Merge pull request #239 from lanl/DanielJ2quick

added LS-EVPFFT-J2 to the source directory. Will merge with other LS-…

.gitattributes

@@ -19,4 +19,5 @@ src/LS-EVPFFT/scripts/** linguist-documentation
 src/Mesh-Builder/examples/** linguist-documentation
 src/Parallel-Solvers/Implicit-Lagrange/Mesh_Examples/** linguist-documentation
 src/Parallel-Solvers/Implicit-Lagrange/MueLu_XML_Examples/** linguist-documentation
-src/Parallel-Solvers/Parallel-Explicit/Example_Yaml_Scripts/** linguist-documentation
+src/Parallel-Solvers/Parallel-Explicit/Example_Yaml_Scripts/** linguist-documentation
+src/LS-EVPFFT-J2/example_lattice_run/** linguist-documentation

src/LS-EVPFFT-J2/example_lattice_run/elastic_parameters.txt

@@ -0,0 +1,2 @@
+1 						ISO
+119800.   0.35    	           		YOUNG(MPa),NU (V+R/2)

src/LS-EVPFFT-J2/example_lattice_run/plastic_parameters.txt

@@ -0,0 +1,5 @@
+SLIP SYSTEMS FOR CUBIC CRYSTAL
+CUBIC             icryst
+   1.   1.   1.   crystal axes (cdim(i))
+   0              nmodesx (total # of modes listed in the file)
+   0              nmodes  (# of modes to be used in the calculation)

src/LS-EVPFFT-J2/example_lattice_run/plastic_parameters_j2.txt

@@ -0,0 +1,4 @@
+PLASTICITY
+J2             icryst
+10 1.0         nrs, edot0
+10.0 10.0 50.0 2.0  sigma0, sigma1, theta0, theta1

src/LS-EVPFFT-J2/example_lattice_run/tension_33.txt

@@ -0,0 +1,48 @@
+2 0 0 0               NPHMX, NMODMX, NTWMMX, NSYSMX
+84 84 64               x-dim, y-dim, z-dim
+2                      number of phases (nph)                         
+1.  1.  1.             RVE dimensions (delt)
+* name and path of microstructure file (filetext)                                
+txfft_gas
+*INFORMATION ABOUT PHASE #1
+1                          igas(iph)
+* name and path of single crystal files (filecryspl, filecrysel) (dummy if igas(iph)=1)
+dummy
+dummy
+*INFORMATION ABOUT PHASE #2
+0                          igas(iph)
+* name and path of single crystal files (filecryspl, filecrysel) (dummy if igas(iph)=1)
+plastic_parameters_j2.txt
+elastic_parameters.txt
+*INFORMATION ABOUT TEST CONDITIONS
+* boundary conditions                                                     
+    1       1       1           iudot     |    flag for vel.grad. 
+    1       1       1                     |    (0:unknown-1:known)        
+    1       1       1                     |            
+                                          |                               
+    0.0     0.0     0.0          udot     |    vel.grad                   
+    0.0     0.0     0.0                   |                               
+    0.0     0.0     1.0                   |                               
+                                          |                               
+    0       0        0           iscau    |    flag for Cauchy            
+            0        0                    |                               
+                     0                    |                               
+                                          |                               
+    0.      0.       0.          scauchy  |    Cauchy stress              
+            0.       0.                   |                               
+                     0.                   @                               
+* other                                                                   
+0.001         eqincr (if ictrl>=0) or tdot (if ictrl=-1)
+-1              ictrl (1-6: strain comp, 0: VM eq, -1: tdot)              
+*INFORMATION ABOUT RUN CONDITIONS                                         
+10               nsteps                                                     
+0.00001         err                                                        
+100              itmax                                                      
+0               IRECOVER read grain states from STRESS.IN  (1) or not (0)?      
+0               ISAVE write grain states in STRESS.OUT (1) or not (0)?                    
+1               IUPDATE update tex & RVE dim (1) or not (0)?
+1               IUPHARD
+1               IWTEX
+1 10             IWFIELDS,IWSTEP
+0               ITHERMO (if ithermo=1, next line is filethermo) 
+dummy

