[ncl-talk] Issues with ESMF_regrid

[Laura Fowler]

Hi Rick:

Thank you for looking into this. The newer mesh I am trying to regrid
has 6488066 cells while the mesh I regridded a couple of years ago had
more cells (6848514). So I did not think that it was the size of the
mesh that was the culprit.

Here is what I found:

1. Using the largest mesh (6848514 cells) and on yellowstone, I tested
the regrid script I used a couple of years ago using ncl/6.3.0 and
ncl/6.4.0. I did not have any issue. You can look at the source,
destination, and weight files in the directories
/glade2/scratch2/laura/ncl/yellowstone.ncl-6.3.0 and
/glade2/scratch2/laura/ncl/yellowstone.ncl-6.4.0. The ncl script is
regrid.to_CMORPHdata.ncl


2. Then, I tested the same script but on cheyenne and I got the same
SIGSEGV using ncl/6.4.0 or ncl/6.3.0. So it seems that it may have to
do with ncl on cheyenne only.


3. Unfortunately, I cannot use yellowstone to regrid my newest mesh
since it is uses the cdf5 format which I cannot read on yellowstone.


Hope that this helps to resolve this issue.
Laura







On Tue, Oct 24, 2017 at 4:19 PM, Rick Brownrigg <brownrig at ucar.edu> wrote:
> Just to follow up on this, the message regarding max-value-size is related
> to the debugger, so fixed limits within the ESMF software are likely not the
> issue.
>
> Nonetheless, the SEGV is occuring in the ESMF software and appears to be
> happening in the NetCDF library, function
> netcdf_expanded.f90::nf90_get_var_2d_fourbyteint().   For anyone else
> looking into this, the line number is 1960, and a link to the current source
> is:
>
> https://github.com/Unidata/netcdf-fortran/blob/master/fortran/netcdf_expanded.f90
>
> (I don't know what version of NetCDF ESMF may be linked against, but that
> line number is in the right function).
>
>
>
> On Tue, Oct 24, 2017 at 3:48 PM, Rick Brownrigg <brownrig at ucar.edu> wrote:
>>
>> Hi Laura,
>>
>> I don't really know much about the regridding process, but what I have
>> been able to surmise running the script:
>>
>> i) NCL reads the MPAS, and creates source*.nc and destination*.nc files.
>> These appear to reflect the geometry of the src/dest grids
>>
>> ii) The actual regridding is is done by ESMF software, with a command:
>>
>>   ESMF_RegridWeightGen --source source_grid_file.nc --destination
>> destination_grid_file.nc --weight
>> weights_onCells.15-3Mesh_to_0.15rectangular.nc --src_type ESMF -i
>>
>> This program SEGVs almost immediately, with a message:
>>
>> "values=<error reading variable: value requires 155713536 bytes, which is
>> more than max-value-size>...."
>>
>> That value is exactly the size of one of the variables in the source*.nc
>> file.  So it looks like some internal limit is being exceeded in the ESMF
>> software.
>>
>> Is this one of the larger MPAS files you've attempted to regrid?  I wonder
>> if anyone else can comment on this?  Those on the glade file system can see
>> all the relevant files under /glade/scratch/brownrig
>>
>> I'm not sure what to tell you as a work-around. Without a debug version of
>> the code, its nearly impossible for me to tell much more or to  detemine
>> what the limits might be. Wish I had a better answer.
>>
>> Rick
>>
>>
>>
>> On Tue, Oct 24, 2017 at 10:13 AM, Laura Fowler <laura at ucar.edu> wrote:
>>>
>>> Hi:
>>>
>>> I am trying to regrid an MPAS unstructured mesh to a rectangular mesh
>>> on cheyenne using ncl/6.4.0. My script crashes with a SIGSEGV and I am
>>> not understanding where this comes from. I have done this successfully
>>> in the past but do not see what I am doing wrong right now, but I
>>> recall that it was with an ealier version of ncl. I am attaching the
>>> output of my script in regrid.to_rectMesh.out.
>>>
>>> The script itself can be found in
>>>
>>> /glade2/scratch2/laura/MPAS.PacificOcean/initialization.centeredPacificOceanMesh.15-3km/regrid.to_rectMesh.ncl.
>>> I also tried to regrid the same MPAS mesh to an other unstructured
>>> mesh and got a similar SIGSEGV (see regrid.to_2621442Mesh.ncl), so I
>>> assume that the errors are the same.
>>>
>>> Hope you can help me figure this one out.
>>> Thanks,
>>> Laura
>>>
>>>
>>> --
>>>
>>> !-------------------------------------------------------------------------------------------------------------
>>> Laura D. Fowler
>>> Mesoscale and Microscale Meteorology Division (MMM)
>>> National Center for Atmospheric Research
>>> P.O. Box 3000, Boulder CO 80307-3000
>>>
>>> e-mail: laura at ucar.edu
>>> phone: 303-497-1628
>>>
>>>
>>> !-------------------------------------------------------------------------------------------------------------
>>>
>>> _______________________________________________
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>>
>



-- 
!-------------------------------------------------------------------------------------------------------------
Laura D. Fowler
Mesoscale and Microscale Meteorology Division (MMM)
National Center for Atmospheric Research
P.O. Box 3000, Boulder CO 80307-3000

e-mail: laura at ucar.edu
phone: 303-497-1628

!-------------------------------------------------------------------------------------------------------------