uniformize regtests output by setting a global output type in the mat…

…rix script (#605)

regtests/bin/matrix_datarmor

@@ -1,16 +1,19 @@
 #!/bin/bash
 # --------------------------------------------------------------------------- #
-# matrix.go: Run matrix of regression tests on target machine.                #
+# matrix_datarmor: Run matrix of regression tests on target machine.          #
 #                                                                             #
 # Remarks:                                                                    #
 # - This version is set up for automatic w3_setenv script and for the         #
 #   IFREMER HPC 'datarmor'. When using this for your own setup and            #
 #   computer, please copy rather than modify.                                 #
 #                                                                             #
 #                                                      Hendrik L. Tolman      #
+#                                                      Mickael Accensi        #
+#                                                                             #
 #                                                      August 2013            #
 #                                                      December 2013          #
 #                                                      April 2018             #
+#                                                      October 2021           #
 #                                                                             #
 #    Copyright 2013 National Weather Service (NWS),                           #
 #       National Oceanic and Atmospheric Administration.  All rights          #
@@ -31,89 +34,88 @@
   echo "Save source codes : $source"
   echo "Save listings     : $list"
 
+# Compiler option. Choose appropriate compiler and set cmplOption to
+# y if using for the first time or using a different compiler
+
+  cmplr=datarmor_intel
+  export cmplOption='y'
 
 # 1. Set up
+
+  export cmplOption='y'
+  export np='28'      #number of mpi tasks
+  export npl='28'     #number of mpi tasks for ufs applications and large setups
+  export npl1='20'    #number of mpi tasks for ufs/large setups (b4b check)
+  export nr='4'       #number of mpi tasks for hybrid
+  export nth='7'      #number of threads
+  export nth1='6'     #number of threads (b4b check)
+
 # 1.a Computer/ user dependent set up
 
   echo '#!/bin/bash'                                        > matrix.head
   echo ' '                                                  >> matrix.head
   echo '#PBS -q mpi_1'                                      >> matrix.head
-  echo '#PBS -l mem=20G'                                    >> matrix.head
-  echo '#PBS -l walltime=48:00:00'                          >> matrix.head
-  echo '#PBS -N ww3_regtest'                                >> matrix.head
+  echo "#PBS -l select=1:ncpus=28:mpiprocs=$nr:ompthreads=$nth:mem=20G"  >> matrix.head
+  echo '#PBS -l walltime=08:00:00'                          >> matrix.head
+  echo "#PBS -N $(basename $(dirname $(dirname $PWD)))"     >> matrix.head
   echo '#PBS -j oe'                                         >> matrix.head
   echo '#PBS -o matrix.out'                                 >> matrix.head
   echo ' '                                                  >> matrix.head
 
   echo "  cd $(dirname $main_dir)/regtests"                 >> matrix.head
   echo ' '                                                  >> matrix.head
 
-# Netcdf modules
-
-  cmplr=datarmor_intel
+# Netcdf, grib and Parmetis modules
 
   echo '  source /usr/share/Modules/3.2.10/init/bash'                                 >> matrix.head
   echo '  module purge'                                                               >> matrix.head
-  echo "  export WW3_PARCOMPN=4"                                                      >> matrix.head
 
   if [ $cmplr = "datarmor_intel_debug" ] || [ $cmplr = "datarmor_intel" ]
   then
+    COMP='INTEL'
     echo '  module load intel-comp/18'                                                >> matrix.head
     echo '  module load impi/2018.1.163'                                              >> matrix.head
-    echo '  export PATH=${PATH}:/home/datawork-wave/NETCDF2019/INTEL/bin'             >> matrix.head
-    echo '  export CPATH=${CPATH}:/home/datawork-wave/NETCDF2019/INTEL/include'       >> matrix.head
-    echo '  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/datawork-wave/NETCDF2019/INTEL/lib'  >> matrix.head
-    echo '  export NETCDF_CONFIG=/home/datawork-wave/NETCDF2019/INTEL/bin/nc-config'  >> matrix.head
-    echo '  export METIS_PATH=/home/datawork-wave/PARMETIS2019/INTEL'                 >> matrix.head
-
   elif [ $cmplr = "datarmor_mpt_debug" ] || [ $cmplr = "datarmor_mpt" ]
   then
+    COMP='MPT'
     echo '  module load intel-comp/18'                                                >> matrix.head
     echo '  module load mpt/2.18'                                                     >> matrix.head
-    echo '  export PATH=${PATH}:/home/datawork-wave/NETCDF2019/MPT/bin'               >> matrix.head
-    echo '  export CPATH=${CPATH}:/home/datawork-wave/NETCDF2019/MPT/include'          >> matrix.head
-    echo '  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/datawork-wave/NETCDF2019/MPT/lib'    >> matrix.head
-    echo '  export NETCDF_CONFIG=/home/datawork-wave/NETCDF2019/MPT/bin/nc-config'    >> matrix.head
-    echo '  export METIS_PATH=/home/datawork-wave/PARMETIS2019/MPT'                   >> matrix.head
-
   elif [ $cmplr = "datarmor_gnu_debug" ] || [ $cmplr = "datarmor_gnu" ]
   then
+    COMP='GNU'
     echo '  module load impi/2018.1.163'                                              >> matrix.head
-    echo '  export PATH=${PATH}:/home/datawork-wave/NETCDF2019/GNU/bin'               >> matrix.head
-    echo '  export CPATH=${CPATH}:/home/datawork-wave/NETCDF2019/GNU/include'          >> matrix.head
-    echo '  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/datawork-wave/NETCDF2019/GNU/lib'    >> matrix.head
-    echo '  export NETCDF_CONFIG=/home/datawork-wave/NETCDF2019/GNU/bin/nc-config'    >> matrix.head
-    echo '  export METIS_PATH=/home/datawork-wave/PARMETIS2019/GNU'                   >> matrix.head
-
   elif [ $cmplr = "datarmor_pgi_debug" ] || [ $cmplr = "datarmor_pgi" ]
   then
+    COMP='PGI'
     echo '  module load pgi/17.10'                                                    >> matrix.head
-    echo '  export PATH=${PATH}:/home/datawork-wave/NETCDF2019/PGI/bin'               >> matrix.head
-    echo '  export CPATH=${CPATH}:/home/datawork-wave/NETCDF2019/PGI/include'          >> matrix.head
-    echo '  export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/datawork-wave/NETCDF2019/PGI/lib'    >> matrix.head
-    echo '  export NETCDF_CONFIG=/home/datawork-wave/NETCDF2019/PGI/bin/nc-config'    >> matrix.head
-    echo '  export METIS_PATH=/home/datawork-wave/PARMETIS2019/PGI'                   >> matrix.head
   fi
 
