MRI-phase-encoding/go.sh

#!/bin/bash
HOST=`hostname`

path_mri=$PWD;   path_bin=$path_mri/bin;   path_build=$path_mri/build
path_src=$path_mri/src;   path_data=$path_mri/data
# Should be same as in cmake config in $path_src

mri_bin="run-mri-phase-encoding"
# Default values
yes="yes";        no="no"

echo base dir path: $path_mri
# Check directory structure
if [[ ! -d $path_src ]]; then
    echo ================ !ERROR! =================
    echo No source folder $path_src
    echo ================ !ERROR! =================
    exit 1
fi
force_new_build=$no
if [[ -a $path_build ]]; then
    echo Found build folder.
else
    echo Creating build folder...
    mkdir build
    force_new_build=$yes
fi
if [[ -a $path_bin ]]; then
    echo Found bin folder.
else
    echo Creating build folder...
    mkdir bin
fi
#############################################################################
#   Compile settings
#############################################################################
echo Cleaning bin
rm -r $path_bin/* >/dev/null 2>&1

# Select OMPI_CXXFLAGS
#debug
#flags_O2="-std=c++11"
flags_O2="-O2 -Wall -std=c++11"
#flags_O2="-O2 -Wall -std=c++11 -stdlib=libc++"
#flags_O2="-O2 -ftemplate-depth-30 -Wall -std=c++11"
flags_debug="-ftemplate-depth-30 -Wall -std=c++11  -stdlib=libc++"
#flags_debug_gcc="-ftemplate-depth-30 -std=c++11  -da -Q"
flags_debug_gcc="-ftemplate-depth-30 -std=c++11 -g -O0" 
flags_O3="-O3 -ffast-math -ftemplate-depth-30 -march=native -mtune=native -mfpmath=both -malign-double -mstackrealign -ftree-vectorize -msse2 -ftree-vectorizer-verbose=5  -Wall  -std=c++11 -stdlib=libc++" 
flags_with_google=" -Ofast -std=c++11 -lm -lrt /usr/lib/libtcmalloc_minimal.so.4 -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -march=native -mtune=native -msse4.2"

export OMPI_CC=gcc
export OMPI_CXX=g++
export OMPI_CXXFLAGS=$flags_O2
#export OMPI_CXXFLAGS=$flags_with_google
#############################################################################
#   Build
#############################################################################
function BuildMRI {
    echo "Building MRI..."
    local path_tmp=`pwd`
    cd $path_build
    flag_cmake=
    echo $PWD
    ls $path_bin
    echo "Doing new build.."
    # echo CC=mpicc CXX=mpic++ VERBOSE=1 cmake $path_mri -DCMAKE_INSTALL_PREFIX="$path_bin"  $flag_cmake
    # CC=mpicc CXX=mpic++ VERBOSE=1 cmake $path_mri \
    #   -DCMAKE_INSTALL_PREFIX="$path_bin" \
    #   $flag_cmake
    # make -j4 
    # make install
    # g++ $path_src/main.cc -o $mri_bin 
    OMPI_CXXFLAGS=$flags_O2 mpic++ -o $mri_bin $path_src/main.cc $path_src/jade.cc $path_src/generator-rf.cc $path_src/lock-in.cc
    cp $mri_bin $path_bin
    cd $path_tmp
}  # end of function BuildMRI
BuildMRI
#############################################################################
#   Run
#############################################################################
echo "Executing $mri_bin on host -> $HOST <-"
MPI_options=
#MPI_options="--bind-to-core"
MPI_size=2
cd $path_bin
time mpirun -np $MPI_size $MPI_options ./$mri_bin