#!/bin/bash # # Usage: build-nemo [options] exec=name cfg=cfgdir \ # srcpath=srcpath \ # [refcfg=cfgdir] \ # [arch=fname] \ # [add_key=keys] \ # [del_key=keys] # Quantities in square brackets are optional # # Purpose: Create a nemo executable or build nemo specifc tools # # Options: # All options begin with a dash (-) and must appear before any other command line arg # Single letter options may be combined, as in "build-nemo -vv ..." # -j num_proc ...number of cpus to use for parallel compilation # -m arch ...Arch specific include file (arch=... will override -m) # -n cfg ...Configuration dir (cfg=... will override -n) # -r refcfg ...Reference configuration dir (refcfg=... will override -r) # ### Incomplete ### -t ...compile a set of nemo tools rather than the ocean model # -v ...increase verbosity (additive) # -h ...show this usage message # -a ...do not use a version specific build-nemo (use the build-nemo found on your PATH) # -b ...use a version specific build-nemo, namely the version specicifed on the command line # If both -a and -b are present then -a takes precedence # -k ...do not delete the tmp dir after compilation is complete (used for debugging) # -d ...compile an executable with debugging symbols (for use with DDT or GDB) # -s ...save executable instead of linking it # # Variable definitions: # srcpath=srcpath ...location of the NEMO source code. # exec=name ...name is the name of the nemo executable to be created # On successful compilation, a file by this name will be saved on RUNPATH # cfg=name ...name is the name of a subdir under the CONFIG dir in the repository # which will contain details of the model configuration (e.g. ORCA2_LIM) # refcfg=name ...name is the name of a subdir under the CONFIG dir in the repository # which will contain a reference configuration # arch=name ...name is the name of an arch specific make include file found in the ARCH # subdir that is used to define compiler switches and libs etc # add_key=keys ...A whitespace separated list of cpp preprocessor keys to be added # for this complie. If there is more than one then keys will need # to be quoted. (e.g. add_keys="key_mpp_mpi key_nproci=8 key_nprocj=4") # del_key=keys ...A whitespace separated list of cpp preprocessor keys to be removed # for this complie. If there is more than one then keys will need # to be quoted. (e.g. del_keys="key_nproci key_nprocj") # # Examples: # build-nemo exec=nemo_v3.4_orca2_lim_exe cfg=ORCA2_LIM srcpath=/path/to/code/ # # -- Build an ORCA2_LIM configuration that uses the nemo code define in srcpath (with # a dir structure the same as the default). # ######################################################################## # # Larry Solheim Sep 2012 # Last update: NCS, 2017-12-18 - merge develop (ocean only) into develop_canesm. # - major conflicts needed to be resolved. # NCS, 2018-08-16 - move compile to in source (in the repo), but # .gitignore compilation related files for VCS. FULLPATH=`type $0|awk '{print $3}'` # pathname of this script Runame=`basename $FULLPATH` usage() { err_exit=0 while getopts e opt; do case $opt in e) err_exit=1 ;; esac done shift `expr $OPTIND - 1` [ -n "$1" ] && echo >&2 "${Runame}:" "$@" echo >&2 " " sed >&2 -n '/^###/q; s/^#$/# /; s/^ *$/# /; 3,$s/^# //p;' "$FULLPATH" if [ $err_exit -eq 0 ]; then exit else exit 1 fi } # Create time stamp to be used in file names etc stamp=`date "+%j%H%M%S"$$` # Identify, by name, the machine this script is running on this_host=`hostname|cut -d'.' -f1` bail(){ echo "${Runame}: *** ERROR *** $1" if [ -z "$keep_tmpd" ] ; then if [ $keep_tmpd -eq 1 ]; then echo "Temporary directory remains in $tmpd" elif [ -z "$tmpd" ]; then cd $CWD rm -fr $tmpd fi fi exit 1 } add2path(){ if echo $PATH|/bin/grep -Evq "'(^|:)'$1'($|:)'" ; then if [ "$2" = "atend" ] ; then PATH=$PATH:$1 else PATH=$1:$PATH fi fi } # echo without return (ie: emulate -n