Reaction Diffusion Tutorial

ExampleCodes/SUNDIALS/Reaction-Diffusion/CMakeLists.txt

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+if (AMReX_SPACEDIM EQUAL 1)
+   return()
+endif ()
+
+# List of source files
+set(_sources main.cpp myfunc.H)
+list(TRANSFORM _sources PREPEND "Source/")
+
+# List of input files
+file( GLOB_RECURSE _input_files LIST_DIRECTORIES false Exec/input* )
+
+setup_tutorial(_sources _input_files)
+
+unset( _sources )
+unset( _input_files   )

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/GNUmakefile

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+# AMREX_HOME defines the directory in which we will find all the AMReX code.
+AMREX_HOME ?= ../../../../../amrex
+
+DEBUG        = FALSE
+USE_MPI      = TRUE
+USE_OMP      = FALSE
+COMP         = gnu
+DIM          = 3
+USE_RPATH    = TRUE
+USE_SUNDIALS = TRUE
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.defs
+
+include ../Source/Make.package
+VPATH_LOCATIONS  += ../Source
+INCLUDE_LOCATIONS += ../Source
+
+ifeq ($(USE_SUNDIALS),TRUE)
+  ifeq ($(USE_CUDA),TRUE)
+    SUNDIALS_ROOT ?= $(TOP)../../../../../sundials/instdir_cuda
+  else
+    SUNDIALS_ROOT ?= $(TOP)../../../../../sundials/instdir
+  endif
+  ifeq ($(NERSC_HOST),perlmutter)
+    SUNDIALS_LIB_DIR ?= $(SUNDIALS_ROOT)/lib64
+  else
+    SUNDIALS_LIB_DIR ?= $(SUNDIALS_ROOT)/lib
+  endif
+
+  USE_CVODE_LIBS ?= TRUE
+  USE_ARKODE_LIBS ?= TRUE
+
+  DEFINES += -DAMREX_USE_SUNDIALS
+  INCLUDE_LOCATIONS += $(SUNDIALS_ROOT)/include
+  LIBRARY_LOCATIONS += $(SUNDIALS_LIB_DIR)
+
+  LIBRARIES += -L$(SUNDIALS_LIB_DIR) -lsundials_cvode
+  LIBRARIES += -L$(SUNDIALS_LIB_DIR) -lsundials_arkode
+  LIBRARIES += -L$(SUNDIALS_LIB_DIR) -lsundials_nvecmanyvector
+  LIBRARIES += -L$(SUNDIALS_LIB_DIR) -lsundials_core
+
+  ifeq ($(USE_CUDA),TRUE)
+    LIBRARIES += -L$(SUNDIALS_LIB_DIR) -lsundials_nveccuda
+  endif
+
+endif
+
+include $(AMREX_HOME)/Src/Base/Make.package
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.rules
+

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/README_sundials

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+SUNDIALS installation guide:
+https://computing.llnl.gov/projects/sundials/faq#inst
+
+Installation
+
+# Download sundials-x.y.z.tar.gz file for SUNDIALS and extract it at the same level as amrex.
+# Update 6/11/24 - v7.0.0. tested
+https://computing.llnl.gov/projects/sundials/sundials-software
+
+>> tar -xzvf sundials-x.y.z.tar.gz # where x.y.z is the version of sundials
+
+# at the same level that amrex is cloned, do:
+
+>> 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-x.y.z
+
+######################
+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-x.y.z
+
+######################
+
+>> 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
+
+# in your inputs file, you will need to have:
+
+# INTEGRATION
+## integration.type can take on the following values:
+## 0 or "ForwardEuler" => Native AMReX Forward Euler integrator
+## 1 or "RungeKutta"   => Native AMReX Explicit Runge Kutta controlled by integration.rk.type
+## 2 or "SUNDIALS"     => SUNDIALS backend controlled by integration.sundials.strategy
+integration.type = <pick a value>
+
+## Native AMReX Explicit Runge-Kutta parameters
+#
+## integration.rk.type can take the following values:
+### 0 = User-specified Butcher Tableau
+### 1 = Forward Euler
+### 2 = Trapezoid Method
+### 3 = SSPRK3 Method
+### 4 = RK4 Method
+integration.rk.type = 3
+
+## If using the SUNDIALS Submodule, then
+## compile with USE_SUNDIALS=TRUE or AMReX_SUNDIALS=ON and
+## set strategy here:
+#
+## integration.sundials.strategy can take the following values:
+### ERK     = ERKStep from ARKode with SSPRK3 Method
+### MRI     = MRIStep from ARKode with Explict Trapezoid Method
+### MRITEST = MRIStep from ARKode modified to use no-op inner f0
+integration.sundials.strategy = ERK

