Custom Query (986 matches)

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.

• Changed the time clock function to measure elapsed time in shared-memory parallel applications from cpu_time to omp_get_wtime. It turns out that cpu_time returns the cumulative elapsed time of all parallel threads instead of a single parallel threads as omp_get_wtime. This resulted into inflated elapsed time values during profiling. Many thanks to Simon Spagnol for ​bringing this to our attention.

• Changed calls to create and open NetCDF files when parallel I/O is activated using CPP options PARALLEL_IO and HDF5. We are using now nf90_create and nf90_open with F90 optional arguments in mod_netcdf.F instead of nf90_create_par and nf90_open_par, respectively.

• The ​release 4.1.2 of the NetCDF library made several internal improvements to parallel I/O performance. However, it broke the logic of writing of scalar variables to the NetCDF-4 (HDF5 format) file. We get now an error when writing scalar variables. If parallel I/O is activated, we need to use an older version of the library until we solve this problem. We don't know if this is a new bug in the library or we need to create/write scalar variables differently. Unfortunately, there is no documentation for how to do this.

• Corrected a bug in the week constraint 4D-Var (W4DPSAS and W4DVAR) when model error is included. It turns out that we were not clearing the model error forcing arrays at the start of each inner-loop in routine frc_weak.F. Many thanks to Andy and Polly for discovering and fixing this serious bug.

• Modify inp_par.F to allow different values of NHIS and NADJ in week constraint 4D-Var applications. Sometimes, it is necessary to have NADJ<<NHIS. Many thanks to Andy for suggesting this change.

• Added local declaration of pfac, rfac, ufac, and vfac arrays in ad_set_avg.F. Many thanks to Andy Moore for reporting this problem.

• Added PARPACK_LIBDIR to the build script (build.bash and build.sh). I missed defining this environmental variable in my previous update to the build script.

• Removed deprecated -xW option to the Intel compiler in the Linux configuration files.