[ncl-talk] ESMF bilinear regridding - error: Segmentation fault (core dumped)
Mirce Morales
mirce.morales at gmail.com
Mon Nov 19 12:24:29 MST 2018
Hi Mary!,
Thank you very much for looking at the script!, I will do the all
the changes you told me, I totally forgot about the "gt." and ".lt". in my
loops., thanks, and I'll try to fix the var problem.
I'll be back in a moment to update you about the error.
Thanks a lot again.
Cheers,
Mirce.
El lun., 19 nov. 2018 a las 11:04, Mary Haley (<haley at ucar.edu>) escribió:
> Mirce,
>
> I don't think the problem is with the regridding per se.
>
> The issue is with one of your "do" loops which is using a double as a loop
> index, and the use of ">" and "<" instead of ".gt." and ".lt".
> You have:
>
> ntime = 100000.d ;Defining the time as double
> ntime = dimsizes(time_1)
>
> do t = 0,ntime-1,1 ;Loop through the time per file
>
> NCL apparently doesn't like the double as a loop argument, which kind of
> surprises me. If you really need t to be double, you could do this:
>
> ntime = dimsizes(time_1)
>
> do it = 0,ntime-1,1 ;Loop through the time per file
> t = todouble(it)
>
> To fix the other problem, change these lines:
>
> if (t < 24)
> if (t>24)
>
> to:
>
> if (t .lt. 24)
> if (t.gt.24)
>
> These changes still don't fix your script, because "var" is undefined when
> the "do v=1,7" loop gets to "v=2", causing an error. I assume you can fix
> this, since it looks like you have some commented code to deal with this.
>
> Good luck,
>
> --Mary
>
> On Mon, Nov 19, 2018 at 10:41 AM Mary Haley <haley at ucar.edu> wrote:
>
>> Hi Mirce,
>>
>> Since the files are on cheyenne, I'll have a look. I'll respond back to
>> ncl-talk if I have any suggestions.
>>
>> --Mary
>>
>>
>> On Sun, Nov 18, 2018 at 11:53 PM Barry Lynn <barry.h.lynn at gmail.com>
>> wrote:
>>
>>> Hello Mirce:
>>>
>>> Is there some number of loops that the program will pass through without
>>> giving a segmentation fault? If so, it may mean that you are running out of
>>> memory.
>>>
>>> Or, you could find the loop it crashes in and see if you can just run
>>> that loop by itself. Or, perhaps, you can run other loops around it, but
>>> not that one indicating a data problem.
>>>
>>> Just some things to check before trying to figure out if the program
>>> itself is broken.
>>>
>>> Barry
>>>
>>> On Mon, Nov 19, 2018 at 2:14 AM Mirce Morales <mirce.morales at gmail.com>
>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am trying to do regrid many variables on ERA5 data using the script
>>>> below. Each file contains many times in it, so I am looping through the
>>>> time and the variables to apply bilinear interpolation. However, my script
>>>> is failing in the time loop.
>>>>
>>>> I tested it without going into the time loop by just defining t = 1,
>>>> and everything worked well...however when I run all my script it
>>>> crashes....This is the error I am getting:
>>>>
>>>> *Segmentation fault (core dumped)*
>>>>
>>>> My script:
>>>>
>>>> ;::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
>>>>
>>>> *load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"*
>>>> *load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"*
>>>> *load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"*
>>>> *load "$NCARG_ROOT/lib/ncarg/nclscripts/contrib/ut_string.ncl"*
>>>> *load "$NCARG_ROOT/lib/ncarg/nclscripts/esmf/ESMF_regridding.ncl"*
>>>>
>>>> *begin*
>>>>
>>>>
>>>> *;----------------------------------------------------------------------*
>>>> *; User settings*
>>>>
>>>> *;----------------------------------------------------------------------*
>>>>
>>>> * ;---------------------------------------------------------------;*
>>>> * ; Set the domain number to agree with the geogrid file and ;*
>>>> * ; the IGRID option in the hydro.namelist for WRF-Hydro ;*
>>>> * ;---------------------------------------------------------------;*
>>>> * domain = "DOMAIN1"*
>>>>
>>>> * ;---------------------------------------------------------------;*
>>>> * ; Set input and output file directories. ;*
>>>> * ;---------------------------------------------------------------;*
>>>> * dirm = "/glade/scratch/mirce/LaSierra/FullDomainForcing/ERA5/"
>>>> ; directory where source forcing data resides*
>>>> * outdir = "./output_regriddes_files/" ; directory where
>>>> regridded forcing data will be placed. set to dirm for overwriting the
>>>> original file*
>>>>
>>>> * ;---------------------------------------------------------------;*
>>>> * ; Set a variable to indicate the timestep of source data ;*
>>>> * ;---------------------------------------------------------------;*
