Here an overview of the applications currently ported in the GRID environment is presented.

User Guides for the application porting for specific applications will be ready as soon as possible.

Installation and porting guides

The following best practices document aims to provide some hints and examples on how to configure and compile some Earth Science related applications on a grid based infrastructure.

NEMO

Application description

NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for oceanographic research, operational oceanography seasonal forecast and climate studies. NEMO includes:

- 5 major components

  • the blue ocean (ocean dynamics, NEMO-OPA);
  • the white ocean (sea-ice, NEMO-LIM);
  • the green ocean (biogeochemistry, NEMO-TOP) ;
  • the adaptative mesh refinement software (AGRIF) ;
  • the assimilation component NEMO_TAM;

- some reference configurations allowing to set-up and validate the applications ;

- a set of scripts and tools (including pre- and post-processing) to use the system.

NEMO is used by a large community: 240 projects in 27 countries (14 in Europe, 13 elsewhere), 350 registered users (numbers for year 2008). See NEMO webpage

NEMO is available under the CeCILL license (public license).

NEMO_3.4

How to compile

Requirements:

  1. FORTRAN90 compliant compiler. Compiler used: native gfortran44;
  2. MPI libraries COMPILED for the architecture and the compiler used. MPI library used: openmpi-1.4.5 (mpich2-1.4.1) gfortran44 static compiled.
  3. NETCDF libraries. NETCDF used: netcdf-4.0.1 gfortran44 compiled

Due to compatibility problems, the code (at present) has to be compiled statically if gfortran44 is not present in the WN(s). Contact your Admin if the needed software is missing or not available.

A. Download or copy the tar file of NEMO package in a machine with at least EMI1 middleware installed, untar it in an appropriate sub-directory.

B. Follow the instructions provided in the website making sure to modify the specific target architecture (configuration) file in the right way as following:

#cat /home/User/NEMO/oofs02/NEMO_3.4/nemo/NEMOGCM/ARCH/ arch-grid.fcm
%NCDF_INC            -I/opt/netcdf-4.0.1-gfortran44/include
%NCDF_LIB            -L/opt/netcdf-4.0.1-gfortran44/lib -lnetcdf
%FC                  /opt/openmpi-1.4.5-gfortran44/bin/mpif90
%FCFLAGS             -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer
%FFLAGS              %FCFLAGS
%LD                  /opt/openmpi-1.4.5-gfortran44/bin/mpif90
%LDFLAGS             -static-libgfortran
%FPPFLAGS            -P -C -traditional
%AR                  ar
%ARFLAGS             -rs
%MK                  gmake
%USER_INC            %NCDF_INC
%USER_LIB            %NCDF_LIB

You can use the executable and submit it to the GRID environment.

Parallel execution

For specific requirements ask the IGI Support Unit.

GLOBO

-- DanieleCesini - 2012-11-16

Topic revision: r2 - 2012-12-13 - EmidioGiorgio
 
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