if not recognized by echo) if [ "X`echo -n`" = "X-n" ]; then echo_n() { echo ${1+"$@"}'\c'; } else echo_n() { echo -n ${1+"$@"}; } fi # Set defaults # The version of code to extract and compile nemo_version='' # The default location of the repository containing nemo source code #nemo_source_repo='git@gitlab.science.gc.ca:CanESM/CanNEMO.git' # Path to copy code from instead of cloning a repo nemo_source_path='' # The name of the executable created by this script nemo_exe='' # Nemo preprocessing keys to be added or removed at compile time nemo_add_cpp_keys='' nemo_del_cpp_keys='' # A boolean flag used to build (or not build) the nemo executable build_nemo_exe=1 # The particular configuration of nemo to be built will be defined by files # in a subdir of the nemo source tree. nemo_config is the name of that subdir nemo_config='' # The reference configuration to be used with nemo_config nemo_ref_config='' # The name of a make include file used to determine compiler name and flags nemo_arch='' # Is this nemo build for a coupled model coupled='' # to officiall "save" the executable or not save_exe='' # Boolean flags used to build (or not build) particular nemo tools build_rebuild_tool=0 build_rebuild_nemo_tool=0 build_weights_tool=0 # Verbosity flag verbose=0 # Flag to remove, or not remove, temporary dir created below keep_tmpd=0 # Number of processors to use during compilation comp_np=12 # Set debug to 0 (turned off, regular optimizations used) debug=0 printf "\n\n ------------------- \n" printf " build-nemo \n" printf " ------------------- \n" # CCRNTMP must be defined #CCRNTMP=/tmp [ ! -d "$CCRNTMP" ] && bail "/tmp is not a directory" # process command line options while getopts j:n:m:r:hktvxds opt do case $opt in m) nemo_arch="$OPTARG" ;; j) comp_np="$OPTARG" ;; n) nemo_config="$OPTARG" ;; r) nemo_ref_config="$OPTARG" ;; v) verbose=`expr $verbose + 1` ;; k) keep_tmpd=1 ;; x) set -x ;; t) build_nemo_exe=0 build_rebuild_tool=1 build_rebuild_nemo_tool=1 build_weights_tool=1 ;; s) save_exe="on" ;; d) debug=1 ;; h) usage ;; -) shift; break ;; # end of options ?) usage -e $USAGE ;; esac done shift `expr $OPTIND - 1` # Process the remaining command line args for arg in "$@"; do case $arg in *=*) var=`echo $arg|awk -F\= '{printf "%s",$1}' -` val=`echo "$arg"|awk '{i=index($0,"=")+1;printf "%s",substr($0,i)}' -` # add this variable definition to the current environment [ -n "$var" ] && eval ${var}=\"\$val\" # preserve quoted assignments case $var in ver) nemo_version="$val" ;; # git version, tag or branch repo) nemo_source_repo="$val" ;; # location of git repository srcpath) nemo_source_path="$val" ;; # location of code in a dir structure (instead of cloning) exec) nemo_exe="$val" ;; # name for the executable created here cfg) nemo_config="$val" ;; # name of subdir in which config lives refcfg) nemo_ref_config="$val" ;; # name of subdir in which ref config lives arch) nemo_arch="$val" ;; # name of file with arch specific make defs # a list of cpp keys to add before compiling nemo add_key) nemo_add_cpp_keys="$val" ;; # a list of cpp keys to remove before compiling nemo del_key) nemo_del_cpp_keys="$val" ;; # if coupled is defined on the cmd line then this value will be used coupled) ;; # Turn on coupling, which requires the coupler code be compiled with nemo cancpl_repo) ;; # location of coupler repository *) bail "Invalid command line arg --> $arg <--" ;; esac ;; *) bail "Invalid command line arg --> $arg <--" ;; esac done # When debugging is requested, the behaviour of this script needs to be adjusted accordingly if [ $debug -eq 1 ]; then # Need to retain the postprocessed source files and store them in a runtime accessible directory keep_tmpd=1 CCRNTMP=$PWD/tmp # Assumed to be in the RUNID directory [ ! -d $CCRNTMP ] && mkdir $CCRNTMP # This directory probably does not exist nemo_arch="$nemo_arch-debug" # Use a version of