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Spiner

Build Status

DOI

DOI

Performance portable utilities for representing and interpolating tabulated data. Named for Brent Spiner. For full documentation, see here.

Performance portability

Spiner is compatible with code on CPU, GPU, and everything in between. We use ports-of-call for this feature.

Building and Installation

Spiner is self-contained. Simply clone it as

git clone --recursive git@github.com:lanl/spiner.git

To build and run unit tests,

mkdir bin
cmake -DSPINER_BUILD_TESTS=ON ..
make -j
make test

and to do convergence testing,

make convergence

after building.

To install,

make install

after configuring and building.

Build options

  • SPINER_USE_HDF enables or disables HDF5. Default is OFF
  • SPINER_USE_KOKKOS enables or disables Kokkos. Default is OFF.
  • SPINER_USE_CUDA enables or disables Cuda. Requires Kokkos. Default is OFF.
  • SPINER_BUILD_TESTS enables or disables tests. Default is OFF. If this is disabled, then configuration only prepares for install and provides targets for in-tree builds, as no build step is necessary.
  • SPINER_HDF5_INSTALL_DIR a hint for cmake about where you may have stashed HDF5.
  • SPINER_KOKKOS_INSTALL_DIR a hint for cmake about where you may have stashed Kokkos.

Including spiner in your project

You can build spiner in-line with your project, or pre-install it. It's header-only and the include directories should have the expected structure. If you build inline, add the following target to your cmake:

target_link_libraries(my_project PRIVATE spiner::spiner)

Dependencies

Spiner relies on ports-of-call for performance portability. It is included as a submodule. Otherwise, Spiner has no dependencies for the databox tool. Simply include it in your project under the spiner directory. It is header-only and requires only a few files:

  • spiner/databox.hpp
  • spiner/interpolation.hpp
  • spiner/spiner_types.hpp
  • spiner/sp5.hpp

To use the build system (rather than simply cloning and including the files) requires cmake.

The testing tooling requires a few different pieces:

  • Unit testing requires Catch2, which is downloaded automatically if needed.
  • Convergence testing requires the scientific python stack, including:
    • python3
    • numpy
    • matplotlib

HDF5

Spiner supports reading and writing DataBox objects into a custom HDF5 format called SP5. To enable this, compile with the appropriate HDF5 linking and the flag -DSPINER_USE_HDF. If you use the cmake build system, just configure with -DSPINER_USE_HDF=ON.

CUDA and Kokkos

Spiner uses the ports-of-call code to optionally support compilation with CUDA, Kokkos, or none of the above. If Kokkos is discoverable by cmake (for example if you installed it with spack), then the build system should find it automatically. Otherwise you can specify a location for Kokkos with SPINER_KOKKOS_INSTALL_DIR.

The following spack install was tested with a V100 GPU:

spack install kokkos-nvcc-wrapper
spack install kokkos~shared+cuda+cuda_lambda+cuda_relocatable_device_code+wrapper cuda_arch=70

and then the following cmake configuration line

cmake -DSPINER_USE_KOKKOS=ON -DSPINER_USE_CUDA=ON -DBUILD_TESTING=ON -DCMAKE_CXX_COMPILER=nvcc_wrapper ..

builds the tests for CUDA.

Clang-Format

Clang-format version 12 is required for committing, and a github workflow is used to check that code meets format requirements. We provide a make target in the build system. After configuration, simply type

make format_spiner

to format the code.

Other versions of clang-format may work. If you would like to try, please examine the diff and see if the formatting appears stable. Otherwise, you may need to upgrade your version of clang-format.

In general, we recommend formatting regularly so that the format calls do not pollute the diffs. If a format call necessarily pollutes the diff, do it as a separate commit.

Features

  • Spiner supports interpolation in arbitrary dimensions, and it's fast in 3d and fewer.
  • Spiner supports interpolation onto "subtables"

Interpolation

Interpolation is linear. Here's an example of interpolation in 3D (2D slice shown). Convergence is second-order, as expected.

convergence plot

Interpolation is fast and portable. Here's performance on several different problem sizes and several different architectures with different parallelism strategies:

performance plot

Contributing

If you use Spiner and need help, submit an issue to the Spiner repository. If you'd like to contribute, just fork and submit a pull request. There's a check list in the PR template, and one of the main Spiner developers will review your PR.

Contributors

Spiner was primarily developed by Jonah Miller in collaboration with

  • Chad Meyer
  • Daniel Holladay
  • Josh Dolence
  • Sriram Swaminarayan

Continuous integration and build system support has been provided by

  • Jonah Miller
  • Karen Tsai
  • Christopher Mauney

Copyright

© (or copyright) 2019-2021. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.

This program is open source under the BSD-3 License. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
  3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE