#!/bin/bash # # svn $Id: build.bash 834 2017-01-25 18:49:17Z arango $ #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: # Copyright (c) 2002-2017 The ROMS/TOMS Group ::: # Licensed under a MIT/X style license ::: # See License_ROMS.txt ::: #::::::::::::::::::::::::::::::::::::::::::::::::::::: Hernan G. Arango ::: # ::: # ROMS/TOMS Compiling Script ::: # ::: # Script to compile an user application where the application-specific ::: # files are kept separate from the ROMS source code. ::: # ::: # Q: How/why does this script work? ::: # ::: # A: The ROMS makefile configures user-defined options with a set of ::: # flags such as ROMS_APPLICATION. Browse the makefile to see these. ::: # If an option in the makefile uses the syntax ?= in setting the ::: # default, this means that make will check whether an environment ::: # variable by that name is set in the shell that calls make. If so ::: # the environment variable value overrides the default (and the ::: # user need not maintain separate makefiles, or frequently edit ::: # the makefile, to run separate applications). ::: # ::: # Usage: ::: # ::: # ./build.bash [options] ::: # ::: # Options: ::: # ::: # -j [N] Compile in parallel using N CPUs ::: # omit argument for all available CPUs ::: # -noclean Do not clean already compiled objects ::: # ::: # Notice that sometimes the parallel compilation fail to find MPI ::: # include file "mpif.h". ::: # ::: #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: parallel=0 clean=1 while [ $# -gt 0 ] do case "$1" in -j ) shift parallel=1 test=`echo $1 | grep '^[0-9]\+$'` if [ "$test" != "" ]; then NCPUS="-j $1" shift else NCPUS="-j" fi ;; -noclean ) shift clean=0 ;; * ) echo "" echo "$0 : Unknown option [ $1 ]" echo "" echo "Available Options:" echo "" echo "-j [N] Compile in parallel using N CPUs" echo " omit argument for all avaliable CPUs" echo "-noclean Do not clean already compiled objects" echo "" exit 1 ;; esac done # Set the CPP option defining the particular application. This will # determine the name of the ".h" header file with the application # CPP definitions. #export ROMS_APPLICATION=UPWELLING export ROMS_APPLICATION=jes77 # Set a local environmental variable to define the path to the directories # where all this project's files are kept. #export MY_ROOT_DIR=${HOME}/ocean/repository #export MY_ROOT_DIR=${HOME}/Project.irus17 #export MY_PROJECT_DIR=${PWD} export MY_ROOT_DIR=${HOME} export MY_PROJECT_DIR=${PWD} # The path to the user's local current ROMS source code. # # If using svn locally, this would be the user's Working Copy Path (WCPATH). # Note that one advantage of maintaining your source code locally with svn # is that when working simultaneously on multiple machines (e.g. a local # workstation, a local cluster and a remote supercomputer) you can checkout # the latest release and always get an up-to-date customized source on each # machine. This script is designed to more easily allow for differing paths # to the code and inputs on differing machines. #export MY_ROMS_SRC=${MY_ROOT_DIR}/branches/arango # export MY_ROMS_SRC=${MY_ROOT_DIR}/trunk # export MY_ROMS_SRC=${MY_ROOT_DIR}/ROMS.trunk export MY_ROMS_SRC=${HOME}/roms2021 # Set path of the directory containing makefile configuration (*.mk) files. # The user has the option to specify a customized version of these files # in a different directory than the one distributed with the source code, # ${MY_ROMS_SRC}/Compilers. If this is the case, the you need to keep # these configurations files up-to-date. export COMPILERS=${MY_ROMS_SRC}/Compilers #export COMPILERS=${HOME}/Compilers # Set tunable CPP options. # # Sometimes it is desirable to activate one or more CPP options to run # different variants of the same application without modifying its header # file. If this is the case, specify each options here using the -D syntax. # Notice also that you need to use shell's quoting syntax to enclose the # definition. Both single or double quotes work. For example, # #export MY_CPP_FLAGS="-DAVERAGES" #export MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDEBUGGING" # # can be used to write time-averaged fields. Notice that you can have as # many definitions as you want by appending values. #export MY_CPP_FLAGS="-D" # Other user defined environmental variables. See the ROMS makefile for # details on other options the user might want to set here. Be sure to # leave the switches meant to be off set to an empty string or commented # out. Any string value (including off) will evaluate to TRUE in # conditional if-statements. export USE_MPI=on # distributed-memory parallelism export USE_MPIF90=on # compile with mpif90 script #export which_MPI=mpich # compile with MPICH library #export which_MPI=mpich2 # compile with MPICH2 library export which_MPI=openmpi # compile with OpenMPI library # export which_MPI=impi # compile with IntelMPI library #export USE_OpenMP=on # shared-memory parallelism #export FORT=ifort export FORT=gfortran #export FORT=pgi #export USE_DEBUG=on # use Fortran debugging flags export USE_LARGE=on # activate 64-bit compilation #export USE_NETCDF4=on # compile with NetCDF-4 library export USE_NETCDF4=on # compile with NetCDF-4 library #export USE_PARALLEL_IO=on # Parallel I/O with Netcdf-4/HDF5 #export USE_MY_LIBS=on # use my library paths below export USE_MY_LIBS=on # use my library paths below # There are several MPI libraries available. Here, we set the desired # "mpif90" script to use during compilation. This only works if the make # configuration file (say, Linux-pgi.mk) in the "Compilers" directory # has the following definition for FC (Fortran Compiler) in the USE_MPI # section: # export FC=mpifort # # that is, "mpif90" defined without any path. Notice that the path # where the MPI library is installed is computer dependent. Recall # that you still need to use the appropriate "mpirun" to execute. if [ -n "${USE_MPIF90:+1}" ]; then case "$FORT" in ifort ) if [ "${which_MPI}" = "mpich" ]; then export PATH=/opt/intelsoft/mpich/bin:$PATH elif [ "${which_MPI}" = "mpich2" ]; then export PATH=/opt/intelsoft/mpich2/bin:$PATH elif [ "${which_MPI}" = "openmpi" ]; then export PATH=/opt/intelsoft/openmpi/bin:$PATH fi ;; pgi ) if [ "${which_MPI}" = "mpich" ]; then export PATH=/opt/pgisoft/mpich/bin:$PATH elif [ "${which_MPI}" = "mpich2" ]; then export PATH=/opt/pgisoft/mpich2/bin:$PATH elif [ "${which_MPI}" = "openmpi" ]; then export PATH=/opt/pgisoft/openmpi/bin:$PATH fi ;; gfortran ) if [ "${which_MPI}" = "mpich2" ]; then export PATH=/usr/bin:$PATH elif [ "${which_MPI}" = "openmpi" ]; then export PATH=/usr/bin:$PATH fi ;; esac fi # If the USE_MY_LIBS is activated above, the path of the libraries # required by ROMS can be set here using environmental variables # which take precedence to the values specified in the make macro # definitions file (Compilers/*.mk). For most applications, only # the location of the NetCDF library is needed during compilation. # # Notice that when the