[MITgcm-support] No output every 4th depth

[Martin Losch]

Hi Mari,

when I get zeros, I usually forgot that the a bathymetry file needs to contain only negative values (and zero).

Martin

> On 16. Nov 2018, at 11:24, Mari Fjalstad Jensen <Mari.F.Jensen at uib.no> wrote:
> 
> Hi again Martin (or others),
> I was a bit quick yesterday, sorry, I only checked one grid cell which looked good.
> However, now I am not able to read the bathymetry-input correctly anymore, and I get zeros at the surface too.
> 
> I added -assume byterecl to the build-options so that it now looks like:
> 
> FC=mpiifort
> CC=mpiicc
> LINK=$FC
> DEFINES='-DWORDLENGTH=4'
> CPP='cpp  -traditional -P'
> NOOPTFLAGS='-O0'
> INCLUDES="-I${NETCDF_DIR}/include -I/opt/cray/mpt/7.1.2/gni/mpich2-pgi/141/include"
> 
> # NetCDF not in use at this time
>    FFLAGS=" -g -r8 -extend_source 132 -convert big_endian -assume byterecl"
>    FOPTIM="-pc=64 -O2"
> 
> Any other guesses? I
> Mari
> 
> On 15/11/2018 17.26, Mari Fjalstad Jensen wrote:
>> Hi Martin,
>> That was a great wild guess; it worked! Thanks a lot!
>> Mari
>> 
>> Den 2018-11-15 12:27 skreiv Martin Losch:
>>> Hi Mari,
>>> 
>>> this is a wild guess: In my intel (ifort) opt files, I always have the
>>> combination of “FFLAGS=$FFLAGS -assume byterecl” with
>>> "DEFINES='-DWORDLENGTH=4’"
>>> 
>>> btw, you don’t need '-DALLOW_USE_MPI -DALWAYS_USE_MPI’, you just need
>>> to specify "genmake2 -mpi”
>>> 
>>> Martin
>>> 
>>>> On 14. Nov 2018, at 22:32, Mari Fjalstad Jensen <Mari.F.Jensen at uib.no> wrote:
>>>> 
>>>> Dear all,
>>>> I've recently moved an existing setup with MITgcm to a new machine. I got the model up and running, and the surface ouput looks reasonable, but I only get ouput at every forth depth. The problem is already in setting up the grid. dRC etc looks fine, but hFacC and similar has a zero at every forth depth.
>>>> The depth.data-output looks like the bathymetry input I give it, so I don't think there is a problem with reading input files. SIZE.h looks correct too.
>>>> I use the same data-file and input as in a previous setup on a different machine, which works fine. Anyway, I've pasted in the data-file, and the build-options (which is what is changed from the other machine)
>>>> Anyone know what the problem could be?
>>>> 
>>>> Thanks for any advice!
>>>> Mari
>>>> 
>>>> build options:
>>>> 
>>>> FC=mpiifort
>>>> CC=mpiicc
>>>> LINK=$FC
>>>> DEFINES='-DWORDLENGTH=4 -DALLOW_USE_MPI -DALWAYS_USE_MPI'
>>>> CPP='cpp  -traditional -P'
>>>> NOOPTFLAGS='-O0'
>>>> INCLUDES="-I${NETCDF_DIR}/include -I/opt/cray/mpt/7.1.2/gni/mpich2-pgi/141/include"
>>>> 
>>>> # NetCDF not in use at this time
>>>>    FFLAGS=" -g -r8 -extend_source 132 -convert big_endian"
>>>>    FOPTIM="-pc=64 -O2"
>>>> 
>>>> 
>>>> data:
>>>> 
>>>> # Continuous equation parameters
>>>> &PARM01
>>>> tRef=30*6.0,
>>>> sRef=30*35.0,
>>>> viscAz=1.E-5,
>>>> # viscAh=20.,
>>>> # viscA4=1.e+9,
>>>> viscC2Smag=2.5,
>>>> no_slip_sides=.TRUE.,
>>>> no_slip_bottom=.TRUE.,
>>>> # diffK4T=1.e+9,
>>>> # diffKhT=30.,
>>>> diffKzT=1.E-5,
>>>> # diffK4S=1.e+9,
>>>> # diffKhS=30.,
>>>> diffKzS=1.E-5,
>>>> f0=1.2e-4,
>>>> beta=0.0E-11,
>>>> tAlpha=0.2E-3,
>>>> sBeta =0.8E-3,
>>>> rigidLid=.FALSE.,
>>>> implicitFreeSurface=.TRUE.,
>>>> staggerTimeStep=.TRUE.,
>>>> eosType='JMD95Z',
>>>> readBinaryPrec=32,
>>>> hFacMin=0.1,
>>>> bottomDragQuadratic=1.e-3,
>>>> implicitDiffusion=.TRUE.,
>>>> implicitViscosity=.TRUE.,
>>>> tempAdvScheme=33,
>>>> saltAdvScheme=33,
>>>> useSingleCpuIO=.TRUE.,
>>>> # vectorInvariantMomentum=.TRUE.,
>>>> ivdc_kappa=1000.0,
>>>> &
>>>> # Elliptic solver parameters
>>>> &PARM02
>>>> cg2dMaxIters=1000,
>>>> cg2dTargetResidual=1.E-11,
>>>> &
>>>> # Time stepping parameters
>>>> &PARM03
>>>> tauCD=0.,
>>>> nIter0=0.,
>>>> nTimeSteps=233280000,
>>>> # startTime=0.0,
>>>> # startTime=235872000,
>>>> # endTime=11.664e+8,
>>>> # endTime=3.1104e+7,
>>>> deltaT=400.0,
>>>> abEps=0.1,
>>>> pChkptFreq=0.0,
>>>> chkptFreq=31104000,
>>>> dumpFreq=2592000,
>>>> monitorFreq=2592000,
>>>> cAdjFreq=0,
>>>> forcing_In_AB=.FALSE.,
>>>> tauThetaClimRelax=0.0,
>>>> &
>>>> # Gridding parameters
>>>> &PARM04
>>>> usingCartesianGrid=.TRUE.,
>>>> usingSphericalPolarGrid=.FALSE.,
>>>> dXspacing=5.e+3,
>>>> dYspacing=5.e+3,
>>>> delZ=20*50,10*100,
>>>> &
>>>> &PARM05
>>>> checkIniTemp=.false.,
>>>> bathyFile='topog.bin',
>>>> &
>>>> 
>>>> 
>>>> 
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>>>> MITgcm-support at mitgcm.org
>>>> http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support
>>> 
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