the requested architecture with debug options [ $build_nemo_exe -eq 1 ] && nemo_exe="$nemo_exe-debug" # Make sure not to clobber an existing optimised executable else # CCRNTMP must be defined CCRNTMP=/tmp [ -z "$CCRNTMP" ] && bail "/tmp must be defined" [ ! -d "$CCRNTMP" ] && bail "/tmp is not a directory" fi if [ $build_nemo_exe -eq 1 ]; then # The name of the executable is not required unless it is to be built [ -z "$nemo_exe" ] && usage -e "A name for the output executable is required on the command line ...exec=name" # The config name is not required unless nemo is to be built [ -z "$nemo_config" ] && usage -e "The name of the configuration is required on the command line ...cfg=cfgname" fi # Determine if this is a coupled build or not if [ -z "$coupled" ]; then # coupled was not defined on the command line ...define it here case $nemo_config in CCC_CANCPL_*) coupled=on ;; *) coupled=off ;; esac fi if [ $coupled = "on" ]; then # Define cancpl repo and commit # Values supplied on the command line will be used, if present, otherwise use these defaults cancpl_repo=${cancpl_repo:=$CCRNSRC/CanCPL} # The coupler repo must be on a locally accessable directory path [ ! -d "$cancpl_repo" ] && usage -e "Coupler repository is not a directory --> $cancpl_repo <--" # Ensure this is a full pathname cancpl_repo=$(cd $cancpl_repo; pwd) # Verify that this is a valid commit # If so then reassign as the full sha1 hash cancpl_ver=$(cd $cancpl_repo; git rev-parse HEAD) || { echo "$(basename $0): Failed to extract the coupler commit from $cancpl_repo"! Is this a true git repo?; exit 1; } fi # This script is intended to be run on the back end case $this_host in xc1*|xc2*|xc3*|xc4*) ;; # This is spica or hadar ...OK *) bail "This should be run on a back end machine" ;; esac # Create a temporary directory and change to it # // Actuall, now compile in source CWD=`pwd` #tmpd=$CCRNTMP/tmp_build_nemo_${this_host}_$stamp #mkdir $tmpd || bail "Cannot create temporary dir $tmpd" #cd $tmpd # Clone the git repo, or copy the srcpath directory if [ -z "$nemo_source_path" ]; then #[ -z "$nemo_version" ] && usage -e "A version number/tag or branch is required on the command line." #[ -z "$nemo_source_repo" ] && usage -e "The source repository name is missing." # Get the code from the repo #git clone $nemo_source_repo CanNEMO #cd CanNEMO #git checkout $nemo_version bail "nemo_source_path not defined" else echo echo "Compiling in: ${nemo_source_path}" #cp -r $nemo_source_path CanNEMO cd $nemo_source_path || bail "Cannot cd in ${nemo_source_path}" if [ -d .git ]; then # If srcpath is a git repo, do some checks branch=`git branch` echo "$nemo_source_path is a git repo...we are using branch $branch" diffs=`git diff --name-only HEAD` if [ ! -z "$diffs" ]; then echo "WARNING: there are local (non-committed) changes in the following files that are being used:" echo $diffs printf "status \n, `git status`" fi fi fi # Define variables containing the current commit and repo path to use as cpp macros during the build NEMO_COMMIT=$(git log -1 --pretty="%H" $nemo_version) NEMO_REPO_PATH=$nemo_source_repo NEMO_CONFIG=$nemo_config NEMO_CANCPL_COMMIT=$cancpl_ver NEMO_CANCPL_REPO_PATH=$cancpl_repo nemo_sfx=`echo "$NEMO_COMMIT" | cut -c1-8` cancpl_sfx=`echo "$NEMO_CANCPL_COMMIT" | cut -c1-8` #nemo_exe_sfx="${nemo_sfx}-${cancpl_sfx}" #if [ $add_nemo_exe_sfx -eq 1 -a -n "$nemo_exe_sfx" ]; then # nemo_exe=${nemo_exe}_$nemo_exe_sfx #fi echo "nemo_version=$nemo_version" echo "NEMO_COMMIT=$NEMO_COMMIT" echo "NEMO_REPO_PATH=$NEMO_REPO_PATH" echo "NEMO_CONFIG=$NEMO_CONFIG" echo "NEMO_CANCPL_COMMIT=$NEMO_CANCPL_COMMIT" echo "NEMO_CANCPL_REPO_PATH=$NEMO_CANCPL_REPO_PATH" echo "nemo_exe=$nemo_exe" printf "\n\n ------------------- \n" printf "\n\n\n" # path_to_nemo is the dir path (relative to the top git source dir) in which nemo code # lives and is used by git archive to extract