src/LS-EVPFFT-J2/scripts/build_scripts/build_ls-evpfft.sh

@@ -0,0 +1,180 @@
+#!/bin/bash -e
+
+show_help() {
+    echo "Usage: source $(basename "$BASH_SOURCE") [OPTION]"
+    echo "Required arguments:"
+    echo "  --heffte_build_type=<fftw|cufft|rocfft>"
+    echo "  --kokkos_build_type=<serial|openmp|pthreads|cuda|hip>"
+    echo " "
+    echo "Optional arguments:"
+    echo "  --build_fftw: builds fftw from scratch"
+    echo "  --build_hdf5: builds hdf5 from scratch"
+    echo "  --machine=<darwin|chicoma|linux|mac> (default: none)"
+    echo "  --num_jobs=<number>: Number of jobs for 'make' (default: 1, on Mac use 1)"
+    echo "  --help: Display this help message"
+    echo " "
+    return 1
+}
+
+# Initialize variables with default values
+heffte_build_type=""
+kokkos_build_type=""
+machine=""
+num_jobs=1
+build_fftw=0
+build_hdf5=0
+
+# Define arrays of valid options
+valid_heffte_build_types=("fftw" "cufft" "rocfft")
+valid_kokkos_build_types=("serial" "openmp" "cuda" "cuda-ampere" "hip")
+valid_machines=("darwin" "chicoma" "linux" "mac")
+
+# Parse command line arguments
+for arg in "$@"; do
+    case "$arg" in
+        --heffte_build_type=*)
+            option="${arg#*=}"
+            if [[ " ${valid_heffte_build_types[*]} " == *" $option "* ]]; then
+                heffte_build_type="$option"
+            else
+                echo "Error: Invalid --heffte_build_type specified."
+                show_help
+                return 1
+            fi
+            ;;
+        --kokkos_build_type=*)
+            option="${arg#*=}"
+            if [[ " ${valid_kokkos_build_types[*]} " == *" $option "* ]]; then
+                kokkos_build_type="$option"
+            else
+                echo "Error: Invalid --kokkos_build_type specified."
+                show_help
+                return 1
+            fi
+            ;;
+        --build_fftw)
+            build_fftw=1
+            ;;
+        --build_hdf5)
+            build_hdf5=1
+            ;;
+        --machine=*)
+            option="${arg#*=}"
+            if [[ " ${valid_machines[*]} " == *" $option "* ]]; then
+                machine="$option"
+            else
+                echo "Error: Invalid --machine specified."
+                show_help
+                return 1
+            fi
+            ;;
+        --num_jobs=*)
+            num_jobs="${arg#*=}"
+            if ! [[ "$num_jobs" =~ ^[0-9]+$ ]]; then
+                echo "Error: Invalid --num_jobs value. Must be a positive integer."
+                show_help
+                return 1
+            fi
+            ;;
+        --help)
+            show_help
+            return 1
+            ;;
+        *)
+            echo "Error: Invalid argument or value specified."
+            show_help
+            return 1
+            ;;
+    esac
+done
+
+# Check if required options are specified
+if [ -z "$heffte_build_type" ] || [ -z "$kokkos_build_type" ]; then
