Frequently Asked Questions¶

How can I tell what version of yt I’m using?¶

If you run into problems with yt and you’re writing to the mailing list or contacting developers on IRC, they will likely want to know what version of yt you’re using. Oftentimes, you’ll want to know both the yt version, as well as the last changeset that was committed to the branch you’re using. To reveal this, go to a command line and type:

$ yt version

yt module located at:
    /Users/username/src/yt-x86_64/src/yt-hg
The supplemental repositories are located at:
    /Users/username/src/yt-x86_64/src/yt-supplemental

The current version and changeset for the code is:

---
Version = 2.7-dev
Changeset = 6bffc737a67a
---

This installation CAN be automatically updated.
yt dependencies were last updated on
Wed Dec  4 15:47:40 MST 2013

To update all dependencies, run "yt update --all".

If the changeset is displayed followed by a “+”, it means you have made modifications to the code since the last changeset.

For more information on this topic, see Updating yt and Its Dependencies.

I upgraded to yt 3.0 but my code no longer works. What do I do?¶

Because there are a lot of backwards-incompatible changes in yt 3.0 (see What’s New and Different in yt 3.0?, it can be a daunting effort in transitioning old scripts from yt 2.x to 3.0. We have tried to describe the basic process of making that transition in Converting Old Scripts to Work with yt 3.0. If you just want to change back to yt 2.x for a while until you’re ready to make the transition, you can follow the instructions in Switching between yt-2.x and yt-3.x.

yt fails saying that it cannot import yt modules¶

This is commonly exhibited with this error: ImportError: cannot import name obtain_rvec. This is likely because you need to rebuild the source. You can do this automatically by running:

cd $YT_HG
python setup.py develop

where $YT_HG is the path to the yt mercurial repository.

This error tends to occur when there are changes in the underlying cython files that need to be rebuilt, like after a major code update or in switching from 2.x to 3.x. For more information on this, see Switching between yt-2.x and yt-3.x.

yt complains that it needs the mpi4py module¶

For yt to be able to incorporate parallelism on any of its analysis (see Parallel Computation With yt), it needs to be able to use MPI libraries. This requires the mpi4py module to be installed in your version of python. Unfortunately, installation of mpi4py is just tricky enough to elude the yt batch installer. So if you get an error in yt complaining about mpi4py like:

ImportError: No module named mpi4py

then you should install mpi4py. The easiest way to install it is through the pip interface. At the command line, type:

pip install mpi4py

What this does is it finds your default installation of python (presumably in the yt source directory), and it installs the mpi4py module. If this action is successful, you should never have to worry about your aforementioned problems again. If, on the other hand, this installation fails (as it does on such machines as NICS Kraken, NASA Pleaides and more), then you will have to take matters into your own hands. Usually when it fails, it is due to pip being unable to find your MPI C/C++ compilers (look at the error message). If this is the case, you can specify them explicitly as per:

env MPICC=/path/to/MPICC pip install mpi4py

So for example, on Kraken, I switch to the gnu C compilers (because yt doesn’t work with the portland group C compilers), then I discover that cc is the mpi-enabled C compiler (and it is in my path), so I run:

module swap PrgEnv-pgi PrgEnv-gnu
env MPICC=cc pip install mpi4py

And voila! It installs! If this still fails for you, then you can build and install from source and specify the mpi-enabled c and c++ compilers in the mpi.cfg file. See the mpi4py installation page for details.

How do I get the convert between code units and physical units for my dataset?¶

Converting between physical units and code units is a common task. In yt-2.x, the syntax for getting conversion factors was in the units dictionary (pf.units['kpc']). So in order to convert a variable x in code units to kpc, you might run:

x = x*pf.units['kpc']

In yt-3.0, this no longer works. Conversion factors are tied up in the length_unit, times_unit, mass_unit, and velocity_unit attributes, which can be converted to any arbitrary desired physical unit:

print "Length unit: ", ds.length_unit
print "Time unit: ", ds.time_unit
print "Mass unit: ", ds.mass_unit
print "Velocity unit: ", ds.velocity_unit

print "Length unit: ", ds.length_unit.in_units('code_length')
print "Time unit: ", ds.time_unit.in_units('code_time')
print "Mass unit: ", ds.mass_unit.in_units('kg')
print "Velocity unit: ", ds.velocity_unit.in_units('Mpc/year')

So to accomplish the example task of converting a scalar variable x in code units to kpc in yt-3.0, you can do one of two things. If x is already a YTQuantity with units in code_length, you can run:

x.in_units('kpc')

However, if x is just a numpy array or native python variable without units, you can convert it to a YTQuantity with units of kpc by running:

x = x*ds.length_unit.in_units('kpc')

For more information about unit conversion, see Fields and Unit Conversion.