the nemo subset of the repository source path_to_nemo=nemo nemo_root=nemo if [ $coupled = "on" ]; then # Add a copy of com_cpl.F90 to the SBC subdir in the nemo tree #gitrip $cancpl_ver src/comm/com_cpl.F90 repo=$cancpl_repo cp ${cancpl_repo}/src/comm/com_cpl.F90 . [ -s com_cpl.F90 ] || bail "Unable to extract com_cpl.F90 from coupler repo $cancpl_repo" # Modify com_cpl.F90 to contain NEMO and CanCPL version info sed '/^#include *"cpl_cppdefs"/d' com_cpl.F90 > tmp_com_cpl.F90 && rm -f com_cpl.F90 tmpfile=tmpf$stamp if [ -n "$NEMO_REPO_PATH" ]; then echo "#define NEMO_REPO_PATH $NEMO_REPO_PATH" | cat - tmp_com_cpl.F90 > $tmpfile mv $tmpfile tmp_com_cpl.F90 fi if [ -n "$NEMO_COMMIT" ]; then echo "#define NEMO_COMMIT $NEMO_COMMIT" | cat - tmp_com_cpl.F90 > $tmpfile mv $tmpfile tmp_com_cpl.F90 fi if [ -n "$NEMO_CONFIG" ]; then echo "#define NEMO_CONFIG $NEMO_CONFIG" | cat - tmp_com_cpl.F90 > $tmpfile mv $tmpfile tmp_com_cpl.F90 fi if [ -n "$NEMO_CANCPL_REPO_PATH" ]; then echo "#define NEMO_CANCPL_REPO_PATH $NEMO_CANCPL_REPO_PATH" | cat - tmp_com_cpl.F90 > $tmpfile mv $tmpfile tmp_com_cpl.F90 fi if [ -n "$NEMO_CANCPL_COMMIT" ]; then echo "#define NEMO_CANCPL_COMMIT $NEMO_CANCPL_COMMIT" | cat - tmp_com_cpl.F90 > $tmpfile mv $tmpfile tmp_com_cpl.F90 fi mv tmp_com_cpl.F90 $nemo_root/NEMO/OPA_SRC/SBC/com_cpl.F90 fi # Make everything user writeable so that an overwrite will clobber existing files chmod -R u+w . if [ $build_nemo_exe -eq 1 ]; then # Build the nemo executable cd $nemo_root/CONFIG if [ -z "$nemo_arch" ]; then nemo_arch=xlf_aix-cccma fi NARCH="-m $nemo_arch" if [ -z "$nemo_ref_config" ]; then REFCFG='' elif [ "$nemo_ref_config" == "$nemo_config" ]; then REFCFG='' else REFCFG="-r $nemo_ref_config" fi if [ -z "$nemo_add_cpp_keys" ]; then NEMO_CPPDEFS='' else NEMO_CPPDEFS="$nemo_add_cpp_keys" fi if [ -z "$nemo_del_cpp_keys" ]; then del_key='' DELKEY='' else del_key='del_key' DELKEY="$nemo_del_cpp_keys" fi # We are currently in the CONFIG dir # Modify cpp_${nemo_config}.fcm to include any user supplied macros cppfcm=cpp_${nemo_config}.fcm if [ -n "$NEMO_CPPDEFS" ]; then [ -f $nemo_config/$cppfcm ] || bail "$nemo_config/$cppfcm is not a regular file" echo "Adding the following cpp defs to $cppfcm :: $NEMO_CPPDEFS" sed 's?$? '"${NEMO_CPPDEFS}?" $nemo_config/$cppfcm > $nemo_config/new_$cppfcm chmod u+w $nemo_config/$cppfcm mv $nemo_config/new_$cppfcm $nemo_config/$cppfcm echo "New $cppfcm file: " cat $nemo_config/$cppfcm fi env='' case $nemo_arch in XC40_CCCma_cray-pe*) env='cray' ;; XC40_CCCma_intel-pe*) env='intel' ;; intel_xc40-cancpl*) env='intel' ;; cray_xc40-cancpl*) env='cray' ;; *) bail "Unknown ARCH $(nemo_arch) - we don't know if this is the Cray or Intel PE" ;; esac if [ $env = 'cray' ]; then module switch PrgEnv-intel PrgEnv-cray else module switch PrgEnv-cray PrgEnv-intel fi module load cray-netcdf module load cray-mpich echo "makenemo -j $comp_np -n $nemo_config $NARCH $REFCFG" ./makenemo -j $comp_np -n $nemo_config $NARCH $REFCFG [ $? -ne 0 ] && bail "Problem building nemo executable" # Copy the executable to the run dir (ocean only) or save in coupled mode #cp $nemo_config/BLD/bin/nemo.exe $tmpd/$nemo_exe #cd $tmpd [ ! -s "$nemo_config/BLD/bin/nemo.exe" ] && bail "Unable to create nemo executable $nemo_exe" if [ "$coupled" = "on" ] || [ "$save_exe" = "on" ]; then # Save the nemo executable to RUNPATH/DATAPATH save $nemo_config/BLD/bin/nemo.exe $nemo_exe || bail "Problem while saving $nemo_exe" #release $nemo_exe echo "Saved $nemo_exe on RUNPATH $RUNPATH" echo "Resetting cfg.txt to HEAD" git checkout HEAD cfg.txt || : else # In ocean-only we copy to the PROD dir ln -s ${nemo_source_path}/nemo/CONFIG/${nemo_config}/BLD/bin/nemo.exe ${CWD}/${nemo_exe} fi fi # Return to the original dir and clean up cd $CWD #if [ $keep_tmpd -eq 1 ]; then # echo "Temporary directory remains in $tmpd" #else # rm -fr $tmpd #fi