Performance portable utilities for representing and interpolating tabulated data. Named for Brent Spiner. For full documentation, see here.
Spiner
is compatible with code on CPU, GPU, and everything in between. We use ports-of-call for this feature.
Spiner
is self-contained. Simply clone it as
git clone --recursive git@gitlab.lanl.gov:jonahm/spiner.git
To build and run unit tests,
mkdir bin
cmake -DBUILD_TESTING=ON ..
make -j
make test
and to do convergence testing,
make convergence
after building.
To install,
make install
after configuring and building.
SPINER_USE_HDF
enables or disables HDF5. Default isOFF
SPINER_USE_KOKKOS
enables or disables Kokkos. Default isOFF
.SPINER_USE_CUDA
enables or disables Cuda. Requires Kokkos. Default isOFF
.BUILD_TESTING
enables or disables tests. Default isOFF
. 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.
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)
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
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
.
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 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
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.
- Spiner supports interpolation in arbitrary dimensions, and it's fast in 3d and fewer.
- Spiner supports interpolation onto "subtables"
Interpolation is linear. Here's an example of interpolation in 3D (2D slice shown). Convergence is second-order, as expected.
Interpolation is fast and portable. Here's performance on several different problem sizes and several different architectures with different parallelism strategies:
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.
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
© (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:
- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
- 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.
- 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.
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