[ncl-talk] ESMF bilinear regridding - error: Segmentation fault (core dumped)

[Mirce Morales]

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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