pykokkos-base 0.0.7rc2

Python bindings to Kokkos Views for data interop

pykokkos-base

Additional Documentation can be found in Wiki

Overview

This package contains the minimal set of bindings for Kokkos interoperability with Python:

• Free-standing function bindings
  • Kokkos::initialize(...)
  • Kokkos::finalize()
  • Kokkos::is_initialized()
  • Kokkos::deep_copy(...)
  • Kokkos::create_mirror(...)
  • Kokkos::create_mirror_view(...)
  • Kokkos::Tools::profileLibraryLoaded()
  • Kokkos::Tools::pushRegion(...)
  • Kokkos::Tools::popRegion()
  • Kokkos::Tools::createProfileSection(...)
  • Kokkos::Tools::destroyProfileSection(...)
  • Kokkos::Tools::startSection(...)
  • Kokkos::Tools::stopSection(...)
  • Kokkos::Tools::markEvent(...)
  • Kokkos::Tools::declareMetadata(...)
  • Kokkos::Tools::Experimental::set_<...>_callback(...)
• Data structures
  • Kokkos::View<...>
  • Kokkos::DynRankView<...>
  • Kokkos_Profiling_KokkosPDeviceInfo
  • Kokkos_Profiling_SpaceHandle

By importing this package in Python, you can pass the supported Kokkos Views and DynRankViews from C++ to Python and vice-versa. Furthermore, in Python, these bindings provide interoperability with numpy and cupy arrays:

import kokkos
import numpy as np

view = kokkos.array([2, 2], dtype=kokkos.double, space=kokkos.CudaUVMSpace,
                    layout=kokkos.LayoutRight, trait=kokkos.RandomAccess,
                    dynamic=False)

arr = np.array(view, copy=False)

Writing Kokkos in Python

In order to write native Kokkos in Python, see pykokkos.

Installation

You can install this package via CMake or Python's setup.py. The important cmake options are:

• ENABLE_VIEW_RANKS (integer)
• ENABLE_LAYOUTS (bool)
• ENABLE_MEMORY_TRAITS (bool)
• ENABLE_INTERNAL_KOKKOS (bool)

By default, CMake will enable the layouts and memory traits options if the Kokkos installation was not built with CUDA support. If Kokkos was built with CUDA support, ENABLE_MEMORY_TRAITS will be disabled by default due to unreasonable compilation times (> 1 hour). The ENABLE_VIEW_RANKS option (defaults to a value of 4) is the max number of ranks for Kokkos::View<...> that can be returned to Python. For example, value of 4 means that views of data type T*, T**, T***, and T**** can be returned to python but T***** and higher cannot. Increasing this value up to 7 can dramatically increase the length of time required to compile the bindings.

Kokkos Installation

If the ENABLE_INTERNAL_KOKKOS option is not specified the first time CMake is run, CMake will try to find an existing Kokkos installation. If no existing installation is found, it will build and install Kokkos from a submodule. When Kokkos is added as a submodule, you can configure the submodule as you would normally configure Kokkos. However, due to some general awkwardness configuring cmake from setup.py (especially via pip install), CMake tries to "automatically" configure reasonable default CMake settings for the Kokkos submodule.

Here are the steps when Kokkos is added as a submodule:

• Does external/kokkos/CMakeLists.txt exists?
  • YES: assumes the submodule is already checked out

    • If compute node does not have internet access, checkout submodule before installing!

  • NO: does .gitmodules exist?
    • YES: git submodule update --init external/kokkos
    • NO: git clone -b master https://github.com/kokkos/kokkos.git external/kokkos
• Set BUILD_SHARED_LIBS=ON
• Set Kokkos_ENABLE_SERIAL=ON
• find_package(OpenMP)
  • Was OpenMP found?
    • YES: set Kokkos_ENABLE_OPENMP=ON
    • NO: find_package(Threads)
      • Was Threads found?
        • YES: set Kokkos_ENABLE_THREADS=ON (if not Windows)
• find_package(CUDA)
  • Was CUDA found?
    • YES: set:
      • Kokkos_ENABLE_CUDA=ON
      • Kokkos_ENABLE_CUDA_UVM=ON
      • Kokkos_ENABLE_CUDA_LAMBDA=ON

