Pull from NOAA-EMC master

model/aux/bash/ww3_ounf_inp2nml.sh

@@ -182,7 +182,7 @@ cat >> $nmlfile << EOF
 !     FIELD%TIMESTRIDE           = '0'                ! Time stride for the output field
 !     FIELD%TIMESTOP             = '29001231 000000'  ! Stop date for the output field
 !     FIELD%TIMECOUNT            = '1000000000'       ! Number of time steps
-!     FIELD%TIMESPLIT            = 6                  ! [4(yearly),6(monthly),8(daily),10(hourly)]
+!     FIELD%TIMESPLIT            = 6                  ! [0(nodate),4(yearly),6(monthly),8(daily),10(hourly)]
 !     FIELD%LIST                 = 'unset'            ! List of output fields
 !     FIELD%PARTITION            = '0 1 2 3'          ! List of wave partitions ['0 1 2 3 4 5']
 !     FIELD%SAMEFILE             = T                  ! All the variables in the same file [T|F]

model/bin/make_makefile.sh

@@ -97,7 +97,7 @@
               shared mpp mpiexp thread GSE prop \
               stress s_ln source stab s_nl snls s_bot s_db miche s_tr s_bs \
               dstress s_ice s_is reflection s_xx \
-              wind windx rwind curr currx mgwind mgprop mggse \
+              wind windx wcor rwind curr currx mgwind mgprop mggse \
               subsec tdyn dss0 pdif tide refrx ig rotag arctic nnt mprf \
               cou oasis agcm ogcm igcm trknc setup pdlib memck uost
   do
@@ -247,6 +247,11 @@
       windx  ) TY='one'
                ID='wind interpolation in space'
                OK='WNX0 WNX1 WNX2' ;;
+#sort:wcor:
+      wcor   ) TY='upto1'
+               ID='wind speed correction'
+               TS='WCOR'
+               OK='WCOR' ;;
 #sort:rwind:
       rwind  ) TY='upto1'
                ID='wind vs. current definition'

model/ftn/w3triamd.ftn

@@ -666,7 +666,10 @@ CONTAINS
         DO IBC = 1, N_OUTSIDE_BOUNDARY
            IX = OUTSIDE_BOUNDARY(IBC)
            !write(*,*) 'TEST1', IX, TMPSTA(1,IX), CCON(IX), COUNTCON(IX), ZBIN(1,IX), ZLIM
-           IF (IX.NE.0) THEN  ! There was a bug in the mesh conversion, OUTSIDE_BOUNDARY(IBC) should not be zero 
+
+           ! OUTSIDE_BOUNDARY(IBC) is defined over the full nodes NODES indexes
+           ! whereas TMPSTA and ZBIN are defined over the clean up list of nodes NX
+           IF ((IX.NE.0).AND.(IX.LE.NX)) THEN
              IF ((TMPSTA(1,IX).EQ.1).AND.(STATUS(IX).EQ.0)  &
                .AND.(ZBIN(1,IX).LT.ZLIM))  TMPSTA(1,IX)=2  
             END IF       

model/ftn/ww3_ounf.ftn

@@ -157,10 +157,9 @@
                                  IOUT, S3, IRET, HASNC4,               &
                                  NBIPART, CNTIPART, NCVARTYPE, IPART,  &
                                  RTDNX, RTDNY
-      INTEGER                 :: TOUT(2), TDUM(2),                     &
-                                 NCIDS(NOGRP,NGRPP,6), STOPDATE(8)
+      INTEGER                 :: TOUT(2), TDUM(2), STOPDATE(8)
 !
-      INTEGER, ALLOCATABLE    :: TABIPART(:)
+      INTEGER, ALLOCATABLE    :: TABIPART(:), NCIDS(:,:,:)
 !
 !/S      INTEGER, SAVE           :: IENT = 0
 !
@@ -383,6 +382,7 @@
       ! Alternative processing of TABIPART to capture requests 
       ! greater than NOSWLL (C.Bunney):
       ALLOCATE(TABIPART(NOSWLL + 1))
+      ALLOCATE(NCIDS(NOGRP,NGRPP,NOSWLL + 1))
       NBIPART=0
       DO I=1,30
         IF(STRINGIPART(I:I) .EQ. ' ') CYCLE
@@ -874,17 +874,21 @@
 