>>>> * dt=3600.0 ; time over which precipitation is accumulated in the
>>>> source dataset in units of seconds*
>>>> * ;(currently set for ERA5 forcing)*
>>>>
>>>> * ;---------------------------------------------------------------;*
>>>> * ; Weight filenames for regridding ;*
>>>> * ;---------------------------------------------------------------;*
>>>> * ;wgtFileName_conserve = "./NLDAS2WRFHydro_weight_conserve.nc"*
>>>> * wgtFileName_bilinear = "./ERA52WRFHydro_weight_bilinear.nc"*
>>>>
>>>> * ;---------------------------------------------------------------;*
>>>> * ; Data field names from the source file to be regridded ;*
>>>> * ;---------------------------------------------------------------;*
>>>> * P_varname = "sp"*
>>>> * T_varname = "t2m"*
>>>> * U_varname = "u10"*
>>>> * V_varname = "v10"*
>>>> * ;Q_varname = "SPF_H_110_HTGL"*
>>>> * PCP_varname = "tp"*
>>>> * DSWR_varname = "msdwswrf"*
>>>> * DLWR_varname = "msdwlwrf"*
>>>>
>>>>
>>>> *;----------------------------------------------------------------------*
>>>> *; read in source and destination files*
>>>>
>>>> *;----------------------------------------------------------------------*
>>>>
>>>> *dstGridName="/glade/work/mirce/DOMAINS/DOMAIN_Files_250m_200/geo_em.d04.nc
>>>> <http://geo_em.d04.nc>"*
>>>>
>>>> * if ( .not.isfilepresent( dstGridName ) ) then*
>>>> * print( " ... source grid file not found : "+ dstGridName )*
>>>> * exit*
>>>> * end if*
>>>>
>>>> *;--- destination grid data*
>>>> * dstfile = addfile( dstGridName ,"r")*
>>>> * dlon2d=dstfile->XLONG_M(0,:,:)*
>>>> * dlat2d=dstfile->XLAT_M(0,:,:)*
>>>> * dims=dimsizes(dlat2d)*
>>>>
>>>> *; flag=0 ; flag for removing accum precip... (should be set to 0
>>>> for NLDAS2 forcing data)*
>>>>
>>>>
>>>> *;----------------------------------------------------------------------*
>>>> *; Open source data files to be regridded...*
>>>>
>>>> *;----------------------------------------------------------------------*
>>>> * system("mkdir "+outdir)*
>>>>
>>>> * srcFileName="download_*"*
>>>>
>>>> * datfils = systemfunc ("ls "+dirm+srcFileName) ; list of file
>>>> names*
>>>>
>>>> * num_datfils = dimsizes(datfils)*
>>>>
>>>>
>>>> * do ifil = 0,num_datfils-1,1 ; loop through datafiles one at a time*
>>>>
>>>> * datfile = addfile( datfils(ifil), "r")*
>>>> * print(datfile)*
>>>>
>>>> * print( " ... Open input file : "+ datfils(ifil) )*
>>>>
>>>> * ;Getting variables for time loop*
>>>> * time_1 = datfile->time*
>>>> * ntime = 100000.d ;Defining the time as double*
>>>> * ntime = dimsizes(time_1)*
>>>>
>>>> * do t = 0,ntime-1,1 ;Loop through the time per file*
>>>>
>>>> * ; It does another do loop to read the variables and do some process
>>>> with them*
>>>>
>>>>
>>>> * end do ; end for time loop*
>>>>
>>>> * end do ; end do for file loop*
>>>>
>>>> *end*
>>>>
>>>>
>>>> ;::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
>>>> The file it is processing has de following attributes:
>>>> Variable: datfile
>>>> Type: file
>>>> filename: download_200901_alltimesdays
>>>> path: /glade/scratch/mirce/LaSierra/FullDomainForcing/ERA5/
>>>> download_200901_alltimesdays.nc
>>>> file global attributes:
>>>> Conventions : CF-1.6
>>>> history : 2018-11-17 21:33:45 GMT by grib_to_netcdf-2.7.0:
>>>> /opt/ecmwf/eccodes/bin/grib_to_netcdf -o /cache/data2/
>>>> adaptor.mars.internal-1542489985.6343107-12063-21-3ffc2cf9-73f5-454d-bc1b-f54dfbfb6454.nc
>>>> /cache/tmp/3ffc2cf9-73f5-454d-bc1b-f54dfbfb6454-adaptor.mars.internal-1542489985.6345837-12063-5-tmp.grib
>>>> dimensions:
>>>> longitude = 1440
>>>> latitude = 721
>>>> time = 744
>>>> variables:
>>>>
>>>> I am sorry that this is quite long, if it's better, the path to the
>>>> data and scripts is the following on Cheyenne:
>>>> */glade/scratch/mirce/LaSierra/FullDomainForcing/ERA5*
>>>>
>>>> I will appreciate any help about this error, in case more information
>>>> is necessary you can tell me and I will add it.
>>>>
>>>> Thanks!,
>>>> Mirce.
>>>>
>>>> _______________________________________________
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>>>
>>>
>>> --
>>> Barry H. Lynn, Ph.D
>>> Senior Associate Scientist, Lecturer,
>>> The Institute of the Earth Science,
>>> The Hebrew University of Jerusalem,
>>> Givat Ram, Jerusalem 91904, Israel
>>> Tel: 972 547 231 170
>>> Fax: (972)-25662581
>>>
>>> C.E.O, Weather It Is, LTD
>>> Weather and Climate Focus
>>> http://weather-it-is.com
>>> Jerusalem, Israel
>>> Local: 02 930 9525
>>> Cell: 054 7 231 170
>>> Int-IS: x972 2 930 9525
>>>
>>> _______________________________________________
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>>
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