libCEED: the CEED API Library

Code for Efficient Extensible Discretization

This repository contains an initial low-level API library for the efficient high-order discretization methods developed by the ECP co-design Center for Efficient Exascale Discretizations (CEED). While our focus is on high-order finite elements, the approach is mostly algebraic and thus applicable to other discretizations in factored form, as explained in the API documentation portion of the Doxygen documentation.

One of the challenges with high-order methods is that a global sparse matrix is no longer a good representation of a high-order linear operator, both with respect to the FLOPs needed for its evaluation, as well as the memory transfer needed for a matvec. Thus, high-order methods require a new "format" that still represents a linear (or more generally non-linear) operator, but not through a sparse matrix.

The goal of libCEED is to propose such a format, as well as supporting implementations and data structures, that enable efficient operator evaluation on a variety of computational device types (CPUs, GPUs, etc.). This new operator description is based on algebraically factored form, which is easy to incorporate in a wide variety of applications, without significant refactoring of their own discretization infrastructure.

The repository is part of the CEED software suite, a collection of software benchmarks, miniapps, libraries and APIs for efficient exascale discretizations based on high-order finite element and spectral element methods. See http://github.com/ceed for more information and source code availability.

The CEED research is supported by the Exascale Computing Project (17-SC-20-SC), a collaborative effort of two U.S. Department of Energy organizations (Office of Science and the National Nuclear Security Administration) responsible for the planning and preparation of a capable exascale ecosystem, including software, applications, hardware, advanced system engineering and early testbed platforms, in support of the nation’s exascale computing imperative.

For more details on the CEED API see http://ceed.exascaleproject.org/ceed-code/.

Building

The CEED library, libceed, is a C99 library with no external dependencies. It can be built using

make

or, with optimization flags

make OPT='-O3 -march=skylake-avx512 -ffp-contract=fast'

These optimization flags are used by all languages (C, C++, Fortran) and this makefile variable can also be set for testing and examples (below).

The library attempts to automatically detect support for the AVX instruction set using gcc-style compiler options for the host. Support may need to be manually specified via

make AVX=1

or

make AVX=0

if your compiler does not support gcc-style options, if you are cross compiling, etc.

Testing

The test suite produces TAP output and is run by:

make test

or, using the prove tool distributed with Perl (recommended)

make prove

Backends

There are multiple supported backends, which can be selected at runtime in the examples:

CEED resource	Backend
/cpu/self/ref/serial	Serial reference implementation
/cpu/self/ref/blocked	Blocked refrence implementation
/cpu/self/memcheck	Memcheck backend, undefined value checks
/cpu/self/opt/serial	Serial optimized C implementation
/cpu/self/opt/blocked	Blocked optimized C implementation
/cpu/self/avx/serial	Serial AVX implementation
/cpu/self/avx/blocked	Blocked AVX implementation
/cpu/self/xsmm/serial	Serial LIBXSMM implementation
/cpu/self/xsmm/blocked	Blocked LIBXSMM implementation
/cpu/occa	Serial OCCA kernels
/gpu/occa	CUDA OCCA kernels
/omp/occa	OpenMP OCCA kernels
/ocl/occa	OpenCL OCCA kernels
/gpu/cuda/ref	Reference pure CUDA kernels
/gpu/cuda/reg	Pure CUDA kernels using one thread per element
/gpu/cuda/shared	Optimized pure CUDA kernels using shared memory
/gpu/cuda/gen	Optimized pure CUDA kernels using code generation
/gpu/magma	CUDA MAGMA kernels

The /cpu/self/*/serial backends process one element at a time and are intended for meshes with a smaller number of high order elements. The /cpu/self/*/blocked backends process blocked batches of eight interlaced elements and are intended for meshes with higher numbers of elements.

The /cpu/self/ref/* backends are written in pure C and provide basic functionality.

The /cpu/self/opt/* backends are written in pure C and use partial e-vectors to improve performance.

The /cpu/self/avx/* backends rely upon AVX instructions to provide vectorized CPU performance.

The /cpu/self/xsmm/* backends rely upon the LIBXSMM package to provide vectorized CPU performance. If linking MKL and LIBXSMM is desired but the Makefile is not detecting MKLROOT, linking libCEED against MKL can be forced by setting the environment variable MKL=1.

The /cpu/self/memcheck/* backends rely upon the Valgrind Memcheck tool to help verify that user QFunctions have no undefined values. To use, run your code with Valgrind and the Memcheck backends, e.g. valgrind ./build/ex1 -ceed /cpu/self/ref/memcheck. A 'development' or 'debugging' version of Valgrind with headers is required to use this backend. This backend can be run in serial or blocked mode and defaults to running in the serial mode if /cpu/self/memcheck is selected at runtime.

