[Wrf-users] Problems with NetCDF Large File Support with geogrid.exe

[Klemens Barfus]

Hi Dom,

many thanks for your help ! The size of individual variables seems to 
have been the problem ('seems' because new output files written in 
NetCDF4 format are much smaller than the same files in NetCDF3 so that 
one could circumvent unconsciously a potential file size limit with this 
solution). I should have read the Unidata NetCDF large file support more 
carefully. Changing to NetCDF4 solved the problem.

Cheers,

Klemens

Dominikus Heinzeller schrieb:
> Hi Klemens,
>
> I am not entirely sure, but: The classical netCDF file format imposes 
> a limit of 4GB on individual variables. With 4000x2500 grid columns 
> (10 million), you are probably facing this problem for the 3D 
> variables. The MPAS website https://mpas-dev.github.io 
> (MPAS-Atmosphere Download -> MPAS-Atmosphere meshes) describes this 
> problem briefly for the 10km mesh with 6 million cells (and three 
> times as many edges).
>
> Can you try to use the NetCDF4 format and see if the problem goes 
> away? NetCDF4 usage is activated by setting the environment variable 
> NETCDF4 to 1 before running ./configure and compiling the model 
> (http://www2.mmm.ucar.edu/wrf/users/docs/user_guide_V3/users_guide_chap5.htm#_Installing_WRF). 
> Make sure to do a ./clean -a beforehand.
>
> Cheers,
>
> Dom
>
>> On 30/04/2017, at 11:52 AM, Klemens Barfus 
>> <klemens.barfus at tu-dresden.de <mailto:klemens.barfus at tu-dresden.de>> 
>> wrote:
>>
>> Dear all,
>>
>> I am working with WRF3.8.1 on the supercomputer of our university and 
>> have problems writing files larger than 2.2 GB from geogrid.exe (may 
>> be from other routines, too).
>> Large file support has been enabled by setting 
>> WRFIO_NCD_LARGE_FILE_SUPPORT to 1. Running geogrid.exe for 4 nested 
>> domains geo_em.d<>.nc for the first three domains are written 
>> properly as '64-bit offset', so I expect that 
>> WRFIO_NCD_LARGE_FILE_SUPPORT is recognized. Errror Message for the 
>> last domain (~4000*2500 gridpoints) is
>>
>> Processing domain 4 of 4
>>   Processing XLAT and XLONG
>> ERROR: Error in ext_pkg_write_commit
>>
>> There are no limitations on the file size in our system (tested as 
>> suggested from 
>> https://www.unidata.ucar.edu/software/netcdf/faq-lfs.html). I run 
>> geogrid.exe with 30GB memory of each CPU to avoid problems due to 
>> insufficient memory.
>>
>> WRF and WPS have been compiled with the following libraries for 
>> application in distributed memory mode:
>>
>> 8) GCCcore/5.3.0
>> 9) binutils/2.26-GCCcore-5.3.0
>> 10) icc/2016.3.210-GCC-5.3.0-2.26
>> 11) ifort/2016.3.210-GCC-5.3.0-2.26
>> 12) iccifort/2016.3.210-GCC-5.3.0-2.26
>> 13) impi/5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26
>> 14) iimpi/2016.03-GCC-5.3.0-2.26
>> 15) imkl/11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26
>> 16) intel/2016.03-GCC-5.3
>> 17) JasPer/1.900.1-intel-2016.03-GCC-5.3
>> 18) zlib/1.2.8-intel-2016.03-GCC-5.3
>> 19) Szip/2.1-intel-2016.03-GCC-5.3
>> 20) HDF5/1.8.16-intel-2016.03-GCC-5.3
>> 21) cURL/7.47.0-intel-2016.03-GCC-5.3
>> 22) netCDF/4.4.0-intel-2016.03-GCC-5.3
>> 23) netCDF-Fortran/4.4.3-intel-2016.03-GCC-5.3
>>
>> Does anybody has an idea, what could be the problem ? Any help is 
>> greatly appreciated !
>>
>> Many thanks for your help in advance !
>>
>> Klemens
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