How do I make a YTQuantity tied to a specific dataset’s units?¶

If you want to create a variable or array that is tied to a particular dataset (and its specific conversion factor to code units), use the ds.quan (for individual variables) and ds.arr (for arrays):

import yt
ds = yt.load(filename)
one_Mpc = ds.quan(1, 'Mpc')
x_vector = ds.arr([1,0,0], 'code_length')

You can then naturally exploit the units system:

print "One Mpc in code_units:", one_Mpc.in_units('code_length')
print "One Mpc in AU:", one_Mpc.in_units('AU')
print "One Mpc in comoving kpc:", one_Mpc.in_units('kpccm')

For more information about unit conversion, see Fields and Unit Conversion.

How do I access the unitless data in a YTQuantity or YTArray?¶

While there are numerous benefits to having units tied to individual quantities in yt, they can also produce issues when simply trying to combine YTQuantities with numpy arrays or native python floats that lack units. A simple example of this is:

# Create a YTQuantity that is 1 kpc in length and tied to the units of
# dataset ds
>>> x = ds.quan(1, 'kpc')

# Try to add this to some non-dimensional quantity
>>> print x + 1

YTUnitOperationError: The addition operator for YTArrays with units (kpc) and (1) is not well defined.

The solution to this means using the YTQuantity and YTArray objects for all of one’s computations, but this isn’t always feasible. A quick fix for this is to just grab the unitless data out of a YTQuantity or YTArray object with the value and v attributes, which return a copy, or with the d attribute, which returns the data itself:

x = ds.quan(1, 'kpc')
x_val = x.v
print x_val

array(1.0)

# Try to add this to some non-dimensional quantity
print x + 1

2.0

For more information about this functionality with units, see Fields and Unit Conversion.

How do I modify whether or not yt takes the log of a particular field?¶

yt sets up defaults for many fields for whether or not a field is presented in log or linear space. To override this behavior, you can modify the field_info dictionary. For example, if you prefer that density not be logged, you could type:

ds = load("my_data")
ds.index
ds.field_info['density'].take_log = False

From that point forward, data products such as slices, projections, etc., would be presented in linear space. Note that you have to instantiate ds.index before you can access ds.field info. For more information see the documentation on Fields in yt and Creating Derived Fields.

I added a new field to my simulation data, can yt see it?¶

Yes! yt identifies all the fields in the simulation’s output file and will add them to its field_list even if they aren’t listed in Field List. These can then be accessed in the usual manner. For example, if you have created a field for the potential called PotentialField, you could type:

ds = load("my_data")
ad = ds.all_data()
potential_field = ad["PotentialField"]

The same applies to fields you might derive inside your yt script via Creating Derived Fields. To check what fields are available, look at the properties field_list and derived_field_list:

print ds.field_list
print ds.derived_field_list

or for a more legible version, try:

for field in ds.derived_field_list:
    print field

What is the difference between yt.add_field() and ds.add_field()?¶

The global yt.add_field() (add_field()) function is for adding a field for every subsequent dataset that is loaded in a particular python session, whereas ds.add_field() (add_field()) will only add it to dataset ds.

Why are the values in my Ray object out of order?¶

Using the Ray objects (YTOrthoRayBase and YTRayBase) with AMR data gives non-contiguous cell information in the Ray’s data array. The higher-resolution cells are appended to the end of the array. Unfortunately, due to how data is loaded by chunks for data containers, there is really no easy way to fix this internally. However, there is an easy workaround.

One can sort the Ray array data by the t field, which is the value of the parametric variable that goes from 0 at the start of the ray to 1 at the end. That way the data will always be ordered correctly. As an example you can:

my_ray = ds.ray(...)
ray_sort = np.argsort(my_ray["t"])
density = my_ray["density"][ray_sort]

There is also a full example in the Line Plots section of the docs.

Someone asked me to make a Pull Request (PR) to yt. How do I do that?¶

A pull request is the action by which you contribute code to yt. You make modifications in your local copy of the source code, then request that other yt developers review and accept your changes to the main code base. For a full description of the steps necessary to successfully contribute code and issue a pull request (or manage multiple versions of the source code) please see Making and Sharing Changes.

