First Impressions of GPUs and PyData

Opportunities and challenges to integrating GPUs into traditional data science workloads

Mike Beaumont

Published in

RAPIDS AI

13 min readDec 17, 2018

By: Matthew Rocklin

I recently moved from Anaconda to NVIDIA within the RAPIDS team, which is building a PyData-friendly GPU-enabled data science stack. For my first week I explored some of the current challenges of working with GPUs in the PyData ecosystem. This post shares my first impressions and also outlines plans for near-term work.

First, lets start with the value proposition of GPUs, significant speed increases over traditional CPUs.

GPU performance

Like many PyData developers, I’m loosely aware that GPUs are sometimes fast, but don’t deal with them often enough to have strong feeling about them.

To get a more visceral feel for the performance differences, I logged into a GPU machine, opened up CuPy (a Numpy-like GPU library developed mostly by Chainer in Japan) and cuDF (a pandas-like library in development at NVIDIA) and did a couple of small speed comparisons:

Compare Numpy and CuPy

>>> import numpy, cupy

>>> x = numpy.random.random((10000, 10000))
>>> y = cupy.random.random((10000, 10000))

>>> %timeit bool((numpy.sin(x) ** 2 + numpy.cos(x) ** 2 == 1).all())
446 ms ± 53.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

>>> %timeit bool((cupy.sin(y) ** 2 + cupy.cos(y) ** 2 == 1).all())
86.3 ms ± 50.7 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

On this mundane example, the GPU computation is a full 5x faster.

Compare pandas and cuDF

>>> import pandas as pd, numpy as np, cudf

>>> pdf = pd.DataFrame({'x': np.random.random(10000000),
                        'y': np.random.randint(0, 10000000, size=10000000)})
>>> gdf = cudf.DataFrame.from_pandas(pdf)

>>> %timeit pdf.x.mean()  # 30x faster
50.2 ms ± 970 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)
>>> %timeit gdf.x.mean()
1.42 ms ± 5.84 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

>>> %timeit pdf.groupby('y').mean()  # 40x faster
1.15 s ± 46.5 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
>>> %timeit gdf.groupby('y').mean()
54 ms ± 182 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

>>> %timeit pdf.merge(pdf, on='y')  # 30x faster
10.3 s ± 38.2 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
>>> %timeit gdf.merge(gdf, on='y')
280 ms ± 856 µs per loop (mean ± std. dev. of 7 runs, 1 loop each)

This is a 30–40x speedup for normal dataframe computing. Operations that previously took ten seconds now process in near-interactive speeds.

These were done naively on one GPU on a DGX machine. The dataframe examples were cherry-picked to find supported operations (see dataframe issues below).

Analysis

This speed difference is potentially transformative to a number of scientific disciplines. I intentionally tried examples that were more generic than typical deep learning workloads today, examples that might represent more traditional scientific computing and data processing tasks.

GPUs seem to offer orders-of-magnitude performance increases over traditional CPUs (at least in the naive cases presented above). This speed difference is an interesting lever for us to push on, and is what made me curious about working for NVIDIA in the first place.

Roadblocks

However, there are many reasons why people don’t use GPUs for general purpose computational programming today. I thought I’d go through a few of them in this blogpost so we can see the sorts of things that we would need to resolve.

Not everyone has a GPU. They can be large and expensive
Installing CUDA-enabled libraries can be tricky, even with conda
Current CUDA-enabled libraries don’t yet form a coherent ecosystem with established conventions

Many of the libraries around RAPIDS need specific help:

cuDF is immature, and needs many simple API and feature improvements
Array computing libraries need protocols to share data and functionality
Deep learning libraries have functionality, but don’t share functionality easily
Deploying Dask on multi-GPU systems can be improved
Python needs better access to high performance communication libraries

This is just my personal experience which, let me be clear, is only limited to a few days. I’m probably wrong about many topics I discuss below.

Not everyone has a GPU

GPUs can be expensive and hard to put into consumer laptops, so there is a simple availability problem. Most people can’t just crack open a laptop, start IPython or a Jupyter notebook, and try something out immediately.

However, most data scientists, actual scientists, and students that I run into today do have some access to GPU resources through their institution. Many companies, labs, and universities today have purchased a GPU cluster that, more often than not, sits under-utilized. These are often an ssh command away, and generally available.