USE_NETCDF4 macro is activated, we need the # serial or parallel version of the NetCDF-4/HDF5 library. The # configuration script NF_CONFIG (available since NetCDF 4.0.1) # is used to set up all the required libraries according to the # installed options (openDAP, netCDF4/HDF5 file format). The # parallel library uses the MPI-I/O layer (usually available # in MPICH2 and OpenMPI) requiring compiling with the selected # MPI library. # # In ROMS distributed-memory applications, you may use either the # serial or parallel version of the NetCDF-4/HDF5 library. The # parallel version is required when parallel I/O is activated # (ROMS cpp option PARALLEL_IO and HDF5). # # However, in serial or shared-memory ROMS applications, we need # to use the serial version of the NetCDF-4/HDF5 to avoid conflicts # with the compiler. We cannot activate MPI constructs in serial # or shared-memory ROMS code. Hybrid parallelism is not possible. # # Recall also that the MPI library comes in several flavors: # MPICH, MPICH2, OpenMPI, etc. if [ -n "${USE_MY_LIBS:+1}" ]; then case "$FORT" in ifort ) # export ESMF_OS=Linux # export ESMF_COMPILER=ifort # export ESMF_BOPT=O # export ESMF_ABI=64 # export ESMF_COMM=mpich # export ESMF_SITE=default # export ARPACK_LIBDIR=/opt/intelsoft/serial/ARPACK if [ -n "${USE_MPI:+1}" ]; then if [ "${which_MPI}" = "mpich" ]; then export ESMF_DIR=/opt/intelsoft/mpich/esmf export MCT_INCDIR=/opt/intelsoft/mpich/mct/include export MCT_LIBDIR=/opt/intelsoft/mpich/mct/lib export PARPACK_LIBDIR=/opt/intelsoft/mpich/PARPACK elif [ "${which_MPI}" = "mpich2" ]; then export ESMF_DIR=/opt/intelsoft/mpich2/esmf export MCT_INCDIR=/opt/intelsoft/mpich2/mct/include export MCT_LIBDIR=/opt/intelsoft/mpich2/mct/lib export PARPACK_LIBDIR=/opt/intelsoft/mpich2/PARPACK elif [ "${which_MPI}" = "openmpi" ]; then export ESMF_DIR=/opt/intelsoft/openmpi/esmf export MCT_INCDIR=/opt/intelsoft/openmpi/mct/include export MCT_LIBDIR=/opt/intelsoft/openmpi/mct/lib export PARPACK_LIBDIR=/opt/intelsoft/openmpi/PARPACK fi fi if [ -n "${USE_NETCDF4:+1}" ]; then if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then if [ "${which_MPI}" = "mpich" ]; then export NF_CONFIG=/opt/intelsoft/mpich/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/intelsoft/mpich/netcdf4/include elif [ "${which_MPI}" = "mpich2" ]; then export NF_CONFIG=/opt/intelsoft/mpich2/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/intelsoft/mpich2/netcdf4/include elif [ "${which_MPI}" = "openmpi" ]; then export NF_CONFIG=/opt/intelsoft/openmpi/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/intelsoft/openmpi/netcdf4/include fi else #export NF_CONFIG=/opt/intelsoft/serial/netcdf4/bin/nf-config export NF_CONFIG=/common/netcdf-fortran-4.4.4_intel/bin/nf-config #export NETCDF_INCDIR=/opt/intelsoft/serial/netcdf4/include export NETCDF_INCDIR=/common/netcdf-fortran-4.4.4_intel/include fi else export NETCDF_INCDIR=/opt/intelsoft/serial/netcdf3/include export NETCDF_LIBDIR=/opt/intelsoft/serial/netcdf3/lib fi ;; pgi ) export ESMF_OS=Linux export ESMF_COMPILER=pgi export ESMF_BOPT=O export ESMF_ABI=64 export ESMF_COMM=mpich export ESMF_SITE=default export ARPACK_LIBDIR=/opt/pgisoft/serial/ARPACK if [ -n "${USE_MPI:+1}" ]; then if [ "${which_MPI}" = "mpich" ]; then export ESMF_DIR=/opt/pgisoft/mpich/esmf export MCT_INCDIR=/opt/pgisoft/mpich/mct/include export MCT_LIBDIR=/opt/pgisoft/mpich/mct/lib export PARPACK_LIBDIR=/opt/pgisoft/mpich/PARPACK elif [ "${which_MPI}" = "mpich2" ]; then