[MITgcm-support] problem reading binary grid file ...
Ufuk Turuncoglu
ufuk.turuncoglu at itu.edu.tr
Fri Apr 22 08:21:15 EDT 2016
Yes. You are right, it solved the problem. Simple but very efficient
information. Some models uses positive and some others negative. It is
hard to follow conventions. Anyway, thanks again.
Regards,
--ufuk
On 22/04/16 15:13, Dimitris Menemenlis wrote:
> maybe you get zeros because you are specifying bathymetry with
> positive instead of negative numbers?
>
> On 04/22/2016 04:00 AM, Ufuk Turuncoglu wrote:
>> Hi,
>>
>> I am trying to create a grid file in binary format using python. In this
>> case, the script is very simple and it writes numpy array using
>> following command in big-endian format,
>>
>> var.astype('>f4').tofile('BATHY_BS.data')
>>
>> Then i am running MITgcm and it produces intermediate files such as
>> Depth.data etc. Then, if i check the Depth.data using following NCL
>> script,
>>
>> begin
>> ;--- parameters ---
>> endian = "BigEndian"
>> nlat = 280 ;264 ;280
>> nlon = 466 ;;570 ;466
>>
>> ;--- set file option ---
>> setfileoption("bin", "ReadByteOrder", endian)
>>
>> ;--- read bathymetry ---
>> h = fbindirread("Depth.data", 0, (/ nlat, nlon /), "float")
>>
>> ;--- plot data ---
>> wks = gsn_open_wks ("newpdf", "check")
>> gsn_define_colormap (wks, "matlab_jet")
>> i = NhlNewColor(wks,0.8,0.8,0.8)
>>
>> ;--- define plot resource ---
>> res = True
>> res at gsnAddCyclic = False
>> res at gsnFrame = False
>> res at gsnLeftString = ""
>> res at gsnRightString = ""
>> res at gsnSpreadColors = True
>> res at gsnSpreadColorEnd = -3
>> res at cnFillOn = True
>> res at cnFillMode = "RasterFill"
>> res at cnInfoLabelOn = False
>> res at cnLinesOn = False
>> res at cnLineLabelsOn = False
>> res at lbLabelBarOn = False
>> res at pmTickMarkDisplayMode = "Always"
>> res at tiXAxisFontHeightF = 0.008
>> res at tiYAxisFontHeightF = 0.008
>> res at tmXBLabelFontHeightF = 0.008
>> res at tmYLLabelFontHeightF = 0.008
>>
>> plot = gsn_csm_contour(wks, h, res)
>> draw(plot)
>> frame(wks)
>> end
>>
>> The output seems wrong and i could not see the correct data and plot
>> have full of zeros. First i thought that it is an issue related with the
>> Python and binary data file but the same NCL script could read other
>> data files (i.e. DXC.data - the delx, dely and delz are provided in data
>> file) generated by MITgcm and BATHY_BS.data file produced by Python
>> script without any problem. As i know that the binary files must be
>> written using single record direct access and the Python script must
>> work at this point. I think that MITgcm could not read Python generated
>> file correctly but i don't know why. Anyway, do you have similar
>> experience? Any suggestion could be helpful. I also try to generate grid
>> data using Fortran but the result is same. You can find the content of
>> my config file to install MITgcm.
>>
>> Regards,
>>
>> --ufuk
>>
>> #!/bin/bash
>> #
>> # $Header: /u/gcmpack/MITgcm/tools/build_options/linux_amd64_ifort11,v
>> 1.6 2011/07/07 22:58:36 jmc Exp $
>> # $Name: checkpoint63a $
>> #
>> # Constantinos Evangelinos
>> #
>> # Build options for the intel 11 & 12 fortran compiler
>> #
>> # Tested on baudelaire (FC 13) with intel compiler v.11.1.073
>> (20100806)
>>
>> # OpenMP : tested on danton (FC 14) using intel compiler v.11.1.046
>> (20090630)
>> # and also v.12.0.4
>> (20110427)
>>
>> #-------
>> # run with OpenMP: needs to set environment var. OMP_NUM_THREADS
>> # and generally, needs to increase the stack-size:
>> # - sh,bash:
>> # > export OMP_NUM_THREADS=2
>> # > export KMP_STACKSIZE=400m
>> # - csh,tcsh:
>> # > setenv OMP_NUM_THREADS 2
>> # > setenv KMP_STACKSIZE 400m
>> #-------
>>
>> FC=mpif90
>> F90C=mpif90
>> CC=icc
>> LINK=mpif90
>>
>> DEFINES='-DWORDLENGTH=4'
>> CPP='cpp -traditional -P'
>> F90FIXEDFORMAT='-fixed -Tf'
>> EXTENDED_SRC_FLAG='-132'
>> GET_FC_VERSION="--version"
>> OMPFLAG='-openmp'
>>
>> NOOPTFLAGS='-O3 -g -fp-model strict'
>> NOOPTFILES=''
>>
>> INCLUDEDIRS=''
>> INCLUDES=''
>> LIBS=''
>>
>> if test "x$GENERIC" != x ; then
>> PROCF=-axSSE4.2,SSE4.1,SSSE3,SSE3,SSE2
>> else
>> PROCF=-xHost
>> fi
>>
>> #FFLAGS="$FFLAGS -m64 -fPIC -convert big_endian -assume byterecl
>> -mcmodel=large"
>> FFLAGS="$FFLAGS -m64 -convert big_endian -assume byterecl -mcmodel large
>> -shared-intel"
>> #FFLAGS="$FFLAGS -m64 -assume byterecl -mcmodel large -shared-intel"
>>
>> #- might want to use '-r8' for fizhi pkg:
>> #FFLAGS="$FFLAGS -r8"
>>
>> if test "x$IEEE" = x ; then #- with optimisation:
>> FOPTIM="-O3 -fp-model strict -align -ip -opt-streaming-stores auto
>> $PROCF -extend_source"
>> else
>> if test "x$DEVEL" = x ; then #- no optimisation + IEEE :
>> FOPTIM="-O3 -fp-model strict -fp-model source -noalign $PROCF
>> -extend_source"
>> else #- development/check options:
>> #FFLAGS="$FFLAGS -debug all -debug-parameters all -fp-model strict"
>> FFLAGS="$FFLAGS -warn all -warn nounused"
>> FOPTIM="-fpe0 -ftz -fp-stack-check -check all -ftrapuv"
>> FOPTIM="$FOPTIM -O3 -fp-model strict -noalign -g -traceback
>> $PROCF"
>> fi
>> fi
>>
>> F90FLAGS=$FFLAGS
>> F90OPTIM=$FOPTIM
>> CFLAGS="-O3 -fp-model strict -ip -m64 -mcmodel large -shared-intel
>> $PROCF"
>>
>> #LIBS='-lmpi -L /opt/netcdf/4.1.2/intel/2011/lib -lnetcdf'
>> LIBS='-lmpi -L /RS/progs/netcdf/4.3.1.1/intel/lib -lnetcdf'
>> #LIBS='-lmpi -L/afs/enea.it/fra/user/sannino2/netcdf-4.1.3/GM/lib
>> -lnetcdf'
>> #INCLUDES='-I/opt//openmpi/1.5.3/intel/2011/include/
>> -I/opt/netcdf/4.1.2/intel/2011/include/'
>> INCLUDES='-I/RS/progs/openmpi/1.10.1/intel/include/
>> -I/RS/progs/netcdf/4.3.1.1/intel/include/'
>>
>>
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>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
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