minor cleaning

compile/croco/jobcomp

-#!/bin/bash
-####################################################
-#               COMPILATION JOB                    #
-####################################################
-
-# This script assumes default compilation options, to
-# change those options : 
-# it can either be  edited to add your own options
-# or take into account the following 
-# environment variables for compilation choices :
-#
-# CROCO_NETCDFLIB      : netcdf library
-# CROCO_NETCDFINC      : netcdf include 
-# CROCO_PRISM_ROOT_DIR : OASIS-MCT directory 
-# CROCO_XIOS_ROOT_DIR  : XIOS directory
-#
-# CROCO_CFT1           : compiler
-# CROCO_FFLAGS1        : compilation otpions
-#
-# Note that environment variables overwrite hard-coded
-# options
-
-#
-# set source, compilation and run directories
-#
-SOURCE="/ccc/work/cont005/gen1140/hourdinc/locean_croco_pisces/croco_locean_v1.00/OCEAN"
-SCRDIR="/ccc/scratch/cont005/gen1140/hourdinc/croco_scratch/c11s2cp_climatoruns_sync_ASAP2020_test_sans_AGRIF_4x24_procs_pdt_600_rst_sans_AGRIF"
-RUNDIR=`pwd`
-ROOT_DIR=$SOURCE/..
-#
-# determine operating system
-#
-OS=`uname`
-echo "OPERATING SYSTEM IS: $OS"
-
-#
-# compiler options
-#
-FC="ifort"
-
-#
-# set MPI directories if needed
-#
-MPIDIR=$
-MPIF90="mpif90"
-MPILIB=""
-MPIINC=""
-
-#
-# set NETCDF directories
-#
-#-----------------------------------------------------------
-# Use : 
-#-lnetcdf           : version netcdf-3.6.3                --
-#-lnetcdff -lnetcdf : version netcdf-4.1.2                --
-#-lnetcdff          : version netcdf-fortran-4.2-gfortran --
-#-----------------------------------------------------------
-NETCDFLIB="$(nf-config --flibs)"
-NETCDFINC="-I$(nf-config --includedir)"
-
-
-#
-# set OASIS-MCT (or OASIS3) directories if needed
-#
-PRISM_ROOT_DIR=../../../oasis3-mct/compile_oa3-mct
-
-#
-# set XIOS directory if needed
-#
-XIOS_ROOT_DIR=$HOME/xios-1.0
-#
-# END OF USER'S MODIFICATIONS
-####################################################
-#
-# Use GNU Make command, else make
-#
-MAKE=make
-which $MAKE > /dev/null 2>&1 || MAKE=make
-
-#
-# clean scratch area
-#
-rm -rf $SCRDIR
-mkdir $SCRDIR
-
-#
-# AGRIF sources directory
-#
-AGRIF_SRC=${ROOT_DIR}/AGRIF
-
-#
-# copy SOURCE code
-#
-
-ls ${SOURCE}/*.F               > /dev/null  2>&1 && \cp ${SOURCE}/*.F   $SCRDIR
-ls ${SOURCE}/*.F90             > /dev/null  2>&1 && \cp ${SOURCE}/*.F90 $SCRDIR
-ls ${SOURCE}/*.h               > /dev/null  2>&1 && \cp ${SOURCE}/*.h   $SCRDIR
-ls ${SOURCE}/Make*             > /dev/null  2>&1 && \cp ${SOURCE}/Make* $SCRDIR
-ls ${SOURCE}/jobcomp           > /dev/null  2>&1 && \cp ${SOURCE}/jobcomp $SCRDIR
-ls ${SOURCE}/amr.in            > /dev/null  2>&1 && \cp ${SOURCE}/amr.in $SCRDIR
-ls ${AGRIF_SRC}                > /dev/null  2>&1 && \cp -r ${AGRIF_SRC} $SCRDIR
-ls ${ROOT_DIR}/XIOS/*.F        > /dev/null  2>&1 && \cp ${ROOT_DIR}/XIOS/*.F $SCRDIR
-ls ${ROOT_DIR}/PISCES/*        > /dev/null  2>&1 && \cp ${ROOT_DIR}/PISCES/* $SCRDIR
-ls ${ROOT_DIR}/PISCES/SED/*    > /dev/null  2>&1 && \cp ${ROOT_DIR}/PISCES/SED/* $SCRDIR
-ls ${ROOT_DIR}/PISCES/kRGB61*  > /dev/null  2>&1 && \cp ${ROOT_DIR}/PISCES/kRGB61* $RUNDIR
-
-if [[ -e "namelist_pisces" ]] ; then
-        echo "  file namelist_pisces exists in Run directory"
-else