Configuring Options via CMake

cmake -DENABLE_LAYOUTS=ON -DENABLE_MEMORY_TRAITS=OFF /path/to/source

Configuring Options via setup.py

There are three ways to configure the options:

1. Via the Python argparse options --enable-<option> and --disable-<option>
2. Setting the PYKOKKOS_BASE_SETUP_ARGS environment variable to the CMake options
3. Passing in the CMake options after a --

All three lines below are equivalent:

python setup.py install --enable-layouts --disable-memory-traits
PYKOKKOS_BASE_SETUP_ARGS="-DENABLE_LAYOUTS=ON -DENABLE_MEMORY_TRAITS=OFF" python setup.py install
python setup.py install -- -DENABLE_LAYOUTS=ON -DENABLE_MEMORY_TRAITS=OFF

Configuring Options via pip

Pip does not handle build options well. Thus, it is recommended to use the PYKOKKOS_BASE_SETUP_ARGS environment variable noted above. However, using the --install-option for pip is possible but each "space" must have it's own --install-option, e.g. all of the following are equivalent: All three lines below are equivalent:

pip install pykokkos-base --install-option=--enable-layouts --install-option=--disable-memory-traits
pip install pykokkos-base --install-option=-- --install-option=-DENABLE_LAYOUTS=ON --install-option=-DENABLE_MEMORY_TRAITS=OFF
pip install pykokkos-base --install-option={--enable-layouts,--disable-memory-traits}
pip install pykokkos-base --install-option={--,-DENABLE_LAYOUTS=ON,-DENABLE_MEMORY_TRAITS=OFF}

pip install pykokkos-base will build against the latest release in the PyPi repository. In order to pip install from this repository, use pip install --user -e .

Differences vs. Kokkos C++

Deep Copy and Host Mirror

If you are not familiar with Kokkos::deep_copy(...), Kokkos::create_mirror(...), Kokkos::create_mirror_view(...), read this Kokkos Wiki entry.

When Kokkos views are allocated on a non-host memory space, this data is not directly accessible in Python. Any attempt to read or modify the data will result in a fatal error. In C++, Kokkos developers usually perform two distinct operations: create a mirror or mirror-view and then execute a deep-copy, e.g.:

// assume MemorySpace is Kokkos::Cuda or similar
Kokkos::View<int*, MemorySpace> a ("a", 10);

// Allocate a view in HostSpace with the layout and padding of a
auto b = create_mirror(a);
// This is always a memcopy
Kokkos::deep_copy (b, a);

// This may not allocate a new view if a is in host space
auto c = Kokkos::create_mirror_view(a);
// This is a no-op if MemorySpace is HostSpace
Kokkos::deep_copy (c, a)

The python equivalent is available via standalone functions:

# assume MemorySpace is kokkos.CudaSpace or similar
a = kokkos.array("a", shape=[10], space=MemorySpace)

# Allocate a view in HostSpace with the layout and padding of a
b = kokkos.create_mirror(a)
# copy memory
kokkos.deep_copy(b, a)

# This may not allocate a new view if a is in host space
c = kokkos.create_mirror_view(a)
# This is a no-op if MemorySpace is HostSpace
kokkos.deep_copy(c, a)

However, this makes it cumbersome to print data in python:

# assume MemorySpace is kokkos.CudaSpace or similar
a = kokkos.array("a", shape=[10], space=MemorySpace)

def print_data(inp):
    v = kokkos.create_mirror_view(inp)
    kokkos.deep_copy(v, inp)
    for i in range(v.shape[0]):
        print(f"v({i}) = {v[i]}")

print_data(a)

Thus, the member functions create_mirror() and create_mirror_view() accept a boolean copy argument which defaults to True, e.g.:

a = kokkos.array("a", shape=[10], space=MemorySpace)

# this:
b = a.create_mirror()

# is implicitly:
b = a.create_mirror(copy=True)

Thus, our print_data function above does not need handle mirror creation because we can replace print_data(a) with print_data(a.create_mirror()) or print_data(a.create_mirror_view()):

# assume MemorySpace is kokkos.CudaSpace or similar
a = kokkos.array("a", shape=[10], space=MemorySpace)

def print_data(v):
    for i in range(v.shape[0]):
        print(f"v({i}) = {v[i]}")

print_data(a.create_mirror_view())