 ! 1.2 Sets the date as ISO8601 convention 
       ! S3 defines the number of characters in the date for the filename
-      ! S3=4-> YYYY, S3=6 -> YYYYMM, S3=10 -> YYYYMMDDHH
+      ! S3=0 -> field, S3=4-> YYYY, S3=6 -> YYYYMM, S3=10 -> YYYYMMDDHH
       ! Setups min and max date format
-      IF (S3.LT.4) S3=4 
+      IF (S3.GT.0 .AND. S3.LT.4) S3=4 
       IF (S3.GT.10) S3=10 
 !
       ! Defines the format of FILETIME
       S5=S3-8
       S4=S3
       OLDTIMEID=TIMEID
+      ! if S3=>nodate then filetime='field'
+      IF (S3.EQ.0) THEN
+        S4=5
+        TIMEID="field"
       ! if S3=>YYYYMMDDHH then filetime='YYYYMMDDTHHZ'
-      IF (S3.EQ.10) THEN 
+      ELSE IF (S3.EQ.10) THEN 
         S4=S4+2 ! add chars for ISO8601 : day T hours Z
         WRITE(FORMAT1,'(A,I1,A,I1,A)') '(I8.8,A1,I',S5,'.',S5,',A1)'
         WRITE (TIMEID,FORMAT1) TIME(1), 'T', &
@@ -3398,9 +3402,6 @@
             FNAMENC(S1+S2+1:S1+S2+3) = '.nc'
             FNAMENC(S1+S2+4:S1+S2+6) = '   '
 
-!/NCO ! For NCEP application, requires fixed netcdf file name
-!/NCO            FNAMENC='ww3.gridded.nc'
-
             ! If the flag frequency is .TRUE., defines the fourth dimension
             IF (FLFRQ) THEN 
               UNITVAR(:)=UNITS

model/ftn/ww3_shel.ftn

@@ -1297,7 +1297,6 @@
             ELSE IF ( J .EQ. 6 ) THEN
 !             IPRT: IX0, IXN, IXS, IY0, IYN, IYS
               CALL NEXTLN ( COMSTR , NDSI , NDSEN )
-              READ (NDSI,*,END=2001,ERR=2002) IPRT, PRTFRM
 !/DEBUGINIT              write(740+IAPROC,*), 'Before reading IPRT'
 !/DEBUGINIT              write(740+IAPROC,*), 'Before read 2002, case 10'
               READ (NDSI,*) IPRT, PRTFRM

model/inp/ww3_ounf.inp

@@ -33,7 +33,7 @@ $
 $
 $ -------------------------------------------------------------------- $
 $ File prefix
-$ number of characters in date [4(yearly),6(monthly),8(daily),10(hourly)]
+$ number of characters in date [0(nodate),4(yearly),6(monthly),8(daily),10(hourly)]
 $ IX and IY ranges [regular:IX NX IY NY, unstructured:IP NP 1 1]
 $
  ww3.         

model/nml/ww3_ounf.nml

@@ -23,7 +23,7 @@
 !     FIELD%TIMESTART            = '19000101 000000'  ! Stop date for the output field
 !     FIELD%TIMESTRIDE           = '0'                ! Time stride for the output field
 !     FIELD%TIMECOUNT            = '1000000000'       ! Number of time steps
-!     FIELD%TIMESPLIT            = 6                  ! [4(yearly),6(monthly),8(daily),10(hourly)]
+!     FIELD%TIMESPLIT            = 6                  ! [0(nodate),4(yearly),6(monthly),8(daily),10(hourly)]
 !     FIELD%LIST                 = 'unset'            ! List of output fields
 !     FIELD%PARTITION            = '0 1 2 3'          ! List of wave partitions ['0 1 2 3 4 5']
 !     FIELD%SAMEFILE             = T                  ! All the variables in the same file

regtests/bin/matrix.base

@@ -1965,9 +1965,9 @@
    echo ' ' >> matrix.body
    if [ "$dist" = 'y' ]
    then 
-     echo "$rtst -s MPI -w work_rg_shel_MPI -i input_rg_shel $ww3 ww3_ts4" >> matrix.body
-     echo "$rtst -s MPI -w work_rg_multi_MPI -i input_rg_multi -m grdset $ww3 ww3_ts4" >> matrix.body
-     echo "$rtst -s MPI -w work_ug_MPI -i input_ug $ww3 ww3_ts4" >> matrix.body
+     echo "$rtst -s MPI -w work_rg_shel_MPI -i input_rg_shel -f -p $mpi -n $np $ww3 ww3_ts4" >> matrix.body
+     echo "$rtst -s MPI -w work_rg_multi_MPI -i input_rg_multi -m grdset -f -p $mpi -n $np $ww3 ww3_ts4" >> matrix.body
+     echo "$rtst -s MPI -w work_ug_MPI -i input_ug -f -p $mpi -n $np $ww3 ww3_ts4" >> matrix.body
    else 
      echo "$rtst -w work_rg_shel -i input_rg_shel $ww3 ww3_ts4" >> matrix.body
      echo "$rtst -w work_rg_multi -i input_rg_multi -m grdset $ww3 ww3_ts4" >> matrix.body

