Parallel Computation With yt

yt has been instrumented with the ability to compute many – most, even – quantities in parallel. This utilizes the package mpi4py to parallelize using the Message Passing Interface, typically installed on clusters.

Capabilities

Currently, yt is able to perform the following actions in parallel:

This list covers just about every action yt can take! Additionally, almost all scripts will benefit from parallelization with minimal modification. The goal of Parallel-yt has been to retain API compatibility and abstract all parallelism.

Setting Up Parallel yt

To run scripts in parallel, you must first install mpi4py as well as an MPI library, if one is not already available on your system. Instructions for doing so are provided on the mpi4py website, but you may have luck by just running:

$ pip install mpi4py

If you have an Anaconda installation of yt and there is no MPI library on the system you are using try:

$ conda install mpi4py

This will install MPICH2 and will interfere with other MPI libraries that are already installed. Therefore, it is preferable to use the pip installation method.

Once mpi4py has been installed, you’re all done! You just need to launch your scripts with mpirun (or equivalent) and signal to yt that you want to run them in parallel by invoking the yt.enable_parallelism() function in your script. In general, that’s all it takes to get a speed benefit on a multi-core machine. Here is an example on an 8-core desktop:

$ mpirun -np 8 python script.py

Throughout its normal operation, yt keeps you aware of what is happening with regular messages to the stderr usually prefaced with:

yt : [INFO   ] YYY-MM-DD HH:MM:SS

However, when operating in parallel mode, yt outputs information from each of your processors to this log mode, as in:

P000 yt : [INFO   ] YYY-MM-DD HH:MM:SS
P001 yt : [INFO   ] YYY-MM-DD HH:MM:SS

in the case of two cores being used.

It’s important to note that all of the processes listed in Capabilities work in parallel – and no additional work is necessary to parallelize those processes.

Running a yt Script in Parallel

Many basic yt operations will run in parallel if yt’s parallelism is enabled at startup. For example, the following script finds the maximum density location in the simulation and then makes a plot of the projected density:

import yt
yt.enable_parallelism()

ds = yt.load("RD0035/RedshiftOutput0035")
v, c = ds.find_max("density")
print(v, c)
p = yt.ProjectionPlot(ds, "x", "density")
p.save()

If this script is run in parallel, two of the most expensive operations - finding of the maximum density and the projection will be calculated in parallel. If we save the script as my_script.py, we would run it on 16 MPI processes using the following Bash command:

$ mpirun -np 16 python2.7 my_script.py

Note

If you run into problems, the you can use Remote and Disconnected Debugging to examine what went wrong.

How do I run my yt job on a subset of available processes

You can set the communicator keyword in the enable_parallelism() call to a specific MPI communicator to specify a subset of available MPI processes. If none is specified, it defaults to COMM_WORLD.

Creating Parallel and Serial Sections in a Script

Many yt operations will automatically run in parallel (see the next section for a full enumeration), however some operations, particularly ones that print output or save data to the filesystem, will be run by all processors in a parallel script. For example, in the script above the lines print(v, c) and p.save() will be run on all 16 processors. This means that your terminal output will contain 16 repetitions of the output of the print statement and the plot will be saved to disk 16 times (overwritten each time).

yt provides two convenience functions that make it easier to run most of a script in parallel but run some subset of the script on only one processor. The first, is_root(), returns True if run on the ‘root’ processor (the processor with MPI rank 0) and False otherwise. One could rewrite the above script to take advantage of is_root() like so:

import yt
yt.enable_parallelism()

ds = yt.load("RD0035/RedshiftOutput0035")
v, c = ds.find_max("density")
p = yt.ProjectionPlot(ds, "x", "density")
if yt.is_root():
    print(v, c)
    p.save()

The second function, only_on_root() accepts the name of a function as well as a set of parameters and keyword arguments to pass to the function. This is useful when the serial component of your parallel script would clutter the script or if you like writing your scripts as a series of isolated function calls. I can rewrite the example from the beginning of this section once more using only_on_root() to give you the flavor of how to use it:

import yt
yt.enable_parallelism()

def print_and_save_plot(v, c, plot, verbose=True):
    if verbose:
       print(v, c)
    plot.save()

ds = yt.load("RD0035/RedshiftOutput0035")
v, c = ds.find_max("density")
p = yt.ProjectionPlot(ds, "x", "density")
yt.only_on_root(print_and_save_plot, v, c, plot, verbose=True)

Types of Parallelism

In order to divide up the work, yt will attempt to send different tasks to different processors. However, to minimize inter-process communication, yt will decompose the information in different ways based on the task.

