[MITgcm-support] netcdf

Sun Dec 22 09:20:19 EST 2013

Hi Dear
Mr Gus Correa ,thank you .
But I do not know where the file of opt  should specify the path to netcdf.
please link netcdf for centose 6?
Please note the installation instructions netcdf?
I have not done much at all with Linux
thank you

On Thu, Dec 19, 2013 at 3:22 PM, Gus Correa <gus at ldeo.columbia.edu> wrote:

> 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
>> @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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>
>
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