Update get wrf archive to cope with multiple day hindcasts

app/get_archive_wrf_file/file/get_wrf_files.sh

+#!/bin/bash
+
+START_DAY=$1
+END_DAY=$2
+WRF_ARCHIVE_DATEFMT=$3
+WRF_ARCHIVE_DIR=$4
+ROSE_DATAC=$5
+
+echo 1
+echo ${START_DAY} 
+
+echo 2
+echo ${END_DAY} 
+
+echo 3
+echo ${WRF_ARCHIVE_DATEFMT} 
+
+echo 4
+echo ${WRF_ARCHIVE_DIR}
+
+echo 5
+echo ${ROSE_DATAC}
+
+
+d=
+n=0
+until [ "$d_comp" = "$END_DAY" ]
+do
+    ((n++))
+    d=$(date -d "$START_DAY + $n days" +${WRF_ARCHIVE_DATEFMT})
+    d_comp=$(date -d "$START_DAY + $n days" +%Y-%m-%d)
+    cp /pml${WRF_ARCHIVE_DIR}/*${d}*/wrfout_d03_* ${ROSE_DATAC}/raw_wrf_file_${n}.nc
+done

app/get_archive_wrf_file/file/merge_files.slurm

+#!/bin/bash --login
+
+# Script to merge the individual runs into month long chunks ready for
+# conversion with wrf_to_fvcom.
+
+module purge
+module load nco
+
+set -eu
+
+# Make sure any symbolic links are resolved to absolute path.
+PBS_O_WORKDIR=$(pwd)
+export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
+
+# Change to the directory from which the job was submitted.
+cd $PBS_O_WORKDIR
+
+year=${year:-2017}
+srcdir=$(readlink -f $PBS_O_WORKDIR/output/)
+binary=$PBS_O_WORKDIR/bin/wrf_to_fvcom_ceto
+start_hour=18 # hour at which the outputs are generated
+wrfnest=${wrfnest:-d03}
+
+for rawmonth in {1..12}; do
+
+    # Sort out our time bracket.
+    yearbefore=$year
+    yearafter=$year
+    before=$(printf %02d $((rawmonth - 1)))
+    month=$(printf %02d $rawmonth)
+    after=$(printf %02d $((rawmonth + 1)))
+
+    # If we're in January or December, reset the before and after month and
+    # year to the appropriate values.
+    if [ $rawmonth -eq 1 ]; then
+        yearbefore=$((year - 1))
+        before=12
+    elif [ $rawmonth -eq 12 ]; then
+        yearafter=$((year + 1))
+        after=01
+    fi
+
+    # We need all the files from the current month plus a couple of days either
+    # side for the FVCOM runs. We need to use an extra pattern of
+    # $year/wrfout_${wrfnest}_$yearbefore-$before* for the start of a given year as
+    # that may have actually been run as the last day of the previous year. In
+    # that instance, the output file will be in the $year directory but will
+    # actually be named $yearbefore. Limit that search to the last few days to
+    # not include the whole month in a non-year-boundary month (i.e. not
+    # January).
+    files=($(\ls -1 $srcdir/$yearbefore/wrfout_${wrfnest}_$yearbefore-$before-{26,27,28,29,30,31}_${start_hour}?00?00 \
+                    $srcdir/$year/wrfout_${wrfnest}_$yearbefore-$before-{26,27,28,29,30,31}_${start_hour}?00?00 \
+                    $srcdir/$year/wrfout_${wrfnest}_$year-$month-??_${start_hour}?00?00 \
+                    $srcdir/$yearafter/wrfout_${wrfnest}_$year-$month-??_${start_hour}?00?00 \
+                    $srcdir/$yearafter/wrfout_${wrfnest}_$yearafter-$after-{01,02,03}_${start_hour}?00?00 2> /dev/null | sort -u))
+
+    # Now convert to FVCOM forcing files. These files have all had their first
+    # time step removed as that's just the initial condition. So, you'd need to
+    # add a -dTime,1,, to the ncrcat command to drop the first time step if
+    # that's not been done. Once they're all converted, ncrcat them all
+    # together into a single file for this month.
+    parallel \(ln -s {} current_{/.}.nc \|\| true\) \&\& $binary -i current_{/.}.nc -o /var/tmp/out_{/.}.nc -latitude 50.0 -hindcast \> \/dev\/null ::: "${files[@]}"
+    parallel rm current_{/.}.nc ::: "${files[@]}"
+    parallel ncrcat -O -h /var/tmp/out_{/.}.nc /var/tmp/trim_{/.}.nc ::: "${files[@]}"
+    parallel rm /var/tmp/out_{/.}.nc ::: "${files[@]}"
+    rm $srcdir/$year/wrfout_${wrfnest}_${year}-${month}.nc || true
+    ncrcat -O -h $(\ls -1 /var/tmp/trim_wrfout_${wrfnest}_{${yearbefore},${year},${yearafter}}-{${before},${month},${after}}-??_*.nc | sort -u) $srcdir/$year/wrfout_${wrfnest}_${year}-${month}.nc
+    parallel rm /var/tmp/trim_{/.}.nc ::: "${files[@]}"
+
+done
+

app/get_archive_wrf_file/rose-app.conf

 [command]
-default = cp /pml${WRF_ARCHIVE_DIR}/*${WRF_ARCHIVE_DATESTR}*/wrfout_d03_* ${ROSE_DATAC}/raw_wrf_file.nc
+default = bash ./get_wrf_files.sh ${START_DAY} ${END_DAY} ${WRF_ARCHIVE_DATEFMT} ${WRF_ARCHIVE_DIR} ${ROSE_DATAC}
+

rose-suite_TAMAR.conf

@@ -18,7 +18,6 @@ MAIL_TO='mbe@pml.ac.uk'
 GRID_NAME='tamar_v2'
 COMMON_FILES_PATH='/users/modellers/modop/Models/FVCOM_tamar_common/'
 ARCHIVE_DIR='data/sthenno1/scratch/modop/Model/FVCOM_tamar/output'
-PLOT_DIR='data/sthenno1/scratch/modop/Model/FVCOM_tamar/plots'
 
 TEMP_ACTIVE='T'
 SALT_ACTIVE='T'
@@ -31,7 +30,7 @@ AIR_PRESSURE_ON='T'
 ## WRF suite settings if any of the above are on
 WRF_RUN_SUITE='wrf'
 WRF_FORECAST_FILE_DIR='/gpfs1/users/modellers/modop/Models/WRF_transfer_dir/'
-WRF_ARCHIVE_DIR='/data/sthenno1/scratch/modop/Model/WRF/output'
+WRF_ARCHIVE_DIR='data/sthenno1/backup/pica/models/WRF/wrf-preprocess-gfs/output'
 WRF_ARCHIVE_DATEFMT='%Y%m%d'