[MITgcm-support] Correct Options File NetCDF Configuration

Phil Underwood p.underwood at uea.ac.uk
Wed Jun 23 13:07:02 EDT 2010


Hi Jean-Michel,

Thank you for getting back to me. I did as you suggested, although it isn't immediately clear to me if I've made the correct amendments to the options file. I've attached a copy of the 'linux_ia32_g77' options file I modified based on the one in the tools/build_options directory. My selection of that file as the foundation was based on the platform, instruction set and compiler of the target system I am working with. I have changed the include and lib paths to match those of the NetCDF installation on the target machine, yet I am still receiving the error.

You'll noticed I have not changed the path name in the if comparison lines as I do not know what the comparison is for. Is this where the problem lies?

Cheers,
Phil

P.S. Incase your servers reject attachments I also include a text version of the file:

#


FC=g77
CC=gcc
DEFINES='-D_BYTESWAPIO -DWORDLENGTH=4'
# CPP='gcc -E -traditional -P -'
CPP='cpp  -traditional -P'
NOOPTFLAGS='-O0'
EXTENDED_SRC_FLAG='-ffixed-line-length-132'

if test "x$IEEE" = x ; then
    #  No need for IEEE-754
    FFLAGS='-Wimplicit -Wunused -Wuninitialized'
    FOPTIM='-O3 -malign-double -funroll-loops'
else
    #  Try to follow IEEE-754
    has_sse2=f
    grep flags /proc/cpuinfo | grep sse2 > /dev/null 2>&1  &&  has_sse2=t

    if test "x$has_sse2" = xt ; then
        FFLAGS='-Wimplicit -Wunused -mfpmath=sse -msse -msse2'
    else
        FFLAGS='-Wimplicit -Wunused -ffloat-store'
    fi
    #  echo 'FFLAGS="'$FFLAGS'"'
    FOPTIM='-O0 -malign-double'
fi

if test -d /usr/include/netcdf-3 ; then
    INCLUDES='-I/cvos/apps/netcdf-4.0.ifc/include'
    if test -d /usr/lib/netcdf-3 ; then
        if test -f /usr/lib/netcdf-3/libnetcdf_g77.a ; then
            LIBS='-L/cvos/apps/netcdf-4.0.ifc/lib -lnetcdf_g77'
        else
            LIBS='-L/cvos/apps/netcdf-4.0.ifc/lib'
        fi
    fi
elif test -d /usr/include/netcdf ; then
    INCLUDES='-I/cvos/apps/netcdf-4.0.ifc/include'
elif test -d /usr/local/netcdf ; then
    INCLUDES='-I/cvos/apps/netcdf-4.0.ifc/include'
    LIBS='-L/cvos/apps/netcdf-4.0.ifc/lib'
fi
GSLINC=''
GSLLIB='-lgsl -lgslcblas'
PAPIINC='-I/usr/local/pkg/papi/papi-3.0.8.1/p4/include'
PAPILIB='-L/usr/local/pkg/papi/papi-3.0.8.1/p4/lib -lpapi'


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On 23 Jun 2010, at 17:00, mitgcm-support-request at mitgcm.org wrote:

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> Today's Topics:
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>   1. Re: [MITgcm Manual] section 6.15 NetCDF	I/O	Integration: MNC
>      (Jean-Michel Campin)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 23 Jun 2010 07:52:41 -0400
> From: Jean-Michel Campin <jmc at ocean.mit.edu>
> To: mitgcm-support at mitgcm.org
> Subject: Re: [MITgcm-support] [MITgcm Manual] section 6.15 NetCDF	I/O
> 	Integration: MNC
> Message-ID: <20100623115241.GA11739 at ocean.mit.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Phil,
> 
> Just 2 commnets:
> 1) Some of the documentation links you are pointed to are from
>  the Release-1 version:
>> http://mitgcm.org/public/sealion/
>  Probably better to look at the latest version:
>> http://mitgcm.org/public/r2_manual/latest/
>  (more recent but not fully up-to-date neither).
> 2) The "WARNING" you are getting are related to failure in compiling/link
>  NetCDF code/library. 
>  When you run "genmake2", there are several tests to check if we have the
>  right things set-up to compile and run with NetCDF. If this step is not
>  successful, then ALLOW_MNC is disable and if you try to run with
>  useMNC=T (data.pkg) you will get this warning message.
>  To fix this, I would recommand to check the optfile you are using for 
>  this platform (and to speed-up this task, you can probably figure out
>   whether this works or  not just by running "genmake2").
> 
> Cheers,
> Jean-Michel
> 
> On Wed, Jun 23, 2010 at 11:55:31AM +0100, Phil Underwood wrote:
>> Comments and questions on page http://mitgcm.org/sealion/online_documents/node229.html
>> 
>> Hi there,
>> 
>> I am currently working on completion of the biogeochemistry tutorial (http://mitgcm.org/public/r2_manual/latest/online_documents/node155.html) and am amending the path names for the "c62g" release of the MITgcm. I have built a test script in order to submit the job to a Sun Grid Engine running on the parallel computing cluster here at my University. Every time the job is completed I get an output file from the system containing the following text:
>> 
>> ***WARNING*** PACKAGES_CHECK: useMNC is TRUE
>> ***WARNING*** but pkg/mnc has not been compiled (#undef ALLOW_MNC)
>> STOP NORMAL END statement executed
>> 
>> This is irrespective of whether the MITgcm is compiled with the -enable=mnc or -disable=mnc switches. I have also commented out #mnc in the "packages.conf" file within the "/MITgcm_c62g/verification/tutorial_dic_adjoffline/code_ad" directory. 
>> 
>> I imagine I would like to use MNC since I am under the impression that using NetCDF is likely to make the process of using the model output quicker. Can you tell me how I can get rid of that warning and exactly what I should in order to get the MITgcm running as I would like.
>> 
>> Regards,
>> Phil
>> 
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
> 
> 
> 
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