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Merge pull request #157 from ajnonaka/sundials_updates
Sundials updates
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‎Docs/source/SUNDIALS_Tutorial.rst‎

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SUNDIALS and Time Integrators
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=============================
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This example code shows how to use the AMReX TimeIntegrator class
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with SUNDIALS backend for integration. It also include two example
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of AMReX native integrators, Forward Euler, and Explicit Runge Kutta.
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Each integration type can be chosen by selecting the corresponding
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inputs file:
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These example codes demonstrate how to use the AMReX TimeIntegrator class
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with SUNDIALS backend for integration.
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- ``inputs_forward_euler`` -- Native AMReX Forward Euler integrator
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The first example code at ``amrex-tutorials/ExampleCodes/SUNDIALS/Single-Rate``
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solves the heat equation:
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- ``inputs_rk3`` -- Native AMReX Explicit Runge Kutta
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.. math:: \frac{\partial\phi}{\partial t} = \nabla^2\phi.
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- ``inputs_sundials_erk`` -- SUNDIALS backend
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The inputs file contains a template for single process time integration strategies.
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Both Runge Kutta and SUNDIALS have additional options which can
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be set by modifying the inputs file. Please see each respective inputs
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file or `AMReX User Guide:Time Integration`_ for more details.
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The second example code at ``amrex-tutorials/ExampleCodes/SUNDIALS/Reaction-Diffusion``
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solves the reaction-diffusion equation, where :math:`R` and :math:`D` are
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user-supplied reaction and diffusion coefficients:
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.. math:: \frac{\partial\phi}{\partial t} = D \nabla^2\phi - R \phi.
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The inputs file contains a template for MRI approaches, where the diffusion process
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can be treated as a "fast" partition relative to the reaction process.
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Please see each respective inputs file or
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`AMReX User Guide:Time Integration`_ for more details.
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.. _`AMReX User Guide:Time Integration`: https://amrex-codes.github.io/amrex/docs_html/TimeIntegration_Chapter.html#

‎ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/GNUmakefile‎

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COMP = gnu
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DIM = 3
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USE_SUNDIALS = TRUE
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SUNDIALS_HOME ?= ../../../../../sundials/instdir
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include $(AMREX_HOME)/Tools/GNUMake/Make.defs
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‎ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/README_sundials‎

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SUNDIALS installation guide:
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https://computing.llnl.gov/projects/sundials/faq#inst
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Refer to https://amrex-codes.github.io/amrex/docs_html/TimeIntegration_Chapter.html
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for SNUDIALS installation, build, and usage instructions.
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Installation
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# You need SUNDIALS v7.1.1 or later.
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# Check https://computing.llnl.gov/projects/sundials/sundials-software to see if it's available for download.
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# If so, download sundials-x.y.z.tar.gz and extract it at the same level as amrex using
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>> tar -xzvf sundials-x.y.z.tar.gz # where x.y.z is the version of sundials
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>> mv sundials-x.y.z sundials-src
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# If v7.1.1. is not available on the website, clone the git repo directly and use the latest version
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# At the same level that amrex is cloned, do:
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>> git clone https://github.com/LLNL/sundials.git
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>> mv sundials sundials-src
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# Next
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>> mkdir sundials
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>> cd sundials
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######################
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HOST BUILD
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######################
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>> mkdir instdir
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>> mkdir builddir
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>> cd builddir
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>> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir/examples -DENABLE_MPI=ON ../../sundials-src
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######################
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NVIDIA/CUDA BUILD
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######################
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# Navigate back to the 'sundials' directory and do:
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>> mkdir instdir_cuda
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>> mkdir builddir_cuda
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>> cd builddir_cuda
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>> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir_cuda -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir_cuda/examples -DENABLE_CUDA=ON -DENABLE_MPI=ON ../../sundials-src
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######################
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>> make -j4
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>> make install
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# in your .bashrc or preferred configuration file, add the following (and then "source ~/.bashrc")
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# If you have a CPU build:
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>> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir/lib/
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# If you have a NVIDIA/CUDA build:
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>> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir_cuda/lib/
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# now you are ready to compile amrex-tutorials/ExampleCodes/SUNDIALS/Exec with:
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>> make -j4 # optional to have 'USE_CUDA=TRUE' as well
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# Refer to inputs to see how to enable different integrators
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Make sure that SUNDIALS_HOME in the GNUmakefile points to the installation directory.

‎ExampleCodes/SUNDIALS/Single-Rate/Exec/GNUmakefile‎

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COMP = gnu
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USE_SUNDIALS = TRUE
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SUNDIALS_HOME ?= ../../../../../sundials/instdir
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include $(AMREX_HOME)/Tools/GNUMake/Make.defs
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‎ExampleCodes/SUNDIALS/Single-Rate/Exec/README_sundials‎

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SUNDIALS installation guide:
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https://computing.llnl.gov/projects/sundials/faq#inst
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Refer to https://amrex-codes.github.io/amrex/docs_html/TimeIntegration_Chapter.html
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for SNUDIALS installation, build, and usage instructions.
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Installation
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# You need SUNDIALS v7.1.1 or later.
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# Check https://computing.llnl.gov/projects/sundials/sundials-software to see if it's available for download.
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# If so, download sundials-x.y.z.tar.gz and extract it at the same level as amrex using
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>> tar -xzvf sundials-x.y.z.tar.gz # where x.y.z is the version of sundials
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>> mv sundials-x.y.z sundials-src
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# If v7.1.1. is not available on the website, clone the git repo directly and use the latest version
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# At the same level that amrex is cloned, do:
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>> git clone https://github.com/LLNL/sundials.git
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>> mv sundials sundials-src
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# Next
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>> mkdir sundials
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>> cd sundials
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######################
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HOST BUILD
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######################
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>> mkdir instdir
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>> mkdir builddir
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>> cd builddir
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>> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir/examples -DENABLE_MPI=ON ../../sundials-src
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######################
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NVIDIA/CUDA BUILD
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######################
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# Navigate back to the 'sundials' directory and do:
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>> mkdir instdir_cuda
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>> mkdir builddir_cuda
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>> cd builddir_cuda
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>> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir_cuda -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir_cuda/examples -DENABLE_CUDA=ON -DENABLE_MPI=ON ../../sundials-src
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######################
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>> make -j4
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>> make install
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# in your .bashrc or preferred configuration file, add the following (and then "source ~/.bashrc")
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# If you have a CPU build:
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>> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir/lib/
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# If you have a NVIDIA/CUDA build:
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>> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir_cuda/lib/
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# now you are ready to compile amrex-tutorials/ExampleCodes/SUNDIALS/Exec with:
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>> make -j4 # optional to have 'USE_CUDA=TRUE' as well
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# Refer to inputs to see how to enable different integrators
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Make sure that SUNDIALS_HOME in the GNUmakefile points to the installation directory.

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