Spatial Decomposition

During this process, the index will be decomposed along either all three axes or along an image plane, if the process is that of projection. This type of parallelism is overall less efficient than grid-based parallelism, but it has been shown to obtain good results overall.

The following operations use spatial decomposition:

Grid Decomposition

The alternative to spatial decomposition is a simple round-robin of data chunks, which could be grids, octs, or whatever chunking mechanism is used by the code frontend begin used. This process allows yt to pool data access to a given data file, which ultimately results in faster read times and better parallelism.

The following operations use chunk decomposition:

Parallelization over Multiple Objects and Datasets

If you have a set of computational steps that need to apply identically and independently to several different objects or datasets, a so-called embarrassingly parallel task, yt can do that easily. See the sections below on Parallelizing over Multiple Objects and Parallelization over Multiple Datasets (including Time Series).

Use of piter()

If you use parallelism over objects or datasets, you will encounter the piter() function. piter is a parallel iterator, which effectively doles out each item of a DatasetSeries object to a different processor. In serial processing, you might iterate over a DatasetSeries by:

for dataset in dataset_series:
    <process>

But in parallel, you can use piter() to force each dataset to go to a different processor:

yt.enable_parallelism()
for dataset in dataset_series.piter():
    <process>

In order to store information from the parallel processing step to a data structure that exists on all of the processors operating in parallel we offer the storage keyword in the piter function. You may define an empty dictionary and include it as the keyword argument storage to piter(). Then, during the processing step, you can access this dictionary as the sto object. After the loop is finished, the dictionary is re-aggregated from all of the processors, and you can access the contents:

yt.enable_parallelism()
my_dictionary = {}
for sto, dataset in dataset_series.piter(storage=my_dictionary):
    <process>
    sto.result = <some information processed for this dataset>
    sto.result_id = <some identfier for this dataset>

print(my_dictionary)

Parallelizing over Multiple Objects

It is easy within yt to parallelize a list of tasks, as long as those tasks are independent of one another. Using object-based parallelism, the function parallel_objects() will automatically split up a list of tasks over the specified number of processors (or cores). Please see this heavily-commented example:

# As always...
import yt
yt.enable_parallelism()

import glob

# The number 4, below, is the number of processes to parallelize over, which
# is generally equal to the number of MPI tasks the job is launched with.
# If num_procs is set to zero or a negative number, the for loop below
# will be run such that each iteration of the loop is done by a single MPI
# task. Put another way, setting it to zero means that no matter how many
# MPI tasks the job is run with, num_procs will default to the number of
# MPI tasks automatically.
num_procs = 4

# fns is a list of all the simulation data files in the current directory.
fns = glob.glob("./plot*")
fns.sort()

# This dict will store information collected in the loop, below.
# Inside the loop each task will have a local copy of the dict, but
# the dict will be combined once the loop finishes.
my_storage = {}

# In this example, because the storage option is used in the
# parallel_objects function, the loop yields a tuple, which gets used
# as (sto, fn) inside the loop.
# In the loop, sto is essentially my_storage, but a local copy of it.
# If data does not need to be combined after the loop is done, the line
# would look like:
#       for fn in parallel_objects(fns, num_procs):
for sto, fn in yt.parallel_objects(fns, num_procs, storage = my_storage):

    # Open a data file, remembering that fn is different on each task.
    ds = yt.load(fn)
    dd = ds.all_data()

    # This copies fn and the min/max of density to the local copy of
    # my_storage
    sto.result_id = fn
    sto.result = dd.quantities.extrema("density")

    # Makes and saves a plot of the gas density.
    p = yt.ProjectionPlot(ds, "x", "density")
    p.save()

# At this point, as the loop exits, the local copies of my_storage are
# combined such that all tasks now have an identical and full version of
# my_storage. Until this point, each task is unaware of what the other
# tasks have produced.
# Below, the values in my_storage are printed by only one task. The other
# tasks do nothing.
if yt.is_root()
    for fn, vals in sorted(my_storage.items()):
        print(fn, vals)

This example above can be modified to loop over anything that can be saved to a Python list: halos, data files, arrays, and more.