regtests/bin/matrix.comp

@@ -19,9 +19,21 @@
 # 1. Set up
 # 1.a Computer/ user dependent set up
 
+  if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]
+  then     
+    printf "\n ERROR ABORTING \n"
+    printf "\n matrix.comp requires 3 arguments: "
+    printf "   1: test type (eg, all or test-name), 2: base directory and 3: reference directory. \n"
+    printf "\n Usage:"
+    printf "    ./bin/matrix.comp all basedir compdir \n\n"
+    exit
+  fi
+
+  ctest=$1
+  base_dir=$2
+  comp_dir=$3
   home_dir=`pwd`
-  base_dir='.'
-  comp_dir='../../EMC_ww3_master/regtests'
+
   rm -rf $home_dir/output
   rm -f $home_dir/matrixDiff.out
 
@@ -58,18 +70,12 @@
   echo '**********************************************************************' >> $home_dir/fulldiff.tmp
 
 
-  if [ "$#" != '1' ] ; then
-    echo "usage: matrix.comp test"
-    echo "       test can be 'all'" ; exit 1 ; fi
-
-  test=$1
-
-  if [ "$test" = 'all' ] ; then
-    test=`ls -d ww3_tp1.? ww3_tp2.? ww3_ts? ww3_tbt1.? ww3_tbt2.? ww3_tic1.? ww3_tic2.? ww3_tig1.? ww3_tp2.1? mww3_test_0?` ; fi
+  if [ "$ctest" = 'all' ] ; then
+    ctest=`ls -d ww3_tp1.? ww3_tp2.? ww3_ts? ww3_tbt1.? ww3_tbt2.? ww3_tic1.? ww3_tic2.? ww3_tig1.? ww3_tp2.1? mww3_test_0?` ; fi
   echo "base directory : $base_dir" >> $home_dir/header.tmp
   echo "comp directory : $comp_dir" >> $home_dir/header.tmp
   echo "test(s)        : "          >> $home_dir/header.tmp
-  echo $test                        >> $home_dir/header.tmp
+  echo $ctest                        >> $home_dir/header.tmp
   echo " "                          >> $home_dir/header.tmp
 
   cat $home_dir/header.tmp
@@ -84,7 +90,7 @@
 # 2.  Looping over tests                                                      #
 # --------------------------------------------------------------------------- #
 
-  for tst in $test
+  for tst in $ctest
   do
     cd $home_dir ; cd $base_dir
     if [ ! -d $tst ]

