Sundials updates

Docs/source/SUNDIALS_Tutorial.rst

@@ -4,20 +4,25 @@
 SUNDIALS and Time Integrators
 =============================
 
-This example code shows how to use the AMReX TimeIntegrator class
-with SUNDIALS backend for integration. It also include two example
-of AMReX native integrators, Forward Euler, and Explicit Runge Kutta.
-Each integration type can be chosen by selecting the corresponding
-inputs file:
+These example codes demonstrate how to use the AMReX TimeIntegrator class
+with SUNDIALS backend for integration.
 
-  - ``inputs_forward_euler`` -- Native AMReX Forward Euler integrator
+The first example code at ``amrex-tutorials/ExampleCodes/SUNDIALS/Single-Rate``
+solves the heat equation:
 
-  - ``inputs_rk3`` -- Native AMReX Explicit Runge Kutta
+.. math:: \frac{\partial\phi}{\partial t} = \nabla^2\phi.
 
-  - ``inputs_sundials_erk`` -- SUNDIALS backend
+The inputs file contains a template for single process time integration strategies.
 
-Both Runge Kutta and SUNDIALS have additional options which can
-be set by modifying the inputs file. Please see each respective inputs
-file or `AMReX User Guide:Time Integration`_ for more details.
+The second example code at ``amrex-tutorials/ExampleCodes/SUNDIALS/Reaction-Diffusion``
+solves the reaction-diffusion equation, where :math:`R` and :math:`D` are
+user-supplied reaction and diffusion coefficients:
+
+.. math:: \frac{\partial\phi}{\partial t} = D \nabla^2\phi - R \phi.
+
+The inputs file contains a template for MRI approaches, where the diffusion process
+can be treated as a "fast" partition relative to the reaction process.
+Please see each respective inputs file or
+`AMReX User Guide:Time Integration`_ for more details.
 
 .. _`AMReX User Guide:Time Integration`: https://amrex-codes.github.io/amrex/docs_html/TimeIntegration_Chapter.html#

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/GNUmakefile

@@ -7,6 +7,7 @@ USE_OMP      = FALSE
 COMP         = gnu
 DIM          = 3
 USE_SUNDIALS = TRUE
+SUNDIALS_HOME ?= ../../../../../sundials/instdir
 
 include $(AMREX_HOME)/Tools/GNUMake/Make.defs
 

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/README_sundials

@@ -1,64 +1,4 @@
-SUNDIALS installation guide:
-https://computing.llnl.gov/projects/sundials/faq#inst
+Refer to https://amrex-codes.github.io/amrex/docs_html/TimeIntegration_Chapter.html
+for SNUDIALS installation, build, and usage instructions.
 
-Installation
-
-# You need SUNDIALS v7.1.1 or later.
-# Check https://computing.llnl.gov/projects/sundials/sundials-software to see if it's available for download.
-# If so, download sundials-x.y.z.tar.gz and extract it at the same level as amrex using
->> tar -xzvf sundials-x.y.z.tar.gz # where x.y.z is the version of sundials
->> mv sundials-x.y.z sundials-src
-
-# If v7.1.1. is not available on the website, clone the git repo directly and use the latest version
-# At the same level that amrex is cloned, do:
-
->> git clone https://github.com/LLNL/sundials.git
->> mv sundials sundials-src
-
-# Next
-
->> mkdir sundials
->> cd sundials
-
-######################
-HOST BUILD 
-######################
-
->> mkdir instdir
->> mkdir builddir
->> cd builddir
-
->> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir/examples -DENABLE_MPI=ON ../../sundials-src
-
-######################
-NVIDIA/CUDA BUILD
-######################
-
-# Navigate back to the 'sundials' directory and do:
-
->> mkdir instdir_cuda
->> mkdir builddir_cuda
->> cd builddir_cuda
-
->> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir_cuda -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir_cuda/examples -DENABLE_CUDA=ON -DENABLE_MPI=ON ../../sundials-src
-
-######################
-
->> make -j4
->> make install
-
-# in your .bashrc or preferred configuration file, add the following (and then "source ~/.bashrc")
-
-# If you have a CPU build:
-
->> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir/lib/
-
-# If you have a NVIDIA/CUDA build:
-
->> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir_cuda/lib/
-
-# now you are ready to compile amrex-tutorials/ExampleCodes/SUNDIALS/Exec with:
-
->> make -j4 # optional to have 'USE_CUDA=TRUE' as well
-
-# Refer to inputs to see how to enable different integrators
+Make sure that SUNDIALS_HOME in the GNUmakefile points to the installation directory.

ExampleCodes/SUNDIALS/Single-Rate/Exec/GNUmakefile

@@ -7,6 +7,7 @@ USE_OMP      = FALSE
 COMP         = gnu
 DIM          = 3
 USE_SUNDIALS = TRUE
+SUNDIALS_HOME ?= ../../../../../sundials/instdir
 
 include $(AMREX_HOME)/Tools/GNUMake/Make.defs
 

ExampleCodes/SUNDIALS/Single-Rate/Exec/README_sundials

@@ -1,64 +1,4 @@
-SUNDIALS installation guide:
-https://computing.llnl.gov/projects/sundials/faq#inst
+Refer to https://amrex-codes.github.io/amrex/docs_html/TimeIntegration_Chapter.html
+for SNUDIALS installation, build, and usage instructions.
 
-Installation
-
-# You need SUNDIALS v7.1.1 or later.
-# Check https://computing.llnl.gov/projects/sundials/sundials-software to see if it's available for download.
-# If so, download sundials-x.y.z.tar.gz and extract it at the same level as amrex using
->> tar -xzvf sundials-x.y.z.tar.gz # where x.y.z is the version of sundials
->> mv sundials-x.y.z sundials-src
-
-# If v7.1.1. is not available on the website, clone the git repo directly and use the latest version
-# At the same level that amrex is cloned, do:
-
->> git clone https://github.com/LLNL/sundials.git
->> mv sundials sundials-src
-
-# Next
-
->> mkdir sundials
->> cd sundials
-
-######################
-HOST BUILD 
-######################
-
->> mkdir instdir
->> mkdir builddir
->> cd builddir
-
->> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir/examples -DENABLE_MPI=ON ../../sundials-src
-
-######################
-NVIDIA/CUDA BUILD
-######################
-
-# Navigate back to the 'sundials' directory and do:
-
->> mkdir instdir_cuda
->> mkdir builddir_cuda
->> cd builddir_cuda
-
->> cmake -DCMAKE_INSTALL_PREFIX=/pathto/sundials/instdir_cuda -DEXAMPLES_INSTALL_PATH=/pathto/sundials/instdir_cuda/examples -DENABLE_CUDA=ON -DENABLE_MPI=ON ../../sundials-src
-
-######################
-
->> make -j4
->> make install
-
-# in your .bashrc or preferred configuration file, add the following (and then "source ~/.bashrc")
-
-# If you have a CPU build:
-
->> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir/lib/
-
-# If you have a NVIDIA/CUDA build:
-
->> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/pathto/sundials/instdir_cuda/lib/
-
-# now you are ready to compile amrex-tutorials/ExampleCodes/SUNDIALS/Exec with:
-
->> make -j4 # optional to have 'USE_CUDA=TRUE' as well
-
-# Refer to inputs to see how to enable different integrators
+Make sure that SUNDIALS_HOME in the GNUmakefile points to the installation directory.