Compilar NetCDF
Instalación de Netcdf con compiladores Intel
IMPORTANTE
A partir de las versión 4.2 de netcdf. esta separado el instalador para C, C++ y Fortran. Siempre instalar primero la versión para C. Averiguar más o usar la versión 3.6.3 (en hydra está la 4.1.3 y creo que va bien)
Para instalar netcdf, primero hay que instalar
http://software.intel.com/en-us/articles/performance-tools-for-software-developers-building-netcdf-with-the-intel-compilers/
Luego descargar la última versión del netcdf para C, Fortran y C++ desde:
http://www.unidata.ucar.edu/downloads/netcdf/index.jsp
Instalar primero la versión del netcdf para C y repetir los siguientes pasos para Fortran y C++
Crear las variables de entorno para compilar netcdf
Intel nuevo (>=10.x)
unset CC CXX F77 FC F90 CPP CXXCPP CFLAGS CXXFLAGS FFLAGS export CC=icc export CXX=icpc export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' export F77=ifort export FC=ifort export F90=ifort export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' export CPP='icc -E' export CXXCPP='icpc -E'
Para incluir el HDF5 y el ZLIB (habiendo instalado previamente el ZLIB en directorio por default y el HDF5 en /usr/local/)
export CPPFLAGS="-I/usr/local/hdf5/include -I=/usr/local/include"
export LDFLAGS="-L/usr/local/hdf5/lib"
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}/usr/local/lib
Comenzamos con la instalacion:
./configure --prefix=/usr/local/netcdf-4.4.1.1 make make check make install
netcdf-fortran
Al momento de instalar el netcdf-fortran es necesario agregar a la variable de entorno LD_LIBRARY_PATH algunos datos ya que al momento de realizar el configure aparece este error:
conftest: error while loading shared libraries: libnetcdf.so.7: cannot open shared object file: No such file or directory
Verificar que datos se encuentran en dicha variable y si hace falta agregar de la siguiente forma:
[root@nautilus netcdf-fortran-4.2]# env | grep LD
LDFLAGS=-L/usr/local/hdf5/lib
OLDPWD=/root
MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic
LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4
[root@nautilus netcdf-fortran-4.2]# export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}
LDFLAGS=-L/usr/local/hdf5/lib
OLDPWD=/root
MIC_LD_LIBRARY_PATH=/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/mic
LD_LIBRARY_PATH=/usr/local/lib:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mpirt/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/../compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/ipp/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/compiler/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/intel64:/opt/intel/composer_xe_2013_sp1.2.144/tbb/lib/intel64/gcc4.4
Se puede apreciar que /usr/local/lib se encuentra agregado. Para que este cambio se mantenga en forma permanente es necesario agregar lo sgte. al /etc/profile
## Agregado para que los compiladores utilicen dicho path tambien 20140515
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}/usr/local/lib
export LD_LIBRARY_PATH
###
Para visualizar las necesidades sobre los path de las librerías al momento de instalar netcdf-fortran se puede acceder a:
http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html
Librerias dinamicas (recomendadas):
export CFLAGS='-O3 -xSSSE3 -ip -no-prec-div' export CXXFLAGS='-O3 -xSSSE3 -ip -no-prec-div' export FFLAGS='-O3 -xSSSE3 -ip -no-prec-div'
Librerias estaticas (no recomendadas):
export CFLAGS='-O3 -xSSSE3 -ip -no-prec-div -static' export CXXFLAGS='-O3 -xSSSE3 -ip -no-prec-div -static' export FFLAGS='-O3 -xSSSE3 -ip -no-prec-div -static'
Intel viejo (<10.x)
export CC=icc export CXX=icpc export CFLAGS='-O3 -xT -ip -no-prec-div -static' export CXXFLAGS='-O3 -xT -ip -no-prec-div -static' export F77=ifort export FC=ifort export F90=ifort export FFLAGS='-O3 -xT -ip -no-prec-div -static' export CPP='icc -E' export CXXCPP='icpc -E'
Portland Completo
export CC=pgcc export CFLAGS="-O2 -Msignextend -V" export FC=pgfortran export F90=pgfortran export F77=pgfortran export FFLAGS="-O2 -w -V" export CXX=pgcpp export CPPFLAGS="-DNDEBUG -DpgiFortran"
Portland simple sin C++
export CC=gcc export FC=pgf90 export FFLAGS="-O2" export CPPFLAGS="-DNDEBUG -DpgiFortran -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE"
En algunos casos para que el make check funcione es necesario exportar la variable de entorno del proxy
export http_proxy=http://proxy1.cima.fcen.uba.ar:3128/
Compilar e instalar
./configure make make check make install
+-------------------------------------------------------------+ | Congratulations! You have successfully installed the netCDF | | Fortran libraries. | | | | You can use script "nf-config" to find out the relevant | | compiler options to build your application. Enter | | | | nf-config --help | | | | for additional information. | | | | CAUTION: | | | | If you have not already run "make check", then we strongly | | recommend you do so. It does not take very long. | | | | Before using netCDF to store important data, test your | | build with "make check". | | | | NetCDF is tested nightly on many platforms at Unidata | | but your platform is probably different in some ways. | | | | If any tests fail, please see the netCDF web site: | | http://www.unidata.ucar.edu/software/netcdf/ | | | | NetCDF is developed and maintained at the Unidata Program | | Center. Unidata provides a broad array of data and software | | tools for use in geoscience education and research. | | http://www.unidata.ucar.edu | +-------------------------------------------------------------+
+-------------------------------------------------------------+ | Congratulations! You have successfully installed the netCDF | | C++ Libaray | | | | CAUTION: | | | | If you have not already run "make check", then we strongly | | recommend you do so. It does not take very long. | | | | Before using netCDF to store important data, test your | | build with "make check". | | | | NetCDF is tested nightly on many platforms at Unidata | | but your platform is probably different in some ways. | | | | If any tests fail, please see the netCDF web site: | | http://www.unidata.ucar.edu/software/netcdf/ | | | | NetCDF is developed and maintained at the Unidata Program | | Center. Unidata provides a broad array of data and software | | tools for use in geoscience education and research. | | http://www.unidata.ucar.edu | +-------------------------------------------------------------+
