Compilar WRF con GCC

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gcc compilation

<hydra> has by default intel C/Fortran compilers. However, <hydra> also has the free gcc compilers.

Here are the instructions followed to compile WRF using the gcc and gfortran compilers. In order to do that, one needs to compile all the required libraries (openmpi, zlib, curl, hdf5 and netcdf) using these compilers. No udunits was installed due to issues with cmake

Required libraries

Here the steps starting from a folder where we will download all the sources called 

/share/tools/Downloads/

These compilation steps are kept inside the file /share/tools/Downloads/compilation.inf

openmpi v3.0.0

  • getting source 
$ wget https://www.open-mpi.org/software/ompi/v3.0/downloads/openmpi-3.0.0.tar.gz
  • Decompressing 
$ tar xvfz openmpi-3.0.0.tar.gz
  • Going there 
$ cd openmpi-3.0.0
  • Creation of the folder where the libraries will be installed 
$ mkdir -p /share/tools/bin/openmpi/3.0.0/gcc
  • Configuring the compilation/installation 
$ ./configure --prefix=/share/tools/bin/openmpi/3.0.0/gcc >& run_configure.log
  • Looking for errors in run_configure.log 
grep -i error run_configure.log

If not make chain (ensuring each steps goes fine) 

$ make all >& run_make.log
$ make test >& run_make_test.log
$ make install >& run_make_install.log

For all the others libraries is similar, but paying attention to provide the right installation folder and the right location of the new compiled libraries

zlib-1.2.11 

 src: https://zlib.net/zlib-1.2.11.tar.gz
 $ ./configure --prefix=/share/tools/bin/zlib/1.2.11/gcc >& run_configure.log
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

hdf5-1.10.1 

 src: hdf5-1.10.1.tar.bz2
 $ export CPP=/usr/bin/cpp
 $ ./configure --enable-fortran --with-zlib=/share/tools/bin/zlib/1.2.11/gcc \ 
   --prefix=/share/tools/bin/hdf5/1.10.1/gcc  >& run_configure.log
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

libcurl-7.60.0 

 src: https://curl.haxx.se/download/curl-7.60.0.tar.gz
 $ ./configure --prefix=/share/tools/bin/curl/7.60.0/gcc >& run_configure.log
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

netcdf-4.5.0 

 src: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz
 $ export LDFLAGS='-L/share/tools/bin/zlib/1.2.11/gcc/lib -L/share/tools/bin/hdf5/1.10.1/gcc/lib 
   -L/share/tools/bin/curl/7.57.0/gcc/lib'
 $ export CPPFLAGS='-I/share/tools/bin/zlib/1.2.11/gcc/include -I/share/tools/bin/hdf5/1.10.1/gcc/include 
   -I/share/tools/bin/curl/7.57.0/gcc/include'
 $ ./configure --enable-netcdf-4 --prefix=/share/tools/bin/netcdf/4.5.0/gcc >& run_configure.log
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

  • Fortran interface 

 src: ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.4.tar.gz
 $ export LD_LIBRARY_PATH=-I/share/tools/bin/netcdf/4.5.0/gcc/lib:${LD_LIBRARY_PATH}
 $ export LDFLAGS='-L/share/tools/bin/zlib/1.2.11/gcc/lib -L/share/tools/bin/hdf5/1.10.1/gcc/lib 
   -L/share/tools/bin/curl/7.57.0/gcc/lib -L/share/tools/bin/netcdf/4.5.0/gcc/lib'
 $ export CPPFLAGS='-I/share/tools/bin/zlib/1.2.11/gcc/include -I/share/tools/bin/hdf5/1.10.1/gcc/include 
   -I/share/tools/bin/curl/7.57.0/gcc/include -I/share/tools/bin/netcdf/4.5.0/gcc/include'
 $ ./configure --prefix=/share/tools/bin/netcdf/4.5.0/gcc >& run_configure.log
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

Jasper

Jasper requiere librerías de JPEG. Si el make devuelve error de JPEG, instalar lo siguiente (o pedir a soporte que lo instale) 

 $ aptitude install libjpeg62-turbo-dev 


 src: http://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.29.tar.gz
 $ ./configure --prefix=/share/tools/bin/jasper/1.900.29/gcc CFLAGS=-fPIC
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

Grib 

 src: https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.27.0-Source.tar.gz
 $ ./configure --prefix=/share/tools/bin/grib/1.13.1/gcc CFLAGS=-fPIC --with-netcdf=/share/tools/bin/netcdf/4.6.1/gcc --with-jasper=/share/tools/bin/jasper/1.900.29/gcc
 $ make >& make.log
 $ make check >& make_check.log
 $ make install >& make_install.log

WRF

Folloing the same folder structure, compilation will be at 

/share/WRF/WRFV3.9.1/gfortran/[type]/WRFV3

In this case there are already two versions:

  • [dmpar]: distributed memory only
  • [dm+sm]: distributed and shared memory

The procedure is similar as in the intel case (here for dmpar) Declaring environment variables: 

$ export NETCDF='/share/tools/bin/netcdf/4.5.0/gcc'
$ export WRFIO_NCD_LARGE_FILE_SUPPORT=1

Decompressing code and renaming 

$ tar xvfz /share/WRF/WRFV3.9.1.1.TAR.gz
$ mv WRF WRFV3
$ cd WRFV3

Running configure. There might be an issue with the netcdfs. In order to do not miss the code, just remove writing permits before running configure 

$ chmod -R -w *
$ configure [choose 34: 32. (serial)  33. (smpar)  34. (dmpar)  35. (dm+sm)   GNU (gfortran/gcc)]
$ chmod -R +w *

One needs to introduce some modifications in the resultant configure.wrf. It is already done, so have a look 

$ cp /share/WRF/WRFV3.9.1/gfortran/dmpar/WRFV3/configure.ifort.dmpar.wrf configure.wrf

Compile 

$ compile em_real >& compile.log

As usual look for errors, but should be fine 

$ grep Error compile.log


Descarga de DATA para ERA-Interim

Para poder descargar la DATA necesaria para correr con el modelo hay que acceder a: https://apps.ecmwf.int/registration/ y registrarse.

Luego de realizar la confirmación y activar la cuenta es necesario ingresar y descargar una key para el usuario con el que nos registramos

Install ECMWF KEY 

   If you don't have an account, please self register at https://apps.ecmwf.int/registration/ and then go to the steps below.

   Login https://apps.ecmwf.int/auth/login/

   Retrieve you key at https://api.ecmwf.int/v1/key/

    Note that the key expires in 1 year. You will receive an email to the registered email address 1 month before the expiration date with the renewal instructions. To check the expiry date of your current key log into www.ecmwf.int, then click here.

  Copy the information in this page and paste it in the file $HOME/.ecmwfapirc

contents of $HOME/.ecmwfapirc (Unix/Linux) or %USERPROFILE%\.ecmwfapirc (Windows)

{
    "url"   : "https://api.ecmwf.int/v1",
    "key"   : "XXXXXXXXXXXXXXXXXXXXXX",
    "email" : "john.smith@example.com"
}

Install client libraries

You can install the ecmwfapi python library by running on Unix/Linux: 

sudo pip install https://software.ecmwf.int/wiki/download/attachments/56664858/ecmwf-api-client-python.tgz

Descargar data necesaria

Para descargar la data necesaria ejecutar lo siguiente: 

soporte@nimbus:/share/DATA/re-analysis/ERA-Interim$ sudo python ERAI_ECMWF_api_pl-sfc.py -y 2005 -m 03

modificando el año y el mes que se utilizan como parámetro

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