In fact, the free-standing kokkos.create_mirror(...) and kokkoos.create_mirror_view(...) simply use this member function and default the copy argument to False:

def create_mirror(src, copy=False):
    """Performs Kokkos::create_mirror"""
    return src.create_mirror(copy)


def create_mirror_view(src, copy=False):
    """Performs Kokkos::create_mirror_view"""
    return src.create_mirror_view(copy)

Example

Overview

This example is designed to emulate a work-flow where the user has code using Kokkos in C++ and writes python bindings to those functions. A python script is used as the "main":

• ex-numpy.py imports the kokkos bindings
• Calls a routine in the "users" python bindings to a C++ function which returns a Kokkos::View
• This view is then converted to a numpy array in python and printed via the numpy capabilities.

Files

• ex-generate.cpp
  • This is the python bindings to the user code
• user.cpp
  • This is the implementation of the user's code which returns a Kokkos::View<double**, Kokkos::HostSpace>
• ex-numpy.py
  • This is the "main"

ex-numpy.py

#!/usr/bin/env python

import argparse
import numpy as np

#
# The python bindings for generate_view are in ex-generate.cpp
# The declaration and definition of generate_view are in user.hpp and user.cpp
# The generate_view function will return a Kokkos::View and will be converted
# to a numpy array
from ex_generate import generate_view, modify_view

#
# Importing this module is necessary to call kokkos init/finalize and
# import the python bindings to Kokkos::View which generate_view will
# return
#
import kokkos


def print_data(label, name, data):
    # write the type info
    print(
        "{:12} : {} (ndim={}, shape={})".format(
            label, type(data).__name__, data.ndim, data.shape
        )
    )

    # print the data
    if data.ndim == 1:
        for i in range(data.shape[0]):
            print("{:8}({}) = {}".format(name, i, data[i]))
    elif data.ndim == 2:
        for i in range(data.shape[0]):
            print(
                "{:8}({}) = [{}]".format(
                    name,
                    i,
                    " ".join("{}".format(data[i, j]) for j in range(data.shape[1])),
                )
            )
    else:
        raise ValueError("only 2 dimensions are supported")


def user_bindings(args):
    # get the kokkos view
    view = generate_view(args.ndim)
    print_data("Kokkos View", "view", view.create_mirror_view())

    # modify view (verify that casting works)
    modify_view(view)
    print_data("Modify View", "view", view.create_mirror_view())

    # wrap the buffer protocal as numpy array without copying the data
    arr = np.array(view.create_mirror_view(), copy=False)
    print_data("Numpy Array", "arr", arr)


def to_numpy(args):
    # get the kokkos view
    view = kokkos.array(
        "python_allocated_view",
        [args.ndim],
        dtype=kokkos.double,
        space=kokkos.DefaultHostMemorySpace,
    )

    for i in range(view.shape[0]):
        view[i] = i * (i % 2)
    print_data("Kokkos View", "view", view)

    # wrap the buffer protocal as numpy array without copying the data
    arr = np.array(view, copy=False)
    print_data("Numpy Array", "arr", arr)


def from_numpy(args):
    arr = np.ones([args.ndim, args.ndim], dtype=np.int32)
    for i in range(args.ndim):
        arr[i, i] = 0

    print_data("Numpy Array", "arr", arr)

    view = kokkos.array(arr, dtype=kokkos.int32, dynamic=True)
    print_data("Kokkos View", "view", view)


if __name__ == "__main__":
    try:
        kokkos.initialize()
        parser = argparse.ArgumentParser()
        parser.add_argument("-n", "--ndim", default=10, help="X dimension", type=int)
        args, argv = parser.parse_known_args()
        print("Executing to numpy...")
        to_numpy(args)
        print("Executing from numpy...")
        from_numpy(args)
        print("Executing user bindings...")
        user_bindings(args)
        kokkos.finalize()
    except Exception as e:
        import sys
        import traceback

        print(f"{e}")
        exc_type, exc_value, exc_traceback = sys.exc_info()
        traceback.print_exception(exc_type, exc_value, exc_traceback)
        sys.exit(1)