Two weeks ago I visited with Joe Hamman, a scientific collaborator at NCAR and UW eScience institute and he said “Oh yeah, we have a GPU cluster at work that I never use”. About 20 minutes later he had a GPU stack installed and was running an experiment very much like what we did above.

Installing CUDA-enabled libraries is complicated by drivers

Before conda packages, wheels, Anaconda, and conda forge, installing the PyData software stack (Numpy, pandas, scikit-learn, Matplotlib) was challenging. This was because users had to match a combination of system libraries, compiler stacks, and Python packages. “Oh, you’re on Mac? First brew install X, then make sure you have gfortran, then pip install scipy”

The ecosystem solved this pain by bringing the entire stack under the single umbrella of conda where everything could be managed consistently, or alternatively was greatly diminished with pip wheels.

Unfortunately, CUDA drivers have to be managed on the system side, so we’re back to matching system libraries with Python libraries, depending on what CUDA version you’re using.

Here are PyTorch’s installation instructions as an example:

CUDA 8.0: conda install pytorch torchvision cuda80 -c pytorch
CUDA 9.2: conda install pytorch torchvision -c pytorch
CUDA 10.0: conda install pytorch torchvision cuda100 -c pytorch
No CUDA: conda install pytorch-cpu torchvision-cpu -c pytorch

Additionally, these conventions differ from the conventions used by Anaconda’s packaging of TensorFlow and NVIDIA’s packaging of RAPIDS. This inconsistency in convention makes it unlikely that a novice user will get a working system if they don’t do some research ahead of time. PyData survives by courting non-expert computer users (they’re often experts in some other field) so this is a challenge.

There is some work happening in Conda that can help with this in the future. Regardless, we will need to develop better shared conventions between the different Python GPU development groups.

No community standard build infrastructure exists

After speaking about this with John Kirkham (Conda Forge maintainer), he suggested that the situation is also a bit like the conda ecosystem before conda-forge, where everyone built their own packages however they liked and uploaded them to anaconda.org without agreeing on a common build environment. As much of the scientific community knows, this inconsistency can lead to a fragmented stack, where certain families of packages work well only with certain packages within their family.

Development teams are fragmented across companies

Many of the large GPU-enabled packages are being developed by large teams within private institutions. There isn’t a strong culture of cross-team collaboration.

After working with the RAPIDS team at NVIDIA for a week my sense is that this is only due to being unaware of how to act, and not any nefarious purpose (or they were very good at hiding that nefarious purpose). I suspect that the broader community will be able to bring these groups more into the open quickly if they engage.

RAPIDS and Dask need specific attention

Now we switch and discuss technical issues in the RAPIDS stack, and Dask’s engagement with GPUs generally. This will be lower-level, but shows the kinds of things that I hope to work on technically over the coming months.

Generally the goal of RAPIDS is to build a data science stack around conventional numeric computation that mimics the PyData/SciPy stack. They seem to be targeting libraries like:

pandas by building a new library, cuDF
scikit-learn / traditional non-deep machine learning by building a new library cuML
Numpy by leveraging existing libraries like CuPy, PyTorch, TensorFlow, and focusing on improving interoperation within the ecosystem

Driven by the standard collection of scientific/data centric applications like imaging, earth science, ETL, finance, and so on.

Now lets talk about the current challenges for those systems. In general, none of this stack is yet mature (except for the array-computing-in-deep-learning case).

cuDF is missing pandas functionality

fWhen I showed cuDF at the top of this post, I ran the following computations, which ran 30–40x as fast as pandas.

gdf.x.mean()
gdf.groupby('y').mean()
gdf.merge(gdf, on='y')

What I failed to show was that many operations erred. The cuDF library has great promise, but still needs work filling out the pandas API.

# There are many holes in the cuDF API
cudf.read_csv(...)      # works
cudf.read_parquet(...)  # fails if compression is present

df.x.mean()  # works
df.mean()    # fails

df.groupby('id').mean()     # works
df.groupby('id').x.mean()   # fails
df.x.groupby(df.id).mean()  # fails

Fortunately, this work is happening quickly (GitHub issues seem to turn quickly into PRs) and is mostly straightforward on the Python side. This is a good opportunity for community members who are looking to have a quick impact. There are lots of low-hanging fruit.

Additionally, there are areas where the cudf semantics don’t match pandas semantics. In general this is fine (not everyone loves pandas semantics) but it makes it difficult as we try to wrap Dask Dataframe around cuDF. We would like to grow Dask Dataframe so that it can accept pandas-like dataframes and so then get out-of-core GPU dataframes on a single node, and distributed GPU dataframes on multi-GPU or multi-node, and we would like to grow cudf so that it can fit into this expectation.

