[MITgcm-support] netcdf

[Gus Correa]

Hi Mohammad

Besides Martin's suggestion of installing from source,
you can also install NetCDF on CentOS 6 using yum and RPM packages.
You can get NetCDF (4.1.1) from the EPEL repository:

https://fedoraproject.org/wiki/EPEL?rd=Epel

First install the EPEL package (make sure to get the CentOS 6 version):

https://fedoraproject.org/wiki/EPEL/FAQ#How_can_I_install_the_packages_from_the_EPEL_software_repository.3F

Then you you can install the netcdf and netcdf-devel packages
(64-bit, if that is what you have, or change x86_64 to i686 if your 
machine is 32-bit ):

# yum install netcdf.x86_64 netcdf-devel.x86_64

I hope this helps,
Gus Correa

On 12/19/2013 07:51 AM, Martin Losch wrote:
> Mohammad,
>
> please have a look at the official netcdf web-site<http://www.unidata.ucar.edu/software/netcdf/>
>
> Ofter there are example builds that you can start from, if you cannot find any instructions for your platform.
>
> BTW: the MITgcm also works without netcdf output. The “mds”-output (pairs of *.data and *.meta files) is an ieee big endian unblocked format and can be easily read into matlab (rdmds in utils/matlab) or python (rdmds in utils/python/MITgcmutils). In general the format is not complicated so you should be able to convince many plotting and post processing tools to read the data
>
> Martin
>
> On Dec 10, 2013, at 4:57 AM, mohammad akbarinasab<akbarinasabmohamad at gmail.com>  wrote:
>
>> Dear MITGCM users
>> I Install mitgcm on CentOS-6.5
>> How I can install NETCDF on CentOS-6.5,
>> Please show me website NETCDF files
>> how I can find path netcdf at CentOS-6.5?
>> Where do I put the file path in opt file
>> (NETCDF )?
>>
>> Meanwhile opt file
>> #!/bin/bash
>>
>> #
>>
>> # $Header: /u/gcmpack/MITgcm/tools/build_options/linux_amd64_gfortran+mpi_generic,v 1.2 2010/12/25 18:25:56 jmc Exp $
>>
>> # $Name: checkpoint63 $
>>
>> #
>>
>> # Tested with gcc-gfortran v4.1.x on FC5, FC6, FC8, using flags
>>
>> # formally for gcc-gfortran 4.3*
>>
>> # + with gcc-gfortran v4.3.x on FC9, FC10
>>
>> # + with gcc-gfortran v4.4.x on FC11,FC12,FC13
>>
>> #
>>
>> # on baudelaire.csail.mit.edu (FC13), uses:
>>
>> # export MPI_GCC_DIR=/srv/software/gcc/gcc-packages/gcc-4.4.5/mpich2/mpich2-1.3
>>
>> # export MPI_INC_DIR=$MPI_GCC_DIR/include
>>
>> # export PATH=$MPI_GCC_DIR/bin:$PATH
>>
>> #
>>
>> #-------
>>
>> # run with OpenMP: needs to set environment var. OMP_NUM_THREADS
>>
>> # and generally, needs to increase the thread stack-size:
>>
>> # - sh,bash:
>>
>> #>  export OMP_NUM_THREADS=2
>>
>> #>  export GOMP_STACKSIZE=400m
>>
>> # - csh,tcsh:
>>
>> #>  setenv OMP_NUM_THREADS 2
>>
>> #>  setenv GOMP_STACKSIZE 400m
>>
>> #-------
>>
>> FC=${FC:=mpif77}
>>
>> F90C=${F90C:=mpif90}
>>
>> CC=${CC:=mpicc}
>>
>> DEFINES='-DWORDLENGTH=4 -DNML_TERMINATOR'