regtests/bin/matrix_ncep

@@ -0,0 +1,157 @@
+#!/bin/bash
+# --------------------------------------------------------------------------- #
+# matrix.go: Run matrix of regression tests on target machine.                #
+#                                                                             #
+# Remarks:                                                                    #
+# - This version is set up for automatic w3_setenv script and for the         #
+#   NOAA RDHPC 'zeus' system. When using this for your own setup and          #
+#   computer, please copy rather than modify.                                 #
+#                                                                             #
+#                                                      Hendrik L. Tolman      #
+#                                                      August 2013            #
+#                                                      December 2013          #
+#                                                      April 2018             #
+#                                                                             #
+#    Copyright 2013 National Weather Service (NWS),                           #
+#       National Oceanic and Atmospheric Administration.  All rights          #
+#       reserved.  WAVEWATCH III is a trademark of the NWS.                   #
+#       No unauthorized use without permission.                               #
+#                                                                             #
+# --------------------------------------------------------------------------- #
+# 0. Environment file
+
+  source $(dirname $0)/../../model/bin/w3_setenv
+  main_dir=$WWATCH3_DIR
+  temp_dir=$WWATCH3_TMP
+  source=$WWATCH3_SOURCE
+  list=$WWATCH3_LIST
+
+  echo "Main directory    : $main_dir"
+  echo "Scratch directory : $temp_dir"
+  echo "Save source codes : $source"
+  echo "Save listings     : $list"
+
+# Set batchq queue to define headers etc (default to original version if empty)
+batchq="slurm"
+
+# 1. Set up
+# 1.a Computer/ user dependent set up
+
+  echo '#!/bin/sh --login'                                   > matrix.head
+  echo ' '                                                  >> matrix.head
+if [ $batchq = "slurm" ]
+then
+  echo '#SBATCH -n 24'                                      >> matrix.head
+  echo '#SBATCH -q batch'                                   >> matrix.head
+  echo '#SBATCH -t 08:00:00'                                >> matrix.head
+  echo '#SBATCH -A marine-cpu'                              >> matrix.head
+  echo '#SBATCH -J ww3_regtest'                             >> matrix.head
+  echo '#SBATCH -o matrix.out'                              >> matrix.head
+else
+  echo '#PBS -l procs=24'                                   >> matrix.head
+  echo '#PBS -q batch'                                      >> matrix.head
+  echo '#PBS -l walltime=08:00:00'                          >> matrix.head
+  echo '#PBS -A marine-cpu'                                 >> matrix.head
+  echo '#PBS -N ww3_regtest'                                >> matrix.head
+  echo '#PBS -j oe'                                         >> matrix.head
+  echo '#PBS -o matrix.out'                                 >> matrix.head
+  echo ' '                                                  >> matrix.head
+fi
+  echo "  cd $(dirname $main_dir)/regtests"                 >> matrix.head
+  echo ' '                                                  >> matrix.head
+
+# Netcdf and Parmetis modules & variables
+
+istheia=`hostname | grep tfe`
+if [ $istheia ]
+then
+  modcomp='intel/14.0.2'
+  modmpi='impi/5.1.2.150'
+  modnetcdf='netcdf/4.3.0'
+fi
+
+  echo "  module load $modcomp $modmpi $modnetcdf"                   >> matrix.head
+  echo "  export WWATCH3_NETCDF=NC4"                        >> matrix.head
+  echo "  export NETCDF_CONFIG=`which nc-config`"           >> matrix.head
+  echo "  export METIS_PATH=/scratch3/NCEPDEV/stmp2/Jessica.Meixner/parmetis-4.0.3"   >> matrix.head
+  echo "  export WW3_PARCOMPN=4"                            >> matrix.head
+  echo ' ' 
+
+# Compiler option. Choose appropriate compiler and set cmplOption to
+# y if using for the first time or using a different compiler
+
+  cmplr=Intel
+  export cmplOption='y'
+
+  if [ "$batchq" = 'slurm' ]
+  then
+    export  mpi='srun'
+  else
+    export  mpi='mpirun'
+  fi
+    export   np='24'
+    export   nr='4'
+    export  nth='6'
+# Compile option
+  if [ "$cmplOption" = 'y' ]
+  then
+     opt="-c $cmplr -S -T"
+  else
+     opt="-S"
+  fi
+# Batch queue option
+  if [ "$batchq" = 'slurm' ]
+  then
+     opt="-b $batchq $opt"
+  fi
+
+# Base run_test command line
+  export rtst="./bin/run_test $opt"
+
+  export  ww3='../model'
+
+# 1.b Flags to do course selection - - - - - - - - - - - - - - - - - - - - - -
+#     Addition selection by commenting out lines as below
+
+  export     shrd='y' # Do shared architecture tests
+  export     dist='y' # Do distributed architecture (MPI) tests
+  export      omp='y' # Threaded (OpenMP) tests
+  export     hybd='n' # Hybrid options
+
+  export   prop1D='y' # 1-D propagation tests (ww3_tp1.X)
+  export   prop2D='y' # 2-D propagation tests (ww3_tp2.X)
+  export     time='y' # time linmited growth
+  export    fetch='y' # fetch linmited growth
+  export   hur1mg='y' # Hurricane with one moving grid
+  export    shwtr='y' # shallow water tests
+  export    unstr='y' # unstructured grid tests
+  export    pdlib='y' # unstr with pdlib for domain decomposition and implicit solver
+  export    smcgr='y' # SMC/Rotated grid test
+  export   mudice='y' # Mud/Ice and wave interaction tests 
+  export   infgrv='y' # Second harmonic generation tests
+  export     uost='y' # ww3_ts4 Unresolved Obstacles Source Term (UOST)
+  export    assim='y' # Restart spectra update
+
+  export  multi01='y' # mww3_test_01 (wetting and drying)
+  export  multi02='y' # mww3_test_02 (basic two-way nesting test))
+  export  multi03='y' # mww3_test_03 (three high and three low res grids).
+  export  multi04='y' # mww3_test_04 (swell on sea mount and/or current)
+  export  multi05='y' # mww3_test_05 (three-grid moving hurricane)
+  export  multi06='y' # mww3_test_06 (curvilinear grid tests)
+  export  multi07='y' # mww3_test_07 (unstructured grid tests)
+  export  multi08='y' # mww3_test_08 (wind and ice tests)
+
+# export   filter='PR3 ST2 UQ'
+                      # The filter does a set of consecutinve greps on the 
+                      # command lines generated by filter.base with the above
+                      # selected options.
+
+# --------------------------------------------------------------------------- #
+# 2.  Execute matrix.base ...                                                 #
+# --------------------------------------------------------------------------- #
+
+  $main_dir/../regtests/bin/matrix.base
+
+# --------------------------------------------------------------------------- #
+# End to the matrix                                                           #
+# --------------------------------------------------------------------------- #