Custom Query (964 matches)

There are some typos in set_scoord.F for Vstretching = 4 introduced in ​src:ticket:494

line 447:
       Cbot=(EXP(theta_b(ng)*Csur)-1.0-r8)/                        &
should be
       Cbot=(EXP(theta_b(ng)*Csur)-1.0_r8)/                        &


line 461:
       Csur=(1.0_r8-COSH(theta_s(ng)*sc_w))/                       &
should be
       Csur=(1.0_r8-COSH(theta_s(ng)*sc_r))/                       &


line 467:
       Cbot=(EXP(theta_b(ng)*Csur)-1.0-r8)/                        &
should be
       Cbot=(EXP(theta_b(ng)*Csur)-1.0_r8)/                        &

Many thanks to Frederic Castruccio for reporting these typos.

The build script (ROMS/Bin/build.bash and ROMS/Bin/build.sh) was improved and updated:

• Mostly all the user tunable parameters are close to each other and better documented:

  # Other user defined environmental variables. See the ROMS makefile for
  # details on other options the user might want to set here. Be sure to
  # leave the switches meant to be off set to an empty string or commented
  # out. Any string value (including off) will evaluate to TRUE in
  # conditional if-statements.
  
   export           USE_MPI=on            # distributed-memory parallelism
   export        USE_MPIF90=on            # compile with mpif90 script
  #export         which_MPI=mpich         # compile with MPICH library
  #export         which_MPI=mpich2        # compile with MPICH2 library
   export         which_MPI=openmpi       # compile with OpenMPI library
  
  #export        USE_OpenMP=on            # shared-memory parallelism
  
   export              FORT=ifort
  #export              FORT=gfortran
  #export              FORT=pgi
  
  #export         USE_DEBUG=on            # use Fortran debugging flags
   export         USE_LARGE=on            # activate 64-bit compilation
  #export       USE_NETCDF4=on            # compile with NetCDF-4 library
  #export   USE_PARALLEL_IO=on            # Parallel I/O with Netcdf-4/HDF5
  
  #export       USE_MY_LIBS=on            # use my library paths below
  

  Notice the new local variable which_MPI to specify which MPI library to use during compilation. You need choose only one and comment the other values.

• The value of local variable USE_MY_LIBS is commented out by default. If you want to use this nice capability, you need to change the paths of the required libraries in your particular computer. Recall that you may want to have different copies of the build script for a particular computer.

• Now we are using the NetCDF-4 configuration script nc-config which is available since NetCDF version 4.0.1. This script loads all the required libraries according to the NetCDF-4 installation options (openDAP, NetCDF4/HDF5 file format). For Example, the logic for the ifort compiler is now:

  if [ -n "${USE_MY_LIBS:+1}" ]; then
    case "$FORT" in
      ifort )
        export            ESMF_OS=Linux
        export      ESMF_COMPILER=ifort
        export          ESMF_BOPT=O
        export           ESMF_ABI=64
        export          ESMF_COMM=mpich
        export          ESMF_SITE=default
  
        if [ -n "${USE_MPI:+1}" ]; then
          if [ "${which_MPI}" = "mpich" ]; then
            export       ESMF_DIR=/opt/intelsoft/mpich/esmf
            export     MCT_INCDIR=/opt/intelsoft/mpich/mct/include
            export     MCT_LIBDIR=/opt/intelsoft/mpich/mct/lib
          elif [ "${which_MPI}" = "mpich2" ]; then
            export       ESMF_DIR=/opt/intelsoft/mpich2/esmf
            export     MCT_INCDIR=/opt/intelsoft/mpich2/mct/include
            export     MCT_LIBDIR=/opt/intelsoft/mpich2/mct/lib
          elif [ "${which_MPI}" = "openmpi" ]; then
            export       ESMF_DIR=/opt/intelsoft/openmpi/esmf
            export     MCT_INCDIR=/opt/intelsoft/openmpi/mct/include
            export     MCT_LIBDIR=/opt/intelsoft/openmpi/mct/lib
          fi
        fi
  
        export        ARPACK_LIBDIR=/opt/intelsoft/serial/ARPACK
        if [ -n "${USE_MPI:+1}" ]; then
          if [ "${which_MPI}" = "mpich" ]; then
            export   PARPACK_LIBDIR=/opt/intelsoft/mpich/PARPACK
          elif [ "${which_MPI}" = "mpich2" ]; then
            export   PARPACK_LIBDIR=/opt/intelsoft/mpich2/PARPACK
          elif [ "${which_MPI}" = "openmpi" ]; then
            export   PARPACK_LIBDIR=/opt/intelsoft/openmpi/PARPACK
          fi
        fi
  