Build and Run

mkdir build
cd build
cmake -DENABLE_EXAMPLES=ON ..
make
python ./ex-numpy.py

Expected Output

[user-bindings]> Generating View... Done.
[user-bindings]> Modifying View... Done.
Executing to numpy...
Kokkos View  : KokkosView_float64_HostSpace_LayoutRight_1 (ndim=1, shape=[10])
view    (0) = 0.0
view    (1) = 1.0
view    (2) = 0.0
view    (3) = 3.0
view    (4) = 0.0
view    (5) = 5.0
view    (6) = 0.0
view    (7) = 7.0
view    (8) = 0.0
view    (9) = 9.0
Numpy Array  : ndarray (ndim=1, shape=(10,))
arr     (0) = 0.0
arr     (1) = 1.0
arr     (2) = 0.0
arr     (3) = 3.0
arr     (4) = 0.0
arr     (5) = 5.0
arr     (6) = 0.0
arr     (7) = 7.0
arr     (8) = 0.0
arr     (9) = 9.0
Executing from numpy...
Numpy Array  : ndarray (ndim=2, shape=(10, 10))
arr     (0) = [0 1 1 1 1 1 1 1 1 1]
arr     (1) = [1 0 1 1 1 1 1 1 1 1]
arr     (2) = [1 1 0 1 1 1 1 1 1 1]
arr     (3) = [1 1 1 0 1 1 1 1 1 1]
arr     (4) = [1 1 1 1 0 1 1 1 1 1]
arr     (5) = [1 1 1 1 1 0 1 1 1 1]
arr     (6) = [1 1 1 1 1 1 0 1 1 1]
arr     (7) = [1 1 1 1 1 1 1 0 1 1]
arr     (8) = [1 1 1 1 1 1 1 1 0 1]
arr     (9) = [1 1 1 1 1 1 1 1 1 0]
Kokkos View  : KokkosDynRankView_int32_HostSpace_LayoutRight (ndim=2, shape=[10, 10, 1, 1, 1, 1, 1])
view    (0) = [0 1 1 1 1 1 1 1 1 1]
view    (1) = [1 0 1 1 1 1 1 1 1 1]
view    (2) = [1 1 0 1 1 1 1 1 1 1]
view    (3) = [1 1 1 0 1 1 1 1 1 1]
view    (4) = [1 1 1 1 0 1 1 1 1 1]
view    (5) = [1 1 1 1 1 0 1 1 1 1]
view    (6) = [1 1 1 1 1 1 0 1 1 1]
view    (7) = [1 1 1 1 1 1 1 0 1 1]
view    (8) = [1 1 1 1 1 1 1 1 0 1]
view    (9) = [1 1 1 1 1 1 1 1 1 0]
Executing user bindings...
Kokkos View  : KokkosView_float64_HostSpace_LayoutRight_2 (ndim=2, shape=[10, 2])
view    (0) = [-1.0 1.0]
view    (1) = [-2.0 2.0]
view    (2) = [-3.0 3.0]
view    (3) = [-4.0 4.0]
view    (4) = [-5.0 5.0]
view    (5) = [-6.0 6.0]
view    (6) = [-7.0 7.0]
view    (7) = [-8.0 8.0]
view    (8) = [-9.0 9.0]
view    (9) = [-10.0 10.0]
Modify View  : KokkosView_float64_HostSpace_LayoutRight_2 (ndim=2, shape=[10, 2])
view    (0) = [-2.0 2.0]
view    (1) = [-4.0 4.0]
view    (2) = [-6.0 6.0]
view    (3) = [-8.0 8.0]
view    (4) = [-10.0 10.0]
view    (5) = [-12.0 12.0]
view    (6) = [-14.0 14.0]
view    (7) = [-16.0 16.0]
view    (8) = [-18.0 18.0]
view    (9) = [-20.0 20.0]
Numpy Array  : ndarray (ndim=2, shape=(10, 2))
arr     (0) = [-2.0 2.0]
arr     (1) = [-4.0 4.0]
arr     (2) = [-6.0 6.0]
arr     (3) = [-8.0 8.0]
arr     (4) = [-10.0 10.0]
arr     (5) = [-12.0 12.0]
arr     (6) = [-14.0 14.0]
arr     (7) = [-16.0 16.0]
arr     (8) = [-18.0 18.0]
arr     (9) = [-20.0 20.0]