-        \cp -f ${ROOT_DIR}/PISCES/namelist_pisces* $RUNDIR
-        echo "  file namelist_pisces copied from source directory"
-fi
-#
-# overwrite with local files
-#
-
-ls *.F90   > /dev/null  2>&1 && \cp -f *.F90 $SCRDIR
-ls *.F     > /dev/null  2>&1 && \cp -f *.F $SCRDIR
-ls *.h     > /dev/null  2>&1 && \cp -f *.h $SCRDIR
-ls *.h90   > /dev/null  2>&1 && \cp -f *.h90 $SCRDIR
-ls Make*   > /dev/null  2>&1 && \cp -f Make* $SCRDIR
-ls jobcomp > /dev/null  2>&1 && \cp -f jobcomp $SCRDIR
-
-# Change directory
-#
-cd $SCRDIR
-#
-# generates LDFLAGS1 according to users notifications
-#
-LDFLAGS1="${CROCO_NETCDFLIB-$NETCDFLIB}"
-CPPFLAGS1="${CROCO_NETCDFINC-$NETCDFINC} -ICROCOFILES/AGRIF_INC"
-#
-# Set compilation options
-#
-if [[ $OS == Linux || $OS == Darwin ]] ; then           # ===== LINUX =====
-	if [[ $FC == ifort || $FC == ifc ]] ; then
-		CPP1="cpp -traditional -DLinux -DIfort"
-		CFT1=ifort
-		FFLAGS1="-O3 -fno-alias -i4 -r8 -fp-model precise"
-#                FFLAGS1="-O0 -g -i4 -r8 -traceback -check all -check bounds \
-#                       -check uninit -CA -CB -CS -ftrapuv -fpe1"
-		LDFLAGS1="$LDFLAGS1"
-	elif [[ $FC == gfortran ]] ; then
-		CPP1="cpp -traditional -DLinux"
-		CFT1=gfortran
-		FFLAGS1="-O3 -fdefault-real-8 -fdefault-double-8"
-#		 FFLAGS1="-O0 -g -fdefault-real-8 -fdefault-double-8 -fbacktrace \
-#			-fbounds-check -finit-real=nan -finit-integer=8888"
-		LDFLAGS1="$LDFLAGS1"
-	fi
-elif [[ $OS == CYGWIN_NT-10.0 ]] ; then  # ======== CYGWIN =======
-        CPP1="cpp -traditional -DLinux"
-        CFT1="gfortran"
-        FFLAGS1="-O4 -fdefault-real-8 -fdefault-double-8 -march=native -mtune=native"
-elif [[ $OS == AIX ]] ; then           # ===== IBM =====
-	CPP1="cpp"
-	CFT1="xlf95 -I$HOME/include/"
-	MAKEAGRIF="Makefile.ibm.64"
-	FFLAGS1="-q64 -qwarn64 -qfixed -qrealsize=8 -qintsize=8 -qhot \
-			-qalias=noaryovrlp -qthreaded -O3 -qarch=pwr4 -qtune=pwr4 -qunroll=yes"
-else
-	echo "Unknown Operating System"
-	exit
-fi
-#
-# determine if AGRIF compilation is required
-#
-unset COMPILEAGRIF
-echo "Checking COMPILEAGRIF..."
-if $($CPP1 testkeys.F | grep -i -q agrifisdefined) ; then
-	echo " => AGRIF activated"
-	COMPILEAGRIF=TRUE
-	FFLAGS1="$FFLAGS1 -IAGRIF"
-	LDFLAGS1="-LAGRIF -lagrif $LDFLAGS1"
-# we use the AGRIF Makedefs.generic definition
-	cp -f Makedefs.generic.AGRIF Makedefs.generic
-fi
-
-#
-# determine if MPI compilation is required
-#
-unset COMPILEMPI
-echo "Checking COMPILEMPI..."
-if $($CPP1 testkeys.F | grep -i -q mpiisdefined) ; then
-	echo " => MPI activated"
-	COMPILEMPI=TRUE
-	LDFLAGS1="$LDFLAGS1 $MPILIB"
-	CPPFLAGS1="$CPPFLAGS1 $MPIINC"
-	FFLAGS1="$FFLAGS1 $MPIINC"
-	CFT1="${MPIF90}"
-fi
-
-#
-# Take environment variables for compiler and options
-#
-FFLAGS1=${CROCO_FFLAGS1-$FFLAGS1}
-CFT1=${CROCO_CFT1-$CFT1}
-
-#
-# determine if XIOS compilation is required
-#
-unset COMPILEXIOS
-echo "Checking COMPILEXIOS..."
-XIOS_ROOT_DIR=${CROCO_XIOS_ROOT_DIR-$XIOS_ROOT_DIR}
-if $($CPP1 testkeys.F | grep -i -q xiosisdefined) ; then
-        echo " => XIOS activated"
-        COMPILEXIOS=TRUE
-        LDFLAGS1="$LDFLAGS1 $XIOS_ROOT_DIR/lib/libxios.a  -lstdc++ -lnetcdff"
-        CPPFLAGS1="$CPPFLAGS1 -I$XIOS_ROOT_DIR/inc"
-        FFLAGS1="$FFLAGS1 -I$XIOS_ROOT_DIR/inc"
-        ln -fs $XIOS_ROOT_DIR/bin/xios_server.exe $RUNDIR/.