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/inputs_forward_euler

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+n_cell = 32
+max_grid_size = 16
+
+nsteps = 1000
+plot_int = 100
+
+dt = 1.e-5
+
+# INTEGRATION
+## integration.type can take on the following values:
+## 0 or "ForwardEuler" => Native AMReX Forward Euler integrator
+## 1 or "RungeKutta"   => Native AMReX Explicit Runge Kutta controlled by integration.rk.type
+## 2 or "SUNDIALS"     => SUNDIALS backend controlled by integration.sundials.strategy
+integration.type = ForwardEuler

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/inputs_rk3

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+n_cell = 32
+max_grid_size = 16
+
+nsteps = 1000
+plot_int = 100
+
+dt = 1.e-5
+
+# INTEGRATION
+## integration.type can take on the following values:
+## 0 or "ForwardEuler" => Native AMReX Forward Euler integrator
+## 1 or "RungeKutta"   => Native AMReX Explicit Runge Kutta controlled by integration.rk.type
+## 2 or "SUNDIALS"     => SUNDIALS backend controlled by integration.sundials.strategy
+integration.type = RungeKutta
+
+## Native AMReX Explicit Runge-Kutta parameters
+#
+## integration.rk.type can take the following values:
+### 0 = User-specified Butcher Tableau
+### 1 = Forward Euler
+### 2 = Trapezoid Method
+### 3 = SSPRK3 Method
+### 4 = RK4 Method
+integration.rk.type = 3

ExampleCodes/SUNDIALS/Reaction-Diffusion/Exec/inputs_sundials

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+n_cell = 32
+max_grid_size = 16
+
+nsteps = 1000
+plot_int = 100
+
+dt = 1.e-5
+
+# Use adaptive time stepping and set integrator relative and absolute tolerances
+# adapt_dt = true
+# reltol   = 1.0e-4
+# abstol   = 1.0e-9
+
+# INTEGRATION
+# integration.type can take on the following values:
+# 0 or "ForwardEuler" => Native AMReX Forward Euler integrator
+# 1 or "RungeKutta"   => Native AMReX Explicit Runge Kutta controlled by integration.rk.type
+# 2 or "SUNDIALS"     => SUNDIALS backend controlled by integration.sundials.type
+#
+# If using the SUNDIALS Submodule, then compile with USE_SUNDIALS=TRUE or
+# AMReX_SUNDIALS=ON
+integration.type = SUNDIALS
+
+# Set the SUNDIALS method type:
+# ERK      = Explicit Runge-Kutta method
+# DIRK     = Diagonally Implicit Runge-Kutta method
+# IMEX-RK  = Implicit-Explicit Additive Runge-Kutta method
+# EX-MRI   = Explicit Multirate Infatesimal method
+# IM-MRI   = Implicit Multirate Infatesimal method
+# IMEX-MRI = Implicit-Explicit Multirate Infatesimal method
+#
+# Optionally select a specific SUNDIALS method by name, see the SUNDIALS
+# documentation for the supported method names
+
+# Use the SUNDIALS default method for the chosen type (fixed or adaptive step sizes)
+integration.sundials.type = ERK
+
+# Use forward Euler (fixed step sizes only)
+# integration.sundials.type = ERK
+# integration.sundials.method = ARKODE_FORWARD_EULER_1_1
+
+# Use backward Euler (fixed step sizes only)
+# integration.sundials.type = DIRK
+# integration.sundials.method = ARKODE_BACKWARD_EULER_1_1

ExampleCodes/SUNDIALS/Reaction-Diffusion/Source/Make.package

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+CEXE_sources += main.cpp
+CEXE_headers += myfunc.H