Parallelization over Multiple Datasets (including Time Series)

The same parallel_objects machinery discussed above is turned on by default when using a DatasetSeries object (see Time Series Analysis) to iterate over simulation outputs. The syntax for this is very simple. As an example, we can use the following script to find the angular momentum vector in a 1 pc sphere centered on the maximum density cell in a large number of simulation outputs:

import yt
yt.enable_parallelism()

# Load all of the DD*/output_* files into a DatasetSeries object
# in this case it is a Time Series
ts = yt.load("DD*/output_*")

# Define an empty storage dictionary for collecting information
# in parallel through processing
storage = {}

# Use piter() to iterate over the time series, one proc per dataset
# and store the resulting information from each dataset in
# the storage dictionary
for sto, ds in ts.piter(storage=storage):
    sphere = ds.sphere("max", (1.0, "pc"))
    sto.result = sphere.quantities.angular_momentum_vector()
    sto.result_id = str(ds)

# Print out the angular momentum vector for all of the datasets
for L in sorted(storage.items()):
    print(L)

Note that this script can be run in serial or parallel with an arbitrary number of processors. When running in parallel, each output is given to a different processor.

You can also request a fixed number of processors to calculate each angular momentum vector. For example, the following script will calculate each angular momentum vector using 4 workgroups, splitting up the pool available processors. Note that parallel=1 implies that the analysis will be run using 1 workgroup, whereas parallel=True will run with Nprocs workgroups.

import yt
yt.enable_parallelism()

ts = yt.DatasetSeries("DD*/output_*", parallel = 4)

for ds in ts.piter():
    sphere = ds.sphere("max", (1.0, "pc))
    L_vecs = sphere.quantities.angular_momentum_vector()

If you do not want to use parallel_objects parallelism when using a DatasetSeries object, set parallel = False. When running python in parallel, this will use all of the available processors to evaluate the requested operation on each simulation output. Some care and possibly trial and error might be necessary to estimate the correct settings for your simulation outputs.

Parallel Performance, Resources, and Tuning

Optimizing parallel jobs in yt is difficult; there are many parameters that affect how well and quickly the job runs. In many cases, the only way to find out what the minimum (or optimal) number of processors is, or amount of memory needed, is through trial and error. However, this section will attempt to provide some insight into what are good starting values for a given parallel task.

Chunk Decomposition

In general, these types of parallel calculations scale very well with number of processors. They are also fairly memory-conservative. The two limiting factors is therefore the number of chunks in the dataset, and the speed of the disk the data is stored on. There is no point in running a parallel job of this kind with more processors than chunks, because the extra processors will do absolutely nothing, and will in fact probably just serve to slow down the whole calculation due to the extra overhead. The speed of the disk is also a consideration - if it is not a high-end parallel file system, adding more tasks will not speed up the calculation if the disk is already swamped with activity.

The best advice for these sort of calculations is to run with just a few processors and go from there, seeing if it the runtime improves noticeably.

Projections, Slices, and Cutting Planes

Projections, slices and cutting planes are the most common methods of creating two-dimensional representations of data. All three have been parallelized in a chunk-based fashion.