+  echo "  export PATH=\${PATH}:/home/datawork-wave/NETCDF2019/${COMP}/bin"             >> matrix.head
+  echo "  export CPATH=\${CPATH}:/home/datawork-wave/NETCDF2019/${COMP}/include"       >> matrix.head
+  echo "  export LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:/home/datawork-wave/NETCDF2019/${COMP}/lib"  >> matrix.head
+  echo "  export NETCDF_CONFIG=/home/datawork-wave/NETCDF2019/${COMP}/bin/nc-config"  >> matrix.head
+  echo "  export METIS_PATH=/home/datawork-wave/PARMETIS2019/${COMP}"                 >> matrix.head
+  echo "  export WW3_PARCOMPN=4"                                                      >> matrix.head
+  echo "  export G2_LIB4=/home/datawork-wave/GRIB2021/${COMP}/lib/libg2.a"            >> matrix.head
+  echo "  export BACIO_LIB4=/home/datawork-wave/GRIB2021/${COMP}/lib/libbacio.a"      >> matrix.head
+  echo "  export JASPER_LIB=/home/datawork-wave/NETCDF2019/${COMP}/lib/libjasper.so"  >> matrix.head
+  echo "  export PNG_LIB=/home/datawork-wave/NETCDF2019/${COMP}/lib/libpng.so"        >> matrix.head
+  echo "  export Z_LIB=/lib64/libz.so.1"                                              >> matrix.head
   echo ' '
 
-# Compiler option. Choose appropriate compiler and set cmplOption to
-# y if using for the first time or using a different compiler
-
-  export cmplOption='y'
-
-  export  mpi='$MPI_LAUNCH'
-  export   np='28'
-  export   nr='14'
-  export  nth='2'
+  export mpi='$MPI_LAUNCH'
 
+# Compile option
   if [ "$cmplOption" = 'y' ]
   then
-     export rtst="./bin/run_test -o both -N -f -S -T -c $cmplr"
+     export opt="-o all -f -c $cmplr -S -T"
   else
-     export rtst="./bin/run_test -o both -N -f -S -T"
+     export opt="-o all -f -S -T"
   fi
 
+# Base run_test command line
+  export rtst="./bin/run_test $opt"
+
   export  ww3='../model'
 
 # 1.b Flags to do course selection - - - - - - - - - - - - - - - - - - - - - -
@@ -122,7 +124,7 @@
   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       hybd='y' # Hybrid options
 
   export     prop1D='y' # 1-D propagation tests (ww3_tp1.X)
   export     prop2D='y' # 2-D propagation tests (ww3_tp2.X)
@@ -138,7 +140,7 @@
   export     infgrv='y' # Second harmonic generation tests
   export       uost='y' # ww3_ts4 Unresolved Obstacles Source Term (UOST)
   export      assim='y' # Restart spectra update
-  export      oasis='y' # Atmosphere, ocean, and ice coupling using oasis
+  export      oasis='y' # Atmosphere, ocean, and ice coupling using OASIS
   export   calendar='y' # Calendar type
   export   confignc='y' # Configurable netCDF meta data (ww3_ounf)
 
@@ -153,13 +155,13 @@
   export    multi09='y' # mww3_test_09 (SMC multi grid test)
   export        ufs='n' # The Unified Forecast System
   export  ufscoarse='n' # Option for small PCs
-  export       grib='n' # grib file field output
+  export       grib='y' # grib file field output
   export  rstrt_b4b='y' # Restart Reproducibility
   export    npl_b4b='y' # MPI task Reproducibility
   export    nth_b4b='y' # Thread Reproducibility
   export       esmf='n' # ESMF coupling
 # export   filter='PR3 ST2 UQ'
-                      # The filter does a set of consecutinve greps on the 
+                      # The filter does a set of consecutive greps on the 
                       # command lines generated by filter.base with the above
                       # selected options.
 