+    echo "Error: --heffte_build_type and --kokkos_build_type are required options."
+    show_help
+    return 1
+fi
+
+# If both arguments are valid, you can use them in your script as needed
+echo "Heffte Build Type: $heffte_build_type"
+echo "Kokkos Build Type: $kokkos_build_type"
+
+# Determine the directory of the current script
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+echo "Script directory: ${SCRIPT_DIR}"
+
+# Determine the parent directory of the script's directory
+PARENT_DIR=$(dirname $(dirname "${SCRIPT_DIR}"))
+
+# make lib directory to store all dependencies
+LIB_DIR="$PARENT_DIR/lib"
+mkdir -p "$LIB_DIR"
+
+# --------setup env for machine
+if [ -n "$machine" ]; then
+    MACHINE_SCRIPT="$PARENT_DIR/scripts/machines/${machine}-env.sh"
+    source  "$MACHINE_SCRIPT" --env_type=$kokkos_build_type
+fi
+
+# --------building heffte
+build_fftw_option=""
+if [ "$build_fftw" -eq 1 ]; then
+  build_fftw_option="--build_fftw"
+fi
+HEFFTE_INSTALL_SCRIPT="$PARENT_DIR/scripts/install_scripts/install_heffte.sh"
+source "$HEFFTE_INSTALL_SCRIPT" --heffte_build_type=$heffte_build_type --num_jobs=$num_jobs $build_fftw_option
+
+# --------building kokkos
+KOKKOS_INSTALL_SCRIPT="$PARENT_DIR/scripts/install_scripts/install_kokkos.sh"
+source "$KOKKOS_INSTALL_SCRIPT" --kokkos_build_type=$kokkos_build_type --num_jobs=$num_jobs
+
+# --------building hdf5
+if [ "$build_hdf5" -eq 1 ]; then
+  HDF5_INSTALL_SCRIPT="$PARENT_DIR/scripts/install_scripts/install_hdf5.sh"
+  source "$HDF5_INSTALL_SCRIPT" --num_jobs=$num_jobs
+fi
+
+# --------building matar
+MATAR_INSTALL_SCRIPT="$PARENT_DIR/scripts/install_scripts/install_matar.sh"
+source "$MATAR_INSTALL_SCRIPT"  --kokkos_build_type=$kokkos_build_type --num_jobs=$num_jobs
+
+# --------building LS-EVPFFT
+LS_EVPFFT_SOURCE_DIR="$PARENT_DIR/src"
+LS_EVPFFT_BUILD_DIR="$PARENT_DIR/ls-evpfft_${heffte_build_type}_${kokkos_build_type}"
+
+# set dependencies directories
+HEFFTE_INSTALL_DIR="$LIB_DIR/heffte/install_heffte_$heffte_build_type"
+KOKKOS_INSTALL_DIR="$LIB_DIR/kokkos/install_kokkos_$kokkos_build_type"
+MATAR_INSTALL_DIR="$LIB_DIR/MATAR/install_MATAR_$kokkos_build_type"
+if [ "$build_hdf5" -eq 1 ]; then
+  HDF5_INSTALL_DIR="$LIB_DIR/hdf5/install_hdf5"
+fi
+
+# Configure LS-EVPFFT using CMake
+cmake_options=(
+    -D CMAKE_BUILD_TYPE=Release
+    -D CMAKE_PREFIX_PATH="$HEFFTE_INSTALL_DIR;$KOKKOS_INSTALL_DIR;$HDF5_INSTALL_DIR;$MATAR_INSTALL_DIR"
+    -D ENABLE_PROFILING=ON
+)
+
+if [ "$heffte_build_type" = "fftw" ]; then
+    cmake_options+=(
+        -D USE_FFTW=ON
+    )   
+elif [ "$heffte_build_type" = "cufft" ]; then
+    cmake_options+=(
+        -D USE_CUFFT=ON
+    )   
+elif [ "$heffte_build_type" = "rocfft" ]; then
+    cmake_options+=(
+      -D USE_ROCFFT=ON
+    )   
+fi
+
+# Configure LS-EVPFFT
+cmake "${cmake_options[@]}" -B "$LS_EVPFFT_BUILD_DIR" -S "$LS_EVPFFT_SOURCE_DIR"
+
+# Build kokkos
+echo "Building LS-EVPFFT..."
+make -C "$LS_EVPFFT_BUILD_DIR" -j"$num_jobs"
+