        if [ -n "${USE_NETCDF4:+1}" ]; then
          if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
            if [ "${which_MPI}" = "mpich" ]; then
              export      NC_CONFIG=/opt/intelsoft/mpich/netcdf4/bin/nc-config
              export  NETCDF_INCDIR=/opt/intelsoft/mpich/netcdf4/include
            elif [ "${which_MPI}" = "mpich2" ]; then
              export      NC_CONFIG=/opt/intelsoft/mpich2/netcdf4/bin/nc-config
              export  NETCDF_INCDIR=/opt/intelsoft/mpich2/netcdf4/include
            elif [ "${which_MPI}" = "openmpi" ]; then
              export      NC_CONFIG=/opt/intelsoft/openmpi/netcdf4/bin/nc-config
              export  NETCDF_INCDIR=/opt/intelsoft/openmpi/netcdf4/include
            fi
          else
            export        NC_CONFIG=/opt/intelsoft/serial/netcdf4/bin/nc-config
            export    NETCDF_INCDIR=/opt/intelsoft/serial/netcdf4/include
          fi
        else
          export      NETCDF_INCDIR=/opt/intelsoft/serial/netcdf3/include
          export      NETCDF_LIBDIR=/opt/intelsoft/serial/netcdf3/lib
        fi
        ;;
  ...
  

  Again, all the above logic is processed when the environmental variable USE_MY_LIBS is not empty and has any non-blank value.

• The above change with the NetCDF4 nc-config script required an update of all the make configuration (*.mk) files in the Compilers directory. This cleaned the logic nicely. Notice that such script is not available for NetCDF 3.x.

Many thanks to Mark Hadfield for ​suggesting this change.

WARNING:

• You need to update the makefile, make configuration (*.mk) scripts, and build (build.bash, build.sh) for all this to work correctly.

• I highly recommend to use the build script when compiling and linking ROMS always. Advanced users that run in various computer architecture may want to have their own Compiles sub-directory somewhere else. I have my customized make configuration files in $HOME/Compilers. So I tell the build script to use those configuration files instead:

  #export         COMPILERS=${MY_ROMS_SRC}/Compilers
   export         COMPILERS=${HOME}/Compilers
  

There has been a lot of traffic in the forum of users struggling how to configure the Test Cases distributed in ROMS. Notice that we introduced last year the test svn repository:

URL:  https://www.myroms.org/svn/src/test

It includes the sub-directory WC13 showing how to run all the 4D-Var algorithms available in ROMS and documented in ​WikiROMS tutorial.

Now I adding several directories which include more Test Cases:

test/
     DAMEE_4/
            /Data/
                 /netcdf3
                 /netcdf4
            /scoord11
            /scoord22
     External/
     WC13/
         /ARRAY_MODES
         /Data
         /Functionals
         /I4DVAR
         /I4DVAR_impact
         /Normalization
         /PSAS
         /PSAS_impact
         /PSAS_sensitivity
         /R4DVAR
         /R4DVAR_impact
         /R4DVAR_sensitivity
         /plotting
     basin/
     benchmark/
     bio_toy/
            /Data
     bl_test/
     canyon/
     double_gyre/
                /AFTE
                /Data
                /FSV
                /FTE
                /Forward
                /OP
                /SOsemi
     estuary_test/
     flt_test/
     grav_adj/
     inlet_test/
               /Data
     kelvin/
     lab_canyon/
     lmd_test/
     riverplume/
     seamount/
     sed_test/
     shoreface/
     soliton/
     test_chan/
     test_head/
              /Data
     upwelling/
     weddell/
     windbasin/

• Notice that there is a directory for each Test Case. The realistic applications are in uppercase whereas the idealized applications are in lowercase. There is also an External sub-directory containing the metadata files varinfo.dat and coupling.dat.

• Each sub-directory contains the necessary header file, standard input scripts, configuration scripts, and build scripts to compile, link, and run each application.

• All the sub-directories show the build script in all its glory. It provides examples of how to manipulate ROMS c-preprocessing options without the need of changing the makefile and/or application header file. Users can start playing with several combinations of the CPP options. Be aware that when making changes it may require the fine-tuning of the application time-step to satisfy CFL constraint.