User Guide

Getting Started

To get started with LEAP you need to have a modern Fortran compiler that supports Fortran 2008 features, such as Intel Fortran Compiler 18x and Gfortran 8x and higher, and follow the instructions below to get third-party libraries and compile the code.

Getting Third-Party Libraries

The following libraries are required to run LEAP:

An MPI distribution (recommended OpenMPI): This library handles the distributed memory aspects and allows the code to run in parallel on large computing systems.
HDF5: This library provides a file format (hdf5) that is widely used for scientific data. It is designed to be scalable, and optimizes IO on distributed systems. There is a nice little tool called HDF View that provides a GUI to look into the meta data in the file.
H5HUT: this is a wrapper around HDF5 that provides a high level API to make using HDF5 easier with block and Lagrangian data.
SZIP: A compression library from the HDF group used by HDF5.
ZLIB: Another compression library used by HDF5.
SILO: A file format for point, structured, and unstructured meshes developed by the Lawrence Livermore National Laboratory.
HYPRE: Scalable linear solvers and multigrid methods developed by the Lawrence Livermore National Laboratory

You may download these libraries from their developper websites and follow their compilation instructions. In general, it is best to use the latest version available.

Configuring a Makefile.in

In order to compile LEAP, you need to create a file called Makefile.in and place it under path/to/leap/src/. This file is machine dependent and the parameters will depend on the compilers you use.

SOL and PHX with GNU compilers
BRIDGES-2 with INTEL compilers

SOL and PHX with GNU compilers

HOMEDIR = $(shell pwd | sed -e 's/\/src.*//')
LDIR  = $(HOMEDIR)/lib
MDIR  = $(HOMEDIR)/mod
ODIR  = $(HOMEDIR)/obj
BDIR  = $(HOMEDIR)/bin

# Compiler and archiver
F90 = mpifort
LD  = mpifort
AR  = ar rcv 
RL  = ranlib

# Flags
LDFLAGS  =
INCFLAGS = -I$(MDIR)
MODFLAGS = -J$(MDIR)
PPFLAGS  = -cpp #-DUSE_GPU
DBGFLAGS = -g -fcheck=all -fbacktrace  -Wall  -Wunderflow  -ffpe-trap=invalid  -fbounds-check -ffree-line-length-none -fallow-invalid-boz -fallow-argument-mismatch
OPTFLAGS = -O3 -march=native -ffree-line-length-none -fPIC -fallow-invalid-boz -fallow-argument-mismatch

#HYPRE
HYPRE_DIR = /path/to/thirdparty/hypre
HYPRE_INC = -I$(HYPRE_DIR)/include
HYPRE_LIB = -Wl,-rpath -Wl,$(HYPRE_DIR)/lib -L$(HYPRE_DIR)/lib \
            -lHYPRE
#HDF5P
HDF5P_DIR = /path/to/thirdparty/hdf5
HDF5P_INC = -I$(HDF5P_DIR)/include
HDF5P_LIB = -Wl,-rpath -Wl,$(HDF5P_DIR)/lib -L$(HDF5P_DIR)/lib \
            -lhdf5 -lhdf5_fortran
#SZIP
SZIP_DIR = /path/to/thirdparty/szip
SZIP_LIB = -Wl,-rpath -Wl,$(SZIP_DIR)/lib -L$(SZIP_DIR)/lib    \
           -lsz
#ZLIB
ZLIB_DIR = /path/to/thirdparty/zlib
ZLIB_LIB = -Wl,-rpath -Wl,$(ZLIB_DIR)/lib -L$(ZLIB_DIR)/lib    \
           -lz
#SILO
SILO_DIR = /path/to/thirdparty/silo
SILO_INC = -I$(SILO_DIR)/include
SILO_LIB = -Wl,-rpath -Wl,$(SILO_DIR)/lib -L$(SILO_DIR)/lib    \
           -lsiloh5 $(HDF5P_LIB) $(SZIP_LIB) $(ZLIB_LIB)        \
           -L/usr/local/lib -lstdc++
#H5HUT  
H5HUT_DIR = /path/to/thirdparty/h5hut
H5HUT_INC = -I$(H5HUT_DIR)/include
H5HUT_LIB = -Wl,-rpath -Wl,$(H5HUT_DIR)/lib -L$(H5HUT_DIR)/lib \
            -lH5hutF -lH5hut