This work has to happen both at the low-level C++/CUDA code, and also at the Python level. The sense I get is that NVIDIA has a ton of people available at the CUDA level, but only a few (very good) people at the Python level who are working to keep up (come help!).

Array computing is robust, but fragmented

The Numpy experience is much smoother, mostly because of the excitement around deep learning over the last few years. Many large tech companies have made their own deep learning framework, each of which contains a partial clone of the Numpy API. These include libraries like TensorFlow, PyTorch, Chainer/CuPy, and others.

This is great because these libraries provide high quality functionality to choose from, but is also painful because the ecosystem is heavily fragmented. Data allocated with TensorFlow can’t be computed on with Numba or CuPy operations.

We can help to heal this rift with a few technical approaches:

A standard to communicate low-level information about GPU arrays between frameworks. This would include information about an array like a device memory pointer, datatype, shape, strides, and so on, similar to what is in the Python buffer protocol today. This would allow people to allocate an array with one framework, but then use computational operations defined in another framework. The Numba team prototyped something like this a few months ago, and the CuPy team seemed happy enough with it. See cupy/cupy #1144. This was also, I believe, accepted into PyTorch.

@property
def __cuda_array_interface__(self):
    desc = {
        'shape': self.shape,
        'typestr': self.dtype.str,
        'descr': self.dtype.descr,
        'data': (self.data.mem.ptr, False),
        'version': 0,
    }
    if not self._c_contiguous:
        desc['strides'] = self._strides
     return desc

A standard way for developers to write backend-agnostic array code. Currently my favorite approach is to use Numpy functions as a lingua franca, and to allow the frameworks to hijack those functions and interpret them as they will.
This was proposed and accepted within Numpy itself in NEP-0018 and has been pushed forward by people like Stephan Hoyer, Hameer Abbasi, Marten van Kerkwijk, and Eric Wieser.
This is also useful for other array libraries, like pydata/sparse and dask array, and would go a long way towards unifying operations with libraries like XArray.

cuML needs features, Scikit-Learn needs datastructure agnosticism

While deep learning on the GPU is commonplace today, more traditional algorithms like GLMs, random forests, preprocessing and so on haven’t received the same thorough treatment.

Fortunately the ecosystem is well prepared to accept work in this space, largely because Scikit Learn established a simple pluggable API early on. Building new estimators in external libraries that connect to the ecosystem well is straightforward.

We should be able to build isolated estimators that can be dropped into existing workflows piece by piece, leveraging the existing infrastructure within other Scikit-Learn-compatible projects.

# This code is aspirational

from sklearn.model_selection import RandomSearchCV
from sklearn.pipeline import make_pipeline
from sklearn.feature_extraction.text import TfidfTransformer

# from sklearn.feature_extraction.text import HashingVectorizer
from cuml.feature_extraction.text import HashingVectorizer  # swap out for GPU versions

# from sklearn.linear_model import LogisticRegression, RandomForest
from cuml.linear_model import LogisticRegression, RandomForest

pipeline = make_pipeline([HashingVectorizer(),  # use Scikit-Learn infrastructure
                          TfidfTransformer(),
                          LogisticRegression()])

RandomSearchCV(pipeline).fit(data, labels)

Note, the example above is aspirational (that cuml code doesn’t exist yet) and probably naive (I don’t know ML well).

However, aside from the straightforward task of building these GPU-enabled estimators (which seems to be routine for the CUDA developers at NVIDIA) there are still challenges around cleanly passing non-Numpy arrays around, coercing only when necessary, and so on that we’ll need to work out within Scikit-Learn.

Fortunately this work has already started because of Dask Array, which has the same problem. The Dask and Scikit-Learn communities have been collaborating to better enable pluggability over the last year. Hopefully this additional use case proceeds along these existing efforts, but now with more support.

Deep learning frameworks are overly specialized

The SciPy/PyData stack thrived because it was modular and adaptable to new situations. There are many small issues around integrating components of the deep learning frameworks into the more general ecosystem.

We went through a similar experience with Dask early on, when the Python ecosystem wasn’t ready for parallel computing. As Dask expanded we ran into many small issues around parallel computing that hadn’t been addressed before because, for the most part, few people used Python for parallelism at the time.