>>
>> CPP='cpp -traditional -P'
>>
>> EXTENDED_SRC_FLAG='-ffixed-line-length-132'
>>
>> GET_FC_VERSION="--version"
>>
>> OMPFLAG='-fopenmp'
>>
>> NOOPTFLAGS='-O0'
>>
>> MPI='true'
>>
>> INCLUDEDIRS='/usr/local/include'
>>
>> LIBDIRS='/usr/local/lib/'
>>
>> if test "x$DEVEL" != x ; then
>>
>> FFLAGS='-g -Wall -W -ffpe-trap=invalid,zero,overflow -fbounds-check'
>>
>> else
>>
>> FFLAGS=''
>>
>> fi
>>
>> # Requires gfortran from 2006 onwards for -fconvert=big-endian
>>
>> FFLAGS="$FFLAGS -fconvert=big-endian -fimplicit-none"
>>
>> # for big objects:
>>
>> FFLAGS="$FFLAGS -fPIC"
>>
>> if test "x$IEEE" = x ; then
>>
>> # No need for IEEE-754
>>
>> FOPTIM='-O3 -funroll-loops'
>>
>> CFLAGS="$FOPTIM -fPIC"
>>
>> else
>>
>> # Try to follow IEEE-754
>>
>> FFLAGS="$FFLAGS -Waliasing -Wampersand -Wsurprising -Wline-truncation"
>>
>> FOPTIM='-O0'
>>
>> CFLAGS="$FOPTIM -fPIC"
>>
>> # to get plenty of warnings :
>>
>> # FFLAGS="$FFLAGS -Wconversion -Wimplicit-interface -Wunused-labels"
>>
>> # more checking (to use with testreport, put DEVEL option in IEEE section):
>>
>> # FOPTIM="$FOPTIM -g -ffpe-trap=invalid,zero,overflow -fbounds-check"
>>
>> fi
>>
>> F90FLAGS=$FFLAGS
>>
>> F90OPTIM=$FOPTIM
>>
>> if [ "x$NETCDF_ROOT" != x ] ; then
>>
>> INCLUDEDIR="${NETCDF_ROOT}/include"
>>
>> INCLUDES="-I${NETCDF_ROOT}/include"
>>
>> LIBDIR="${NETCDF_ROOT}/lib"
>>
>> LIBS="-L${NETCDF_ROOT}/lib"
>>
>> elif [ "x$NETCDF_HOME" != x ]; then
>>
>> INCLUDEDIR="${NETCDF_HOME}/include"
>>
>> INCLUDES="-I${NETCDF_HOME}/include"
>>
>> LIBDIR="${NETCDF_HOME}/lib"
>>
>> LIBS="-L${NETCDF_HOME}/lib"
>>
>> elif [ "x$NETCDF_INC" != x -a "x$NETCDF_LIB" != x ]; then
>>
>> NETCDF_INC=`echo $NETCDF_INC | sed 's/-I//g'`
>>
>> NETCDF_LIB=`echo $NETCDF_LIB | sed 's/-L//g'`
>>
>> INCLUDEDIR="${NETCDF_INC}"
>>
>> INCLUDES="-I${NETCDF_INC}"
>>
>> LIBDIR="${NETCDF_LIB}"
>>
>> LIBS="-L${NETCDF_LIB}"
>>
>> elif [ "x$NETCDF_INCDIR" != x -a "x$NETCDF_LIBDIR" != x ]; then
>>
>> INCLUDEDIR="${NETCDF_INCDIR}"
>>
>> INCLUDES="-I${NETCDF_INCDIR}"
>>
>> LIBDIR="${NETCDF_LIBDIR}"
>>
>> LIBS="-L${NETCDF_LIBDIR}"
>>
>> elif test -d /usr/include/netcdf-3 ; then
>>
>> INCLUDES='-I/usr/include/netcdf-3'
>>
>> LIBS='-L/usr/lib/netcdf-3 -L/usr/lib64/netcdf-3'
>>
>> elif test -d /usr/local/netcdf ; then
>>
>> INCLUDES='-I/usr/local/netcdf'
>>
>> elif test -d /usr/local/netcdf ; then
>>
>> INCLUDES='-I/usr/local/netcdf/include'
>>
>> LIBS='-L/usr/local/netcdf/lib'
>>
>> elif test -d /usr/local/include/netcdf.inc ; then
>>
>> INCLUDES='-I/usr/local/include'
>>
>> LIBS='-L/usr/local/lib64'
>>
>> fi
>>
>> MPI_HEADER_FILES='mpif.h mpif-mpi-io.h'
>>
>> MPI_HEADER_FILES_INC='/usr/local/include/mpif.h /usr/local/include/mpif-mpi-io.h'
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
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