  • Projections: projections are parallelized utilizing a quad-tree approach. Data is loaded for each processor, typically by a process that consolidates open/close/read operations, and each grid is then iterated over and cells are deposited into a data structure that stores values corresponding to positions in the two-dimensional plane. This provides excellent load balancing, and in serial is quite fast. However, the operation by which quadtrees are joined across processors scales poorly; while memory consumption scales well, the time to completion does not. As such, projections can often be done very fast when operating only on a single processor! The quadtree algorithm can be used inline (and, indeed, it is for this reason that it is slow.) It is recommended that you attempt to project in serial before projecting in parallel; even for the very largest datasets (Enzo 1024^3 root grid with 7 levels of refinement) in the absence of IO the quadtree algorithm takes only three minutes or so on a decent processor.
  • Slices: to generate a slice, chunks that intersect a given slice are iterated over and their finest-resolution cells are deposited. The chunks are decomposed via standard load balancing. While this operation is parallel, it is almost never necessary to slice a dataset in parallel, as all data is loaded on demand anyway. The slice operation has been parallelized so as to enable slicing when running in situ.
  • Cutting planes: cutting planes are parallelized exactly as slices are. However, in contrast to slices, because the data-selection operation can be much more time consuming, cutting planes often benefit from parallelism.

Object-Based

Like chunk decomposition, it does not help to run with more processors than the number of objects to be iterated over. There is also the matter of the kind of work being done on each object, and whether it is disk-intensive, cpu-intensive, or memory-intensive. It is up to the user to figure out what limits the performance of their script, and use the correct amount of resources, accordingly.

Disk-intensive jobs are limited by the speed of the file system, as above, and extra processors beyond its capability are likely counter-productive. It may require some testing or research (e.g. supercomputer documentation) to find out what the file system is capable of.

If it is cpu-intensive, it’s best to use as many processors as possible and practical.

For a memory-intensive job, each processor needs to be able to allocate enough memory, which may mean using fewer than the maximum number of tasks per compute node, and increasing the number of nodes. The memory used per processor should be calculated, compared to the memory on each compute node, which dictates how many tasks per node. After that, the number of processors used overall is dictated by the disk system or CPU-intensity of the job.

Domain Decomposition

The various types of analysis that utilize domain decomposition use them in different enough ways that they are be discussed separately.

Halo-Finding

Halo finding, along with the merger tree that uses halo finding, operates on the particles in the volume, and is therefore mostly chunk-agnostic. Generally, the biggest concern for halo finding is the amount of memory needed. There is subtle art in estimating the amount of memory needed for halo finding, but a rule of thumb is that the HOP halo finder is the most memory intensive (HaloFinder()), and Friends of Friends (FOFHaloFinder()) being the most memory-conservative. For more information, see Halo Analysis.

Volume Rendering

The simplest way to think about volume rendering, is that it load-balances over the i/o chunks in the dataset. Each processor is given roughly the same sized volume to operate on. In practice, there are just a few things to keep in mind when doing volume rendering. First, it only uses a power of two number of processors. If the job is run with 100 processors, only 64 of them will actually do anything. Second, the absolute maximum number of processors is the number of chunks. In order to keep work distributed evenly, typically the number of processors should be no greater than one-eighth or one-quarter the number of processors that were used to produce the dataset. For more information, see 3D Visualization and Volume Rendering.

Additional Tips

  • Don’t be afraid to change how a parallel job is run. Change the number of processors, or memory allocated, and see if things work better or worse. After all, it’s just a computer, it doesn’t pass moral judgment!
  • Similarly, human time is more valuable than computer time. Try increasing the number of processors, and see if the runtime drops significantly. There will be a sweet spot between speed of run and the waiting time in the job scheduler queue; it may be worth trying to find it.
  • If you are using object-based parallelism but doing CPU-intensive computations on each object, you may find that setting num_procs equal to the number of processors per compute node can lead to significant speedups. By default, most mpi implementations will assign tasks to processors on a ‘by-slot’ basis, so this setting will tell yt to do computations on a single object using only the processors on a single compute node. A nice application for this type of parallelism is calculating a list of derived quantities for a large number of simulation outputs.
  • It is impossible to tune a parallel operation without understanding what’s going on. Read the documentation, look at the underlying code, or talk to other yt users. Get informed!
  • Sometimes it is difficult to know if a job is cpu, memory, or disk intensive, especially if the parallel job utilizes several of the kinds of parallelism discussed above. In this case, it may be worthwhile to put some simple timers in your script (as below) around different parts.
import yt
import time