export ESMF_DIR=/opt/pgisoft/mpich2/esmf export MCT_INCDIR=/opt/pgisoft/mpich2/mct/include export MCT_LIBDIR=/opt/pgisoft/mpich2/mct/lib export PARPACK_LIBDIR=/opt/pgisoft/mpich2/PARPACK elif [ "${which_MPI}" = "openmpi" ]; then export ESMF_DIR=/opt/pgisoft/openmpi/esmf export MCT_INCDIR=/opt/pgisoft/openmpi/mct/include export MCT_LIBDIR=/opt/pgisoft/openmpi/mct/lib export PARPACK_LIBDIR=/opt/pgisoft/openmpi/PARPACK fi fi if [ -n "${USE_NETCDF4:+1}" ]; then if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then if [ "${which_MPI}" = "mpich" ]; then export NF_CONFIG=/opt/pgisoft/mpich/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/pgisoft/mpich/netcdf4/include elif [ "${which_MPI}" = "mpich2" ]; then export NF_CONFIG=/opt/pgisoft/mpich2/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/pgisoft/mpich2/netcdf4/include elif [ "${which_MPI}" = "openmpi" ]; then export NF_CONFIG=/opt/pgisoft/openmpi/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/pgisoft/openmpi/netcdf4/include fi else export NF_CONFIG=/opt/pgisoft/serial/netcdf4/bin/nf-config export NETCDF_INCDIR=/opt/pgisoft/serial/netcdf4/include fi else export NETCDF_INCDIR=/opt/pgisoft/serial/netcdf3/include export NETCDF_LIBDIR=/opt/pgisoft/serial/netcdf3/lib fi ;; gfortran ) export ESMF_OS=Linux export ESMF_COMPILER=gfortran export ESMF_BOPT=O export ESMF_ABI=64 export ESMF_COMM=mpich export ESMF_SITE=default export ARPACK_LIBDIR=/opt/gfortransoft/serial/ARPACK if [ -n "${USE_MPI:+1}" ]; then if [ "${which_MPI}" = "mpich2" ]; then export ESMF_DIR=/opt/gfortransoft/mpich2/esmf export MCT_INCDIR=/opt/gfortransoft/mpich2/mct/include export MCT_LIBDIR=/opt/gfortransoft/mpich2/mct/lib export PARPACK_LIBDIR=/opt/gfortransoft/mpich2/PARPACK elif [ "${which_MPI}" = "openmpi" ]; then export ESMF_DIR=/opt/gfortransoft/openmpi/esmf export MCT_INCDIR=/opt/gfortransoft/openmpi/mct/include export MCT_LIBDIR=/opt/gfortransoft/openmpi/mct/lib export PARPACK_LIBDIR=/opt/gfortransoft/openmpi/PARPACK fi fi if [ -n "${USE_NETCDF4:+1}" ]; then if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then if [ "${which_MPI}" = "mpich2" ]; then export NF_CONFIG=/usr/bin export NETCDF_INCDIR=/usr/include elif [ "${which_MPI}" = "openmpi" ]; then export NF_CONFIG=/usr/bin export NETCDF_INCDIR=/usr/include fi else export NF_CONFIG=/usr/bin export NETCDF_INCDIR=/usr/include fi else export NETCDF_INCDIR=/usr/bin export NETCDF_LIBDIR=/usr/lib fi ;; esac fi #export MPI_INCDIR=/usr/lib/x86_64-linux-gnu/openmpi/include #export MPI_ROOT=/usr/lib/x86_64-linux-gnu/openmpi # The rest of this script sets the path to the users header file and # analytical source files, if any. See the templates in User/Functionals. # # If applicable, use the MY_ANALYTICAL_DIR directory to place your # customized biology model header file (like fennel.h, nemuro.h, ecosim.h, # etc). export MY_HEADER_DIR=${MY_PROJECT_DIR} export MY_ANALYTICAL_DIR=${MY_PROJECT_DIR} # Put the binary to execute in the following directory. export BINDIR=${MY_PROJECT_DIR} # Put the f90 files in a project specific Build directory to avoid conflict # with other projects. export SCRATCH_DIR=${MY_PROJECT_DIR}/Build # Go to the users source directory to compile. The options set above will # pick up the application-specific code from the appropriate place. cd ${MY_ROMS_SRC} # Remove build directory. if [ $clean -eq 1 ]; then make clean fi # Compile (the binary will go to BINDIR set above). if [ $parallel -eq 1 ]; then make $NCPUS else make fi