#!

/bin/bash # # svn $Id$ #:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: # Copyright (c) 2002-2011 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 $1 grep -P '^\d+$'` if [ "$test" != "" ]; then NCPUS="-j $1" shift else NCPUS="-j" fi ;; -noclean ) shift

clean=0 ;; * ) echo echo echo echo echo echo echo echo echo exit ;; esac done "" "$0 : Unknown option [ $1 ]" "" "Available Options:" "" "-j [N] Compile in parallel using N CPUs" " omit argument for all avaliable CPUs" "-noclean Do not clean already compiled objects" "" 1

# 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=ESTUARY_TEST

# Set a local environmental variable to define the path to the directories # where all this project's files are kept. export export # # # # # # # # # MY_ROOT_DIR=${HOME}/ocean/repository MY_PROJECT_DIR=${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. MY_ROMS_SRC=${MY_ROOT_DIR}/branches/arango MY_ROMS_SRC=${MY_ROOT_DIR}/trunk

#export export # # # # #

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, ${MY_ROMS_SRC}/Compilers. If this is the case, the you need to keep these configurations files up-to-date. COMPILERS=${MY_ROMS_SRC}/Compilers COMPILERS=${HOME}/Compilers

export #export # # # # # # # #

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="${MY_CPP_FLAGS} -DDEBUGGING" # # can be used to write time-averaged fields. Notice that you can have as # many definitions as you want by appending values. export #export #export #export export #setenv # # # # # MY_CPP_FLAGS="-DAVERAGES" MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDEBUGGING" MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDIAGNOSTICS_TS" MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDIAGNOSTICS_UV" MY_CPP_FLAGS="${MY_CPP_FLAGS} -DGLS_MIXING" MY_CPP_FLAGS="${MY_CPP_FLAGS} -DMY25_MIXING"

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. USE_MPI=on USE_MPIF90=on which_MPI=mpich which_MPI=mpich2 which_MPI=openmpi USE_OpenMP=on FORT=ifort FORT=gfortran FORT=pgi USE_DEBUG=on USE_LARGE=on USE_NETCDF4=on USE_PARALLEL_IO=on USE_MY_LIBS=on # # # # use Fortran debugging flags activate 64-bit compilation compile with NetCDF-4 library Parallel I/O with Netcdf-4/HDF5 # # # # # distributed-memory parallelism compile with mpif90 script compile with MPICH library compile with MPICH2 library compile with OpenMPI library

export export #export #export export #export export #export #export #export export #export #export #export # # # # # # # # # # #

# shared-memory parallelism

# 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: FC := mpif90 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=/opt/gfortransoft/mpich2/bin:$PATH elif [ "${which_MPI}" = "openmpi" ]; then export PATH=/opt/gfortransoft/openmpi/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 NC_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 export

ESMF_COMM=mpich 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 NC_CONFIG=/opt/intelsoft/mpich/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/intelsoft/mpich/netcdf4/include elif [ "${which_MPI}" = "mpich2" ]; then export NC_CONFIG=/opt/intelsoft/mpich2/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/intelsoft/mpich2/netcdf4/include elif [ "${which_MPI}" = "openmpi" ]; then export NC_CONFIG=/opt/intelsoft/openmpi/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/intelsoft/openmpi/netcdf4/include fi else export NC_CONFIG=/opt/intelsoft/serial/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/intelsoft/serial/netcdf4/include fi else export NETCDF_INCDIR=/opt/intelsoft/serial/netcdf3/include export NETCDF_LIBDIR=/opt/intelsoft/serial/netcdf3/lib fi ;; pgi ) export export export export export export ESMF_OS=Linux ESMF_COMPILER=pgi ESMF_BOPT=O ESMF_ABI=64 ESMF_COMM=mpich 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 NC_CONFIG=/opt/pgisoft/mpich/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/pgisoft/mpich/netcdf4/include elif [ "${which_MPI}" = "mpich2" ]; then export NC_CONFIG=/opt/pgisoft/mpich2/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/pgisoft/mpich2/netcdf4/include elif [ "${which_MPI}" = "openmpi" ]; then export NC_CONFIG=/opt/pgisoft/openmpi/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/pgisoft/openmpi/netcdf4/include fi else export NC_CONFIG=/opt/pgisoft/serial/netcdf4/bin/nc-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 export export export export export ESMF_OS=Linux ESMF_COMPILER=gfortran ESMF_BOPT=O ESMF_ABI=64 ESMF_COMM=mpich 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 [ "${which_MPI}" = "mpich2" ]; then export NC_CONFIG=/opt/gfortransoft/mpich2/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/gfortransoft/mpich2/netcdf4/include elif [ "${which_MPI}" = "openmpi" ]; then export NC_CONFIG=/opt/gfortransoft/openmpi/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/gfortransoft/openmpi/netcdf4/include fi else export NC_CONFIG=/opt/gfortransoft/serial/netcdf4/bin/nc-config export NETCDF_INCDIR=/opt/gfortransoft/serial/netcdf4/include fi else export NETCDF_INCDIR=/opt/gfortransoft/serial/netcdf3/include export NETCDF_LIBDIR=/opt/gfortransoft/serial/netcdf3/lib fi ;; esac fi # # # # # # 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