-        $CPP1 -P -traditional -imacros cppdefs.h  ${ROOT_DIR}/XIOS/field_def.xml_full $RUNDIR/field_def.xml
-        $CPP1 -P -traditional -imacros cppdefs.h  ${ROOT_DIR}/XIOS/domain_def.xml $RUNDIR/domain_def.xml
-        $CPP1 -P -traditional -imacros cppdefs.h  ${ROOT_DIR}/XIOS/file_def.xml $RUNDIR/file_def.xml
-        $CPP1 -P -traditional -imacros cppdefs.h  ${ROOT_DIR}/XIOS/iodef.xml $RUNDIR/iodef.xml
-fi
-
-#
-# determine if OASIS compilation is required
-#
-unset COMPILEOASIS
-echo "Checking COMPILEOASIS..."
-PRISM_ROOT_DIR=${CROCO_PRISM_ROOT_DIR-$PRISM_ROOT_DIR}
-if $($CPP1 testkeys.F | grep -i -q oacplisdefined) ; then
-    echo " => OASIS activated"
-    CHAN=MPI1
-    LIBPSMILE="${PRISM_ROOT_DIR}/lib/libpsmile.${CHAN}.a \
-		${PRISM_ROOT_DIR}/lib/libmct.a  \
-		${PRISM_ROOT_DIR}/lib/libmpeu.a \
-		${PRISM_ROOT_DIR}/lib/libscrip.a"
-    PSMILE_INCDIR="-I${PRISM_ROOT_DIR}/build/lib/psmile.${CHAN} \
-		-I${PRISM_ROOT_DIR}/build/lib/mct"
-    COMPILEOASIS=TRUE
-    LDFLAGS1="$LDFLAGS1 $LIBPSMILE $NETCDFLIB"
-    CPPFLAGS1="$CPPFLAGS1 ${PSMILE_INCDIR} $NETCDFINC"
-    FFLAGS1="$FFLAGS1 ${PSMILE_INCDIR} $NETCDFINC"
-fi
-#
-# prepare and compile the library
-#
-if [[ $COMPILEAGRIF ]] ; then
-#
-# compile the AGRIF librairy
-#
-	if [[ $COMPILEMPI ]] ; then
-		$MAKE -C AGRIF FC="$CFT1" CPP="$CPP1" CPPFLAGS="-DAGRIF_MPI $MPIINC" FFLAGS="$FFLAGS1"
-	else
-		$MAKE -C AGRIF FC="$CFT1" CPP="$CPP1" FFLAGS="$FFLAGS1"
-	fi
-	if [[ $OS == Darwin ]] ; then          # DARWIN
-# run RANLIB on Darwin system
-		ranlib AGRIF/libagrif.a
-	fi
-#
-	mkdir CROCOFILES
-	mkdir -p CROCOFILES/AGRIF_MODELFILES
-	mkdir -p CROCOFILES/AGRIF_INC
-	$CPP1 amr.in | grep -v -e ! -e '#' -e % -e '*' > CROCOFILES/amr.scrum
-	mv AGRIF/conv CROCOFILES/.
-	for i in *.h *.h90 ; do
-		echo $i
-		cat cppdefs.h $i | cpp -P | grep -v -e ! -e '#' -e % -e '*' > CROCOFILES/$i
-	done
-	mv -f CROCOFILES/private_scratch_AMR.h CROCOFILES/private_scratch.h
-fi
-
-#
-# determine if OPENMP compilation is needed
-#
-unset COMPILEOMP
-echo "Checking COMPILEOMP..."
-if $($CPP1 testkeys.F | grep -i -q openmp) ; then
-	COMPILEOMP=TRUE
-	if [[ $OS == Linux || $OS == Darwin ]] ; then 
-		if [[ $FC == gfortran ]] ; then
-			FFLAGS1="$FFLAGS1 -fopenmp"
-		elif [[ $FC == ifort || $FC == ifc ]] ; then
-			FFLAGS1="$FFLAGS1 -openmp"
-		else
-			FFLAGS1="$FFLAGS1 -openmp"
-		fi
-	elif [[ $OS == CYGWIN_NT-10.0 ]] ; then
-        FFLAGS1=="$FFLAGS1 -fopenmp"
-	elif [[ $OS == AIX ]] ; then
-		FFLAGS1="$FFLAGS1 -qsmp=omp"
-		CFT1="xlf95_r"
-	fi
-fi
-
-#
-# rewrite Makedefs according to previous flags
-# with openmp flags if needed
-#
-rm -f Makedefs
-echo 's?$(FFLAGS1)?'$FFLAGS1'?g' > flags.tmp
-echo 's?$(LDFLAGS1)?'$LDFLAGS1'?g' >> flags.tmp
-echo 's?$(CPP1)?'$CPP1'?g' >> flags.tmp
-echo 's?$(CFT1)?'$CFT1'?g' >> flags.tmp
-echo 's?$(CPPFLAGS1)?'$CPPFLAGS1'?g' >> flags.tmp
-sed -f flags.tmp Makedefs.generic > Makedefs
-rm -f flags.tmp
-
-#
-# compile croco
-#
-$MAKE depend
-$MAKE
-  
-[[ -f croco  ]] && mv croco $RUNDIR
-[[ -f partit ]] && mv partit $RUNDIR
-[[ -f ncjoin ]] && mv ncjoin  $RUNDIR
-#