[ncl-talk] ESMF bilinear regridding - error: Segmentation fault (core dumped)
Mary Haley
haley at ucar.edu
Mon Nov 19 10:41:59 MST 2018
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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