P4est.jl

P4est.jl is lightweight wrapper for the p4est C library, which allows to manage multiple connected adaptive quadtrees/octrees in parallel.
Author trixi-framework
Popularity
9 Stars
Updated Last
1 Year Ago
Started In
October 2020

P4est.jl

Build Status Codecov Coveralls License: MIT GitHub commits since tagged version

P4est.jl is a Julia package that wraps p4est, a C library to manage multiple connected adaptive quadtrees or octrees in parallel.

Installation

If you have not yet installed Julia, please follow the instructions for your operating system. P4est.jl works with Julia v1.5.

P4est.jl is a registered Julia package. Hence, you can install it by executing the following commands in the Julia REPL:

julia> import Pkg; Pkg.add("P4est")

P4est.jl depends on the binary distribution of the p4est library, which is available in the Julia package P4est_jll.jl and which is automatically installed as a dependency.

Note: Currently, P4est_jll.jl is not available under Windows and provides only serial binaries without MPI support. Both limitations are planned to be lifted in the future.

Note: On MacOS, you need to have Xcode installed to be able to use this package.

You can configure P4est.jl to use a custom build of p4est by setting the following environment variables and building P4est.jl again afterwards:

  1. Set JULIA_P4EST_PATH.

    You can set the environment variable JULIA_P4EST_PATH to the install prefix of your p4est library. P4est.jl will then assume to find the corresponding library as joinpath(ENV["JULIA_P4EST_PATH"], "lib", "libp4est.{so,dylib,dll}") and the include files in joinpath(ENV["JULIA_P4EST_PATH"], "include").

  2. Set JULIA_P4EST_LIBRARY and JULIA_P4EST_INCLUDE.

    Alternatively, you can specify the p4est library and the include directory directly. Note that JULIA_P4EST_LIBRARY expects the full path to the p4est library, while JULIA_P4EST_INCLUDE must be the full path to the directory with the p4est header files.

For example, if your custom p4est build is installed to /opt/p4est, you can use it from P4est.jl by executing

julia --project -e 'ENV["JULIA_P4EST_PATH"] = "/opt/p4est"; using Pkg; Pkg.build("P4est"; verbose=true)'

P4est.jl supports p4est both with and without MPI enabled. By default, it uses the p4est library from the binary Julia package P4est_jll, which currently is not compiled with MPI support. However, you may specify a custom p4est build with MPI enabled using the environment variables desribed above. In this case, you need to set a few additional variables to make sure that P4est.jl can create the correct C bindings:

  1. Set JULIA_P4EST_USES_MPI to yes.

    This is always required, since it tells P4est.jl to use the MPI include directory while generating the C bindings.

  2. Set JULIA_P4EST_MPI_PATH.

    You can set the environment variable JULIA_P4EST_MPI_PATH to the install prefix of your MPI library. P4est.jl will then assume to find the corresponding include files in joinpath(ENV["JULIA_P4EST_MPI_PATH"], "include").

  3. Set JULIA_P4EST_MPI_INCLUDE.

    Alternatively, you can specify the MPI include directory directly. Note that JULIA_P4EST_MPI_INCLUDE must be the full path to the directory with the mpi.h header file. Please note that you should specify the path to the MPI version with which you also built the parallel version of p4est, in order to avoid errors from mismatching definitions.

For example, if your custom p4est build is installed to /opt/p4est and was built using the MPI library installed to /opt/mpich, you can use it from P4est.jl by executing

julia --project -e 'ENV["JULIA_P4EST_PATH"] = "/opt/p4est";
                    ENV["JULIA_P4EST_USES_MPI"] = "yes";
                    ENV["JULIA_P4EST_MPI_PATH"] = "/opt/mpich";
                    using Pkg; Pkg.build("P4est"; verbose=true)'

Usage

In the Julia REPL, first load the package P4est.jl

julia> using P4est

You can then access the full p4est API that is defined by the headers. For example, to create a periodic connectivity and check its validity, execute the following lines:

julia> conn_ptr = p4est_connectivity_new_periodic()
Ptr{p4est_connectivity} @0x0000000001ad2080

julia> p4est_connectivity_is_valid(conn_ptr)
1

julia> p4est_ptr = p4est_new_ext(sc_MPI_Comm(0), conn_ptr, 0, 2, 0, 0, C_NULL, C_NULL)
Into p4est_new with min quadrants 0 level 2 uniform 0
New p4est with 1 trees on 1 processors
Initial level 2 potential global quadrants 16 per tree 16
Done p4est_new with 10 total quadrants
Ptr{p4est} @0x00000000029e9fc0

julia> p4est_ = unsafe_wrap(p4est_ptr)
p4est(mpicomm=0, mpisize=1, mpirank=0, mpicomm_owned=0, data_size=0x0000000000000000, user_pointer=Ptr{Nothing} @0x0000000000000000, revision=0, first_local_tree=0, last_local_tree=0, local_num_quadrants=10, global_num_quadrants=10, global_first_quadrant=Ptr{Int64} @0x00000000025b2880, global_first_position=Ptr{p4est_quadrant} @0x0000000001ee1390, connectivity=Ptr{p4est_connectivity} @0x000000000256de60, trees=Ptr{sc_array} @0x0000000002210e20, user_data_pool=Ptr{sc_mempool} @0x0000000000000000, quadrant_pool=Ptr{sc_mempool} @0x00000000020a5820, inspect=Ptr{p4est_inspect} @0x0000000000000000)

julia> p4est_.connectivity == conn_ptr
true

julia> p4est_.connectivity.num_trees
1

As can be seen, unsafe_wrap allows to convert pointers to p4est C structs to the corresponding Julia wrapper type provided by CBinding.jl. Once converted, CBinding.jl will automatically wrap pointers nested structures (such as Ptr{p4est_connectivity} in p4est_ in the example above) with the corresponding Julia type.

Many functions and types in p4est have been documented with comments by the p4est authors; you can access this documentation as you would for any Julia-native entity through ?:

help?> p4est_memory_used
search: p4est_memory_used p4est_mesh_memory_used p4est_ghost_memory_used p4est_connectivity_memory_used P4EST_HAVE_MEMORY_H @P4EST_HAVE_MEMORY_H

  ๐ฃ๐ฅ.@cextern p4est_memory_used(p4est::๐ฃ๐ฅ.Ptr{p4est_t})::size_t


  Calculate local memory usage of a forest structure. Not collective. The memory used on the current rank is returned. The connectivity structure is not counted since it is not owned; use
  p4estconnectivitymemory_usage (p4est->connectivity).

  Parameters
  ============

    โ€ข    p4est: Valid forest structure.

  Returns
  =========

            Memory used in bytes.


  Reference
  ===========

  p4est.h:177 (~/.julia/artifacts/bb31421737f71afecd6a7760afa471cd27c9d211/include/p4est.h:177:21)

For more information on how to use p4est via P4est.jl, please refer to the documentation for p4est itself or to the header files (*.h) in the p4est repository.

Authors

P4est.jl was initiated by Michael Schlottke-Lakemper (University of Cologne, Germany), Hendrik Ranocha (KAUST, Saudi Arabia), and Alexander Astanin (University of Cologne, Germany). Together, they are the principal developers of P4est.jl. The p4est library itself is written by Carsten Burstedde, Lucas C. Wilcox, and Tobin Isaac.

License and contributing

P4est.jl is licensed under the MIT license (see LICENSE.md). p4est itself is licensed under the GNU General Public License, version 2.

Used By Packages

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