src/LS-EVPFFT-J2/scripts/install_scripts/install_fftw.sh

@@ -0,0 +1,116 @@
+#!/bin/bash -e
+
+show_help() {
+    echo "Usage: source $(basename "$BASH_SOURCE") [OPTION]"
+    echo "Valid options:"
+    echo "  --num_jobs=<number>: Number of jobs for 'make' (default: 1, on Mac use 1)"
+    echo "  --help: Display this help message"
+    return 1
+}
+
+# Initialize variables with default values
+num_jobs=1
+
+# Parse command line arguments
+for arg in "$@"; do
+    case "$arg" in
+        --num_jobs=*)
+            num_jobs="${arg#*=}"
+            if ! [[ "$num_jobs" =~ ^[0-9]+$ ]]; then
+                echo "Error: Invalid --num_jobs value. Must be a positive integer."
+                show_help
+                return 1
+            fi
+            ;;
+        --help)
+            show_help
+            return 1
+            ;;
+        *)
+            echo "Error: Invalid argument or value specified."
+            show_help
+            return 1
+            ;;
+    esac
+done
+
+# Determine the script's directory
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+echo "Script location: $SCRIPT_DIR"
+
+# Determine the parent directory of the script's directory
+PARENT_DIR=$(dirname $(dirname "${SCRIPT_DIR}"))
+
+# make lib directory to store all dependencies
+LIB_DIR="$PARENT_DIR/lib"
+mkdir -p "$LIB_DIR"
+
+# Define FFTW directories
+FFTW_SOURCE_DIR="$LIB_DIR/fftw-3.3.10"
+FFTW_INSTALL_DIR="$LIB_DIR/fftw-3.3.10/install_fftw"
+FFTW_BUILD_DIR="$LIB_DIR/fftw-3.3.10/build_fftw"
+
+# Check if the 'fftw-3.3.10' directory exists in the lib directory; if not, clone it
+if [ ! -d "$FFTW_SOURCE_DIR" ]; then
+  echo "Directory 'fftw' does not exist in '$LIB_DIR', downloading 'fftw'...."
+  wget -P "$LIB_DIR" "http://www.fftw.org/fftw-3.3.10.tar.gz"
+  tar -C "$LIB_DIR" -zxvf "$LIB_DIR/fftw-3.3.10.tar.gz"
+else
+  echo "Directory 'fftw' exists in '$LIB_DIR', skipping 'fftw' download"
+fi
+
+# Check to avoid reinstalling FFTW which might take time
+if [ -d "$FFTW_INSTALL_DIR" ]; then
+    echo "FFTW already installed, to reinstall FFTW delete $FFTW_INSTALL_DIR and $FFTW_BUILD_DIR"
+    return 0
+fi
+
+# Configure fftw
+config_options=(
+    CFLAGS='-O3 -DNDEBUG -fPIC'
+    --prefix=${FFTW_INSTALL_DIR}
+    --enable-mpi
+    --enable-threads
+    --enable-openmp
+    #--enable-avx
+    #--enable-avx2
+    #--enable-avx512
+)
+
+current_dir=$(pwd)
+# have to mkdir and cd because configure does not provide option for build_dir
+mkdir -p "$FFTW_BUILD_DIR"
+cd "$FFTW_BUILD_DIR"
+# Run configure
+"$FFTW_SOURCE_DIR/configure" "${config_options[@]}"
+
+echo "Building double precision fftw..."
+make -C "$FFTW_BUILD_DIR" -j"$num_jobs"
+
+echo "Installing double precision fftw..."
+make -C "$FFTW_BUILD_DIR" install
+
+# cleanup before installing single precision
+make distclean
+
+# Configure for single precision
+config_options+=(
+    --enable-float
+)
+
+# Run configure for single precision
+"$FFTW_SOURCE_DIR/configure" "${config_options[@]}"
+
+echo "Building single precision fftw..."
+make -C "$FFTW_BUILD_DIR" -j"$num_jobs"
+
+echo "Installing single precision fftw..."
+make -C "$FFTW_BUILD_DIR" install
+
+#cleanup
+make distclean
+
+cd "$current_dir"
+
+echo "fftw installation complete."
+