@@ -169,6 +171,7 @@
 
   $main_dir/../regtests/bin/matrix.base
 
+  $main_dir/../regtests/bin/matrix_divider_p.sh
 # --------------------------------------------------------------------------- #
 # End to the matrix                                                           #
 # --------------------------------------------------------------------------- #

regtests/bin/matrix_milhydro

@@ -65,9 +65,9 @@
 # Compile option
   if [ "$cmplOption" = 'y' ]
   then
-     opt="-c $cmplr -S -T"
+     opt="-o all -c $cmplr -S -T"
   else
-     opt="-S"
+     opt="-o all -S"
   fi
 # Batch queue option
   if [ "$batchq" = 'slurm' ]

regtests/bin/matrix_ncep

@@ -164,9 +164,9 @@
 # Compile option
   if [ "$cmplOption" = 'y' ]
   then
-     opt="-c $cmplr -S -T"
+     opt="-o all -c $cmplr -S -T"
   else
-     opt="-S"
+     opt="-o all -S"
   fi
 # Batch queue option
   if [ "$batchq" = 'slurm' ]

regtests/bin/matrix_s4

@@ -121,9 +121,9 @@
 # Compile option
   if [ "$cmplOption" = 'y' ]
   then
-     opt="-c $cmplr -S -T"
+     opt="-o all -c $cmplr -S -T"
   else
-     opt="-S"
+     opt="-o all -S"
   fi
 # Batch queue option
   opt="-b $batchq $opt"

regtests/bin/matrix_ukmo_cray

@@ -104,9 +104,9 @@ fi
 
   if [ "$cmplOption" = 'y' ]
   then
-     export rtst="./bin/run_test -c $cmplr -S"
+     export rtst="./bin/run_test -o both -c $cmplr -S"
   else
-     export rtst="./bin/run_test -S"
+     export rtst="./bin/run_test -o both -S"
   fi
 
   export  ww3='../model'

regtests/bin/run_test

@@ -469,8 +469,7 @@ fi
 
 # 3.b2 Preprocess cdl files into nc files ----------------------------------- #
 
-filescdl=$path_i/*.cdl
-for f in $filescdl
+for f in $(find $path_i/ -type f -name "*.cdl")
 do
   echo "Converting $f to NetCDF"
   # take action on each file.  Note that converted file is in $path_w

regtests/ww3_tic2.2/input/ww3_outp_spec.inp

@@ -2,17 +2,6 @@ $ WAVEWATCH III Point output post-processing
 $ ------------------------------------------
   19680606 120000   3600. 1
 $
-   1
-   2
-   3
-   4
-   5
-   6
-   7
-   8
-   9
-  10
-  11
   -1
 $
    1

regtests/ww3_tic2.2/input/ww3_outp_tab50.inp

@@ -2,30 +2,6 @@ $ WAVEWATCH III Point output post-processing
 $ ------------------------------------------
   19680606 000000  600. 9999
 $
-   1
-   2
-   3
-   4
-   5
-   6
-   7
-   8
-   9
-  10
-  11
-  12
-  13
-  14
-  15
-  16
-  17
-  18
-  19
-  20
-  21
-  22
-  23
-  24
   -1
 $
    2

regtests/ww3_tic2.2/input/ww3_outp_tab51.inp

@@ -2,8 +2,6 @@ $ WAVEWATCH III Point output post-processing
 $ ------------------------------------------
   19680606 000000    900. 49
 $
-$  1
-  16
   -1
 $
    2

regtests/ww3_tic2.2/input_IC2/ww3_outp_spec.inp

@@ -2,17 +2,6 @@ $ WAVEWATCH III Point output post-processing
 $ ------------------------------------------
   19680606 120000   3600. 1
 $
-   1
-   2
-   3
-   4
-   5
-   6
-   7
-   8
-   9
-  10
-  11
   -1
 $
    1

regtests/ww3_tic2.2/input_IC2/ww3_outp_tab50.inp

@@ -2,30 +2,6 @@ $ WAVEWATCH III Point output post-processing
 $ ------------------------------------------
   19680606 000000  600. 9999
 $
-   1
-   2
-   3
-   4
-   5
-   6
-   7
-   8
-   9
-  10
-  11
-  12
-  13
-  14
-  15
-  16
-  17
-  18
-  19
-  20
-  21
-  22
-  23
-  24
   -1
 $
    2

regtests/ww3_tic2.2/input_IC2/ww3_outp_tab51.inp

@@ -2,8 +2,6 @@ $ WAVEWATCH III Point output post-processing
 $ ------------------------------------------
   19680606 000000    900. 49
 $
-$  1
-  16
   -1
 $
    2