The /*/occa backends rely upon the OCCA package to provide cross platform performance.

The /gpu/cuda/* backends provide GPU performance strictly using CUDA.

The /gpu/magma backend relies upon the MAGMA package.

Examples

libCEED comes with several examples of its usage, ranging from standalone C codes in the /examples/ceed directory to examples based on external packages, such as MFEM, PETSc, and Nek5000. Nek5000 v18.0 or greater is required.

To build the examples, set the MFEM_DIR, PETSC_DIR and NEK5K_DIR variables and run:

# libCEED examples on CPU and GPU
cd examples/ceed
make
./ex1-volume -ceed /cpu/self
./ex1-volume -ceed /gpu/occa
./ex2-surface -ceed /cpu/self
./ex2-surface -ceed /gpu/occa
cd ../..

# MFEM+libCEED examples on CPU and GPU
cd examples/mfem
make
./bp1 -ceed /cpu/self -no-vis
./bp3 -ceed /gpu/occa -no-vis
cd ../..

# Nek5000+libCEED examples on CPU and GPU
cd examples/nek
make
./nek-examples.sh -e bp1 -ceed /cpu/self -b 3
./nek-examples.sh -e bp3 -ceed /gpu/occa -b 3
cd ../..

# PETSc+libCEED examples on CPU and GPU
cd examples/petsc
make
./bps -problem bp1 -ceed /cpu/self
./bps -problem bp2 -ceed /gpu/occa
./bps -problem bp3 -ceed /cpu/self
./bps -problem bp4 -ceed /gpu/occa
./bps -problem bp5 -ceed /cpu/self
./bps -problem bp6 -ceed /gpu/occa
cd ../..

cd examples/petsc
./area -problem cube -ceed /cpu/self -petscspace_degree 3
./area -problem cube -ceed /gpu/occa -petscspace_degree 3
./area -problem sphere -ceed /cpu/self -petscspace_degree 3 -dm_refine 2
./area -problem sphere -ceed /gpu/occa -petscspace_degree 3 -dm_refine 2
cd ../..

cd examples/navier-stokes
make
./navierstokes -ceed /cpu/self
./navierstokes -ceed /gpu/occa
cd ../..

The above code assumes a GPU-capable machine with the OCCA backend enabled. Depending on the available backends, other Ceed resource specifiers can be provided with the -ceed option.

Benchmarks

A sequence of benchmarks for all enabled backends can be run using

make benchmarks

The results from the benchmarks are stored inside the benchmarks/ directory and they can be viewed using the commands (requires python with matplotlib):

cd benchmarks
python postprocess-plot.py petsc-bps-bp1-*-output.txt
python postprocess-plot.py petsc-bps-bp3-*-output.txt

Using the benchmarks target runs a comprehensive set of benchmarks which may take some time to run. Subsets of the benchmarks can be run using the scripts in the benchmarks folder.

For more details about the benchmarks, see benchmarks/README.md

Install

To install libCEED, run

make install prefix=/usr/local

or (e.g., if creating packages),

make install prefix=/usr DESTDIR=/packaging/path

Note that along with the library, libCEED installs kernel sources, e.g. OCCA kernels are installed in $prefix/lib/okl. This allows the OCCA backend to build specialized kernels at run-time. In a normal setting, the kernel sources will be found automatically (relative to the library file libceed.so). However, if that fails (e.g. if libceed.so is moved), one can copy (cache) the kernel sources inside the user OCCA directory, ~/.occa using

$(OCCA_DIR)/bin/occa cache ceed $(CEED_DIR)/lib/okl/*.okl

This will allow OCCA to find the sources regardless of the location of the CEED library. One may occasionally need to clear the OCCA cache, which can be accomplished by removing the ~/.occa directory or by calling $(OCCA_DIR)/bin/occa clear -a.

To install libCEED for Python, run

python setup.py build install

with the desired setuptools options, such as --user.

Alternatively, if libCEED is installed in the directory specified by the environment variable CEED_DIR, then run

pip install .

pkg-config

In addition to library and header, libCEED provides a pkg-config file that can be used to easily compile and link. For example, if $prefix is a standard location or you set the environment variable PKG_CONFIG_PATH,

cc `pkg-config --cflags --libs ceed` -o myapp myapp.c

will build myapp with libCEED. This can be used with the source or installed directories. Most build systems have support for pkg-config.

Contact

You can reach the libCEED team by emailing [email protected] or by leaving a comment in the issue tracker.

Copyright

The following copyright applies to each file in the CEED software suite, unless otherwise stated in the file:

Copyright (c) 2017, Lawrence Livermore National Security, LLC. Produced at the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights reserved.

See files LICENSE and NOTICE for details.