README.rst

MPP_PREP

Description

MPP_PREP proposes possible domain decompositions for a given bathymetric file, which is particularly intersting when we want to eliminate land-only domain. All solution are proposed and written to output file. The ratio between the effective number of computed point and the total number of points in the domain is given and is probably a major criteria for choosing a domain decomposition.

Tools mpp_optimiz_zoom_nc.exe as been tested on one eORCA12 and one eORCA025 configuration at trunk@10036

Tools mppopt_showproc_nc.exe has not been tested.

Method

Use mpp_init like code for setting up the decomposition and evaluate the efficiency of the decomposition.

How to compile it

MPP_PREP is compiled in the same manner as all the other tools. The compilation script is maketools and the option are very similar to makenemo.

Here an example of how to compile MPP_PREP on the MetOffice XC40 HPC:

$ ./maketools -n MPP_PREP -m XC40_METO

Usage

the MPP_PREP executable is named mpp_optimiz_zoom_nc.exe. The input file needed are:

• a netcdf file containing a variable with 0 on land and data > 0 on ocean (typically a bathymetry file)
• a namelist to specify the number of vertical levels, netcdf input file, variable and dimension names (...). A namelist template is available in the file 'namelist'. Default namelist is set up for input file domain_cfg.nc (output of Domaincfg tool) and will find decomposition between 100 and 4000 processors.

$ ./mpp_optimiz_zoom_nc.exe -h
  usage : mpp_optimize [ -h ]  [-keep jpni jpnj] [ -o file out ]
               [ -modulo val ] [-r ratio] [-minocean procs] -n namelist

     PURPOSE :
         This program is build to optimize the domain beakdown into
         subdomain for mpp computing.
         Once the grid size, and the land/sea mask is known, it looks
         for all the possibilities within a range of setting parameters
         and determine the optimal.

         Optimization is done with respect to the maximum number of
         sea processors and to the maximum numbers of procs (nn_procmax)

         Optional optimization can be performed taking into account
         the maximum available processor memory rn_ppmcal. This is
         activated if ln_memchk is set true in the namelist

         Additional criteria can be given on the command line to reduce
         the amount of possible choices.

     ARGUMENTS :
         -n namelist : indicate the name of the namelist to use

     OPTIONS :
         -h : print this help message
         -keep jpni jpnj : print a file suitable for plotting,
                 corresponding to the given decomposition
         -o output file : give the name of the output file
                 default is processor.layout
         -modulo val : only retain decomposition whose total number
                 of util processors (sea) are a multiple of val
         -r ratio : only retain decomposition with a ratio computed/global
                 less or equal to the given ratio
         -minocean procs : only retain decomposition with a number of
                 ocean procs greater of equal to procs

     REQUIRED FILES :
       A bathymetric file and an ad-hoc namelist are required.
       The file name of the bathymetry is specified in the namelist

     OUTPUT :
       processor.layout : an ascii file with all found possibilities

     SEE ALSO :
       script screen.ksh helps a lot in the analysis of the output file.

STOP

Example

Here is an example of usage of ./mpp_optimiz_zoom_nc.exe on the the eORCA025 bathymetry. We keep in the output only domain decomposition with a ratio (computed/global) lower than 1, using namelist_eORCA025 and output the list of domain decomposition in processor.layout_eORCA025

$ ./mpp_optimiz_zoom_nc.exe -r 1 -n namelist_eORCA025 -o processor.layout_eORCA025

 ocean/land file used is: domcfg_eORCA025.nc
 variable used to find ocean domain is: bottom_level
 Dimensions (jpi x jpj) are:  1442 x 1207

Loop over all the decompositions (can take a while) ...

STOP

The output for one specific decomposition contains this information:

 iresti= 14  irestj= 9
--> Total number of domains  1612

 jpni= 31  jpnj= 52
 jpi=  49  jpj=  26
 Number of ocean processors        1074
 Number of land processors         538
 Mean ocean coverage per domain    0.7542637596508307
 Minimum ocean coverage            7.849293761E-4
 Maximum ocean coverage            1.
 nb of proc with coverage         < 10 %  68
 nb of proc with coverage 10 < nb < 30 %  99
 nb of proc with coverage 30 < nb < 50 %  59
 Number of computed points         1368276
 Overhead of computed points       -372218
 % sup (computed / global)         0.786142349

Sorting phase

The processor.layout can be very long and hard to exploit. To sort out what is the best model decomposition for a specific application, there is a suggestion at the end of the processor.layout file. Otherwise you can use the python script find_layout.py to dig into it.

$ python2.7 find_layout.py
usage: find_layout.py [-h] -f layout_file --rmax max_ratio --noce min/max_noce

Below an example to extract all decomposition with a ratio (computed/global) < 0.8 and a number of ocean domain between 300 and 350. All the decomposition fitting the criterions are listed. At the end, a summary of the one with the smallest ratio, the largest number of ocean domains and the smallest computed domain.