yt.enable_parallelism()

ds = yt.load("DD0152")
t0 = time.time()
bigstuff, hugestuff = StuffFinder(ds)
BigHugeStuffParallelFunction(ds, bigstuff, hugestuff)
t1 = time.time()
for i in range(1000000):
    tinystuff, ministuff = GetTinyMiniStuffOffDisk("in%06d.txt" % i)
    array = TinyTeensyParallelFunction(ds, tinystuff, ministuff)
    SaveTinyMiniStuffToDisk("out%06d.txt" % i, array)
t2 = time.time()

if yt.is_root()
    print("BigStuff took %.5e sec, TinyStuff took %.5e sec" % (t1 - t0, t2 - t1))
  • Remember that if the script handles disk IO explicitly, and does not use a built-in yt function to write data to disk, care must be taken to avoid race-conditions. Be explicit about which MPI task writes to disk using a construction something like this:
if yt.is_root()
    file = open("out.txt", "w")
    file.write(stuff)
    file.close()
  • Many supercomputers allow users to ssh into the nodes that their job is running on. Many job schedulers send the names of the nodes that are used in the notification emails, or a command like qstat -f NNNN, where NNNN is the job ID, will also show this information. By ssh-ing into nodes, the memory usage of each task can be viewed in real-time as the job runs (using top, for example), and can give valuable feedback about the resources the task requires.

An Advanced Worked Example

Below is a script used to calculate the redshift of first 99.9% ionization in a simulation. This script was designed to analyze a set of 100 outputs on Gordon, running on 128 processors. This script goes through three phases:

  1. Define a new derived field, which calculates the fraction of ionized hydrogen as a function only of the total hydrogen density.
  2. Load a time series up, specifying parallel = 8. This means that it will decompose into 8 jobs. So if we ran on 128 processors, we would have 16 processors assigned to each output in the time series.
  3. Creating a big cube that will hold our results for this set of processors. Note that this will be only for each output considered by this processor, and this cube will not necessarily be filled in in every cell.
  4. For each output, distribute the grids to each of the sixteen processors working on that output. Each of these takes the max of the ionized redshift in their zone versus the accumulation cube.
  5. Iterate over slabs and find the maximum redshift in each slab of our accumulation cube.

At the end, the root processor (of the global calculation) writes out an ionization cube that contains the redshift of first reionization for each zone across all outputs.

import yt
from yt.utilities.parallel_tools.parallel_analysis_interface \
    import communication_system

import h5py
import time
import numpy as np

@yt.derived_field(name="IonizedHydrogen", units="",
                  display_name=r"\frac{\rho_{HII}}{\rho_H}")
def IonizedHydrogen(field, data):
    return data["HII_Density"]/(data["HI_Density"]+data["HII_Density"])

ts = yt.DatasetSeries("SED800/DD*/*.index", parallel=8)

ionized_z = np.zeros(ts[0].domain_dimensions, dtype="float32")

t1 = time.time()
for ds in ts.piter():
    z = ds.current_redshift
    for g in parallel_objects(ds.index.grids, njobs = 16):
        i1, j1, k1 = g.get_global_startindex() # Index into our domain
        i2, j2, k2 = g.get_global_startindex() + g.ActiveDimensions
        # Look for the newly ionized gas
        newly_ion = ((g["IonizedHydrogen"] > 0.999)
                   & (ionized_z[i1:i2,j1:j2,k1:k2] < z))
        ionized_z[i1:i2,j1:j2,k1:k2][newly_ion] = z
        g.clear_data()

print("Iteration completed  %0.3e" % (time.time()-t1))
comm = communication_system.communicators[-1]
for i in range(ionized_z.shape[0]):
    ionized_z[i,:,:] = comm.mpi_allreduce(ionized_z[i,:,:], op="max")
    print("Slab % 3i has minimum z of %0.3e" % (i, ionized_z[i,:,:].max()))
t2 = time.time()
print("Completed.  %0.3e" % (t2-t1))

if comm.rank == 0:
    f = h5py.File("IonizationCube.h5", "w")
    f.create_dataset("/z", data=ionized_z)