Various libraries didn’t release the GIL (thanks for the work pandas, scikit-image, and others!)
Various libraries weren’t threadsafe in some cases (like h5py, and even Scikit-Learn in one case)
Function serialization still needed work (thanks cloudpickle developers!)
Compression libraries were unmaintained (like LZ4)
Networking libraries weren’t used to high bandwidth workloads (thanks Tornado devs!)

These issues were fixed by a combination of Dask developers and the broader community (it’s amazing what people will do if you provide a well-scoped and well-described problem on GitHub). These libraries were designed to be used with other libraries, and so they were well incentivized to improve their usability by the broader ecosystem.

Today deep learning frameworks have these same problems. They rarely serialize well, aren’t threadsafe when called by external threads, and so on. This is to be expected, most people using a tool like TensorFlow or PyTorch are operating almost entirely within those frameworks. These projects aren’t being stressed against the rest of the ecossytem (no one puts PyTorch arrays as columns in pandas, or pickles them to send across a wire). Taking tools that were designed for narrow workflows and encouraging them towards general purpose collaboration takes time and effort, both technically and socially.

The non-deep-learning OSS community has not yet made a strong effort to engage the deep-learning developer communities. This should be an interesting social experiment between two different of dev cultures. I suspect that these different groups have different styles and can learn from each other.

Note: Chainer/CuPy is a notable exception here. The Chainer library (another deep learning framework) explicitly separates its array library, CuPy, which makes it easier to deal with. This, combined with a strict adherence to the Numpy API, is probably why they’ve been the early target for most ongoing Python OSS interactions.

Dask needs convenience scripts for GPU deployment

On high-end systems it is common to have several GPUs on a single machine. Programming across these GPUs is challenging because you need to think about data locality, load balancing, and so on.

Dask is well-positioned to handle this for users. However, most people using Dask and GPUs today have a complex setup script that includes a combination of environment variables, dask-worker calls, additional calls to CUDA profiling utilities, and so on. We should make a simple LocalGPUCluster Python object that people can easily call within a local script, similar to how they do today for LocalCluster.

Additionally, this problem applies to the multi-gpu-multi-node case, and will require us to be creative with the existing distributed deployment solutions (like dask-kubernetes, dask-yarn, and dask-jobqueue). Of course, adding complexity like this without significantly impacting the non-GPU case and adding to community maintenance costs will be an interesting challenge, and will require creativity.

Python needs High Performance Communication libraries

High-end GPU systems often use high-end networking. This is especially important when our compute times drop significantly because communication time may quickly become our new bottleneck if we reduce computation time with GPUs.

Last year Antoine worked to improve Tornado’s handling of high-bandwidth connections to get about 1GB/s per process on Infiniband networks from Python. We may need to go well above this, both for Infiniband and for more exotic networking solutions. In particular NVIDIA has systems that support efficient transfer directly between GPU devices without going through host memory.

There is already work here that we can leverage. The OpenUCX project offloads exotic networking solutions (like Infiniband) to a uniform API. They’re now working to provide a Python accessible API that we can then then connect to Dask. This is good also for Dask-CPU users because Infiniband connections will become more efficient (HPC users rejoice) and also for the general Python HPC community, which will finally have a reasonable Python API for high performance networking. This work currently targets the Asyncio event loop.

As an aside, this is the kind of work I’d like to see coming out of NVIDIA (and other large technology companies) in the future. It helps to connect Python users to their specific hardware yes, but also helps lots of other systems and provides general infrastructure applicable across the community at the same time.

Come help!

This post started with the promise of 5–40x speed improvements (at least for some simple computations), and then outlined many of the challenges to getting there. These challenges are serious, but also mostly straightforward technical and social engineering problems. There is a lot of basic work with a high potential payoff.

NVIDIA’s plan to build a GPU-compatible data science stack seems ambitious, but they seem to be treating the problem seriously, and seem willing to put resources and company focus behind the problem.

If any of the work above sounds interesting to you please engage either as an…

Individual: either as an open source contributor (RAPIDS is Apache 2.0 licensed and seems to be operating as a normal OSS project on GitHub) or as an employee (see active job postings). There is lots of exciting work to do here. Or as an…
Institution: You may already have both an under-utilized cluster of GPUs within your institution, and also large teams of data scientists familiar with the Python but unfamiliar with CUDA. NVIDIA seems eager to find partners who are interested in mutual arrangements to build out functionality for specific domains. Please reach out if this sounds familiar.

Originally published at matthewrocklin.com on December 17, 2018.