BRIDGES-2 with INTEL compilers

HOMEDIR = $(shell pwd | sed -e 's/\/src.*//')
LDIR  = $(HOMEDIR)/lib
MDIR  = $(HOMEDIR)/mod
ODIR  = $(HOMEDIR)/obj
BDIR  = $(HOMEDIR)/bin

# Compiler and archiver
F90 = mpif90
LD  = mpif90
AR  = ar rcv
RL  = ranlib

# Flags
FLAGS   =
F90FLAGS =
F77FLAGS =
LDFLAGS  = -march=core-avx2
INCFLAGS = -I$(MDIR)
MODFLAGS = -module $(MDIR)
DBGFLAGS = -g -CB -CS -traceback -debug all -ftrapuv -check all -check noarg_temp_created -WB
OPTFLAGS = -O3 -march=core-avx2 -ip

#HYPRE
HYPRE_DIR = /path/to/thirdparty/hypre
HYPRE_INC = -I$(HYPRE_DIR)/include
HYPRE_LIB = -Wl,-rpath -Wl,$(HYPRE_DIR)/lib -L$(HYPRE_DIR)/lib \
            -lHYPRE
#HDF5P
HDF5P_DIR = /path/to/thirdparty/hdf5
HDF5P_INC = -I$(HDF5P_DIR)/include
HDF5P_LIB = -Wl,-rpath -Wl,$(HDF5P_DIR)/lib -L$(HDF5P_DIR)/lib \
            -lhdf5 -lhdf5_fortran
#SZIP
SZIP_DIR = /path/to/thirdparty/szip
SZIP_LIB = -Wl,-rpath -Wl,$(SZIP_DIR)/lib -L$(SZIP_DIR)/lib    \
           -lsz
#ZLIB
ZLIB_DIR = /path/to/thirdparty/zlib
ZLIB_LIB = -Wl,-rpath -Wl,$(ZLIB_DIR)/lib -L$(ZLIB_DIR)/lib    \
           -lz
#SILO
SILO_DIR = /path/to/thirdparty/silo
SILO_INC = -I$(SILO_DIR)/include
SILO_LIB = -Wl,-rpath -Wl,$(SILO_DIR)/lib -L$(SILO_DIR)/lib    \
           -lsiloh5 $(HDF5P_LIB) $(SZIP_LIB) $(ZLIB_LIB)        \
           -L/usr/local/lib -lstdc++
#H5HUT  
H5HUT_DIR = /path/to/thirdparty/h5hut
H5HUT_INC = -I$(H5HUT_DIR)/include
H5HUT_LIB = -Wl,-rpath -Wl,$(H5HUT_DIR)/lib -L$(H5HUT_DIR)/lib \
            -lH5hutF -lH5hut

Compiling LEAP

After getting the third-party libraries and configuring Makefile.in, you may now compile LEAP. Go to /path/to/leap/src and run the following commands:

cd /path/to/leap/src
make debug

This will compile the code with debug flags. When coding for LEAP, it's best to compile in debug mode, since the compilation is much faster, and the compiler will pick up on any potential mistakes in the new code.

For production runs, compile in opt(imized) mode

cd /path/to/leap/src
make opt

This will instruct the compiler to turn on optimization flags. The compilation will take longer than in debug mode, but the code will run significantly faster!

When running make with debug and opt flags, the compiler will build the LEAP library and compile the main program in /path/to/leap/src/leap.f90. The binaries will be placed in /path/to/leap/bin. The library and mod files will be placed in /path/to/leap/lib and /path/to/leap/mod.

If for any reason you need to restart from a clean slate, you can delete all compilation files with the following

cd /path/to/leap/src
make clean

LEAP also has a limited number of tests. If you would like to compile those too run

make tests