Someone asked me to file an issue or a bug report for a bug I found. How?¶

See Submit a bug report and Making and Sharing Changes.

How can I get some sample data for yt?¶

Many different sample datasets can be found at http://yt-project.org/data/ . These can be downloaded, unarchived, and they will each create their own directory. It is generally straight forward to load these datasets, but if you have any questions about loading data from a code with which you are unfamiliar, please visit Loading Data.

To make things easier to load these sample datasets, you can add the parent directory to your downloaded sample data to your yt path. If you set the option test_data_dir, in the section [yt], in ~/.yt/config, yt will search this path for them.

This means you can download these datasets to /big_drive/data_for_yt , add the appropriate item to ~/.yt/config, and no matter which directory you are in when running yt, it will also check in that directory.

I can’t scroll-up to previous commands inside python¶

If the up-arrow key does not recall the most recent commands, there is probably an issue with the readline library. To ensure the yt python environment can use readline, run the following command:

$ ~/yt/bin/pip install gnureadline

yt seems to be plotting from old data¶

yt does check the time stamp of the simulation so that if you overwrite your data outputs, the new set will be read in fresh by yt. However, if you have problems or the yt output seems to be in someway corrupted, try deleting the .yt and .harray files from inside your data directory. If this proves to be a persistent problem add the line:

from yt.config import ytcfg; ytcfg["yt","serialize"] = "False"

to the very top of your yt script. Turning off serialization is the default behavior in yt-3.0.

How can I change yt’s log level?¶

yt’s default log level is INFO. However, you may want less voluminous logging, especially if you are in an IPython notebook or running a long or parallel script. On the other hand, you may want it to output a lot more, since you can’t figure out exactly what’s going wrong, and you want to output some debugging information. The yt log level can be changed using the Configuration File, either by setting it in the $HOME/.yt/config file:

[yt]
loglevel = 10 # This sets the log level to "DEBUG"

which would produce debug (as well as info, warning, and error) messages, or at runtime:

from yt.config import ytcfg
ytcfg["yt","loglevel"] = "40" # This sets the log level to "ERROR"

which in this case would suppress everything below error messages. For reference, the numerical values corresponding to different log levels are:

Can I always load custom data objects, fields, and quantities with every dataset?¶

The plugin file is a means of modifying the available fields, quantities, data objects and so on without modifying the source code of yt. The plugin file will be executed if it is detected. It must be located in a .yt folder in your home directory and be named my_plugins.py:

$HOME/.yt/my_plugins.py

The code in this file can add fields, define functions, define datatypes, and on and on. It is executed at the bottom of yt.mods, and so it is provided with the entire namespace available in the module yt.mods. For example, if I created a plugin file containing:

def _myfunc(field, data):
    return np.random.random(data["density"].shape)
add_field("some_quantity", function=_myfunc, units='')

then all of my data objects would have access to the field “some_quantity”. Note that the units must be specified as a string, see Fields and Unit Conversion for more details on units and derived fields.

You can also define other convenience functions in your plugin file. For instance, you could define some variables or functions, and even import common modules:

import os

HOMEDIR="/home/username/"
RUNDIR="/scratch/runs/"

def load_run(fn):
    if not os.path.exists(RUNDIR + fn):
        return None
    return load(RUNDIR + fn)

In this case, we’ve written load_run to look in a specific directory to see if it can find an output with the given name. So now we can write scripts that use this function:

from yt.mods import *

my_run = load_run("hotgasflow/DD0040/DD0040")

And because we have imported from yt.mods we have access to the load_run function defined in our plugin file.

How do I cite yt?¶

If you use yt in a publication, we’d very much appreciate a citation! You should feel free to cite the ApJS paper with the following BibTeX entry:

@ARTICLE{2011ApJS..192....9T,
   author = {{Turk}, M.~J. and {Smith}, B.~D. and {Oishi}, J.~S. and {Skory}, S. and
     {Skillman}, S.~W. and {Abel}, T. and {Norman}, M.~L.},
    title = "{yt: A Multi-code Analysis Toolkit for Astrophysical Simulation Data}",
  journal = {\apjs},
archivePrefix = "arXiv",
   eprint = {1011.3514},
 primaryClass = "astro-ph.IM",
 keywords = {cosmology: theory, methods: data analysis, methods: numerical },
     year = 2011,
    month = jan,
   volume = 192,
    pages = {9-+},
      doi = {10.1088/0067-0049/192/1/9},
   adsurl = {http://adsabs.harvard.edu/abs/2011ApJS..192....9T},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}