>>>> straightforward to implement.
>>>>
>>>> In the existing system we have a mechanism for aliasing fields. What
>>>> we can do is provide an additional translation system where we
>>>> enumerate the fields that are available for items in UniversalFields,
>>>> and then construct aliases to those. This would mean changing what is
>>>> aliased in existing non-Enzo frontends, and adding aliases in Enzo.
>>>> The style of name Casey proposes is what I woudl also agree with:
>>>> underscores, lower cases, and erring on the side of verbosity. The
>>>> fields off hand that we would need to do this for (in their current
>>>> enzo-isms):
>>>>
>>>> x-velocity => velocity_x (same for y, z)
>>>> Density => density
>>>> TotalEnergy => ?
>>>> GasEnergy => thermal_energy_specific (and thermal_energy_density)
>>>> Temperature => temperature
>>>>
>>>> and so on.
>>>>
>>>> Once we have these aliases in place, an overall cleanup of
>>>> UniversalFields should take place. One place we should clean up is
>>>> ensuring that there are no conditionals; rather than conditionals
>>>> inside the functions, we should place those conditionals inside the
>>>> parameter file types. So for instance, if you have a field that is
>>>> calculated differently depending on the parameter HydroMethod (in Enzo
>>>> for instance) you simply set a validator on the field requiring the
>>>> parameter be set to a particular value, and then only the field which
>>>> satisfies that validator will be called when requested.
>>>>
>>>> So we've gotten rid of a bunch of enzo-isms in the parameter files;
>>>> after fields, what else can we address? And, I'd be up for sprinting
>>>> on this (which should take just a few hours) basically any time next
>>>> week or after. I'd also be up for talking more about geometry
>>>> refactoring, if anyone is interested, but it's not quite to the point
>>>> that I think I am satisfied enough with the architecture to request
>>>> input / contributions. Sometimes (especially with big architectural
>>>> things like this) I think it's a shame we do all of our work
>>>> virtually, as I think a lot of this would be easier to bang out in
>>>> person for a couple hours.
>>>>
>>>> -Matt
>>>>
>>>> On Wed, Mar 28, 2012 at 6:14 PM, Casey W. Stark<caseywstark(a)gmail.com>
>>>> wrote:
>>>>>
>>>>> Hi Nathan.
>>>>>
>>>>> I'm also worried about this and I agree that fields with the same name
>>>>> should all be consistent. I would support some sort of cleanup of
>>>>> frontend
>>>>> fields, and I can get the Nyx fields in line and help with Enzo.
>>>>>
>>>>> I doubt we can do this, but I would prefer changing the field names as
>>>>> part
>>>>> of the removing enzo-isms and geometry handling refactoring pushes. For
>>>>> instance, the field in Orion could be thermal_energy_density and the
>>>>> field
>>>>> in Enzo could be specific_thermal_energy. I also noticed this issue
>>>>> when I
>>>>> was using "Density" in Enzo (proper density in cgs) and "density" in
>>>>> Nyx
>>>>> (comoving density in cgs).
>>>>>
>>>>> Best,
>>>>> Casey
>>>>>
>>>>>
>>>>> On Wed, Mar 28, 2012 at 1:47 PM, Nathan Goldbaum<goldbaum(a)ucolick.org>
>>>>> wrote:
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> On IRC today we noticed that Orion defines its ThermalEnergy field per
>>>>>> unit volume but Enzo and FLASH define ThermalEnergy per unit mass. Is
>>>>>> this
>>>>>> a problem? Since yt defaults to the Enzo field names, should we try
>>>>>> to make
>>>>>> sure that all fields are defined using the same units as in Enzo? Is
>>>>>> there
>>>>>> a convention for how different codes should define derived fields that
>>>>>> are
>>>>>> aliased to Enzo fields?
>>>>>>
>>>>>> One problem for this particular example is that the Pressure field is
>>>>>> defined in terms of ThermalEnergy in universal_fields.py so the units
>>>>>> of
>>>>>> ThermalEnergy become important if a user merely wants the gas pressure
>>>>>> in
>>>>>> the simulation.
>>>>>>
>>>>>> One possible solution for this issue would be the units overhaul we're
>>>>>> planning. If all fields are associated with a unit object, we can
>>>>>> simply
>>>>>> query the units to ensure that units are taken care of correctly and
>>>>>> code-to-code comparisons aren't sensitive to the units chosen for
>>>>>> fields in
>>>>>> the frontend.
>>>>>>
>>>>>> Personally, I think it would be best if we could make sure that all of
>>>>>> the
>>>>>> fields aliased to Enzo fields have the same units.
>>>>>>
>>>>>> Nathan Goldbaum
>>>>>> Graduate Student
>>>>>> Astronomy& Astrophysics, UCSC
>>>>>>
>>>>>> goldbaum(a)ucolick.org
>>>>>> http://www.ucolick.org/~goldbaum
>>>>>>
>>>>>> _______________________________________________
>>>>>> yt-dev mailing list
>>>>>> yt-dev(a)lists.spacepope.org
>>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> yt-dev mailing list
>>>>> yt-dev(a)lists.spacepope.org
>>>>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>>>>>
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>>>>
>>>> !DSPAM:10175,4f74e5073356450621218!
>>>>
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>>>
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6 years, 11 months
Install script issue
by Andrew Myers
Hello yt developers,
I don't know if this is a "bug," exactly, but I noticed an issue when doing
a clean install of yt today involving the h5py install. Namely, it looks
like if you have an non-empty CFLAGS environment variable (which can happen
without your knowledge if you load certain module files in a supercomputing
environment, for example), the h5py build will proceed without getting the
"-fno-strict-aliasing" flag and the resulting module will not work. You can
get around this either by 1) clobbering CFLAGS, or 2) adding
"-fno-strict-aliasing" to it and re-running the script.
It seems like the install script should either detect this and work around
it, or else warn you that the h5py build has gone of the rails after the
installation, because the tracebacks you get from trying to use the
whacked-out h5py module are not very illuminating. I would do this myself,
but I'm not sure my shell scripting skills are up to the task.
Thanks,
Andrew
6 years, 11 months
