[ncl-talk] fatal:NclMalloc Failed:[errno=12] Segmentation fault

[Rick Brownrigg]

Hi,

Errno=12 is "Cannot allocate memory".

That dox variable looks to be about 2.6GB, and I can't quite tell, but it
looks like you may be creating another 2 variables of comparable size(?)
How much memory does you machine have?  Can you tell how far the script
gets executed (i.e., perhaps put some print statements at strategic places
in the script to see how far it gets).

Rick

On Mon, Dec 3, 2018 at 2:18 PM Amal Inge <amalingenieur89 at gmail.com> wrote:

> Dear NCL experts,
> i tried to run the script attached but i had this error: fatal:NclMalloc
> Failed:[errno=12] Segmentation fault
> what should be the solution please knowing that i have enough space in the
> memory ?
> many thanks
>
>
> netcdf dox_med_1.4-101 {
> dimensions:
>     longitude = 670 ;
>     latitude = 253 ;
>     depth = 18 ;
>     time = UNLIMITED ; // (215 currently)
> variables:
>     float longitude(longitude) ;
>         longitude:standard_name = "longitude" ;
>         longitude:long_name = "longitude" ;
>         longitude:units = "degrees_east" ;
>         longitude:axis = "X" ;
>     float latitude(latitude) ;
>         latitude:standard_name = "latitude" ;
>         latitude:long_name = "latitude" ;
>         latitude:units = "degrees_north" ;
>         latitude:axis = "Y" ;
>     float depth(depth) ;
>         depth:standard_name = "depth" ;
>         depth:long_name = "depth" ;
>         depth:units = "m" ;
>         depth:positive = "down" ;
>         depth:axis = "Z" ;
>         depth:_CoordinateAxisType = "Height" ;
>         depth:_CoordinateZisPositive = "down" ;
>     double time(time) ;
>         time:standard_name = "time" ;
>         time:long_name = "time" ;
>         time:units = "seconds since 1970-01-01 00:00:00" ;
>         time:calendar = "standard" ;
>         time:axis = "T" ;
>     float dox(time, depth, latitude, longitude) ;
>         dox:standard_name =
> "mole_concentration_of_dissolved_molecular_oxygen_in_sea_water" ;
>         dox:long_name = "Mole concentration of Dissolved Molecular Oxygen
> in sea water" ;
>         dox:units = "millimol m-3" ;
>         dox:_FillValue = 1.e+20f ;
>         dox:missing_value = 1.e+20f ;
>         dox:_ChunkSizes = 1, 22, 84, 161 ;
>
> // global attributes:
>         :CDI = "Climate Data Interface version 1.8.1 (
> http://mpimet.mpg.de/cdi)" ;
>         :Conventions = "CF-1.0" ;
>         :source = "3DVAR-OGSTM-BFM" ;
>         :institution = "OGS (Istituto Nazionale di Oceanografia e di
> Geofisica Sperimentale) , Sgonico (Trieste) - Italy" ;
>         :references = "Please check in CMEMS catalogue the INFO section
> for product MEDSEA_ANALYSIS_FORECAST_BIO_006_008 -
> http://marine.copernicus.eu/" ;
>         :comment = "Please check in CMEMS catalogue the INFO section for
> product MEDSEA_ANALYSIS_FORECAST_BIO_006_008 -
> http://marine.copernicus.eu/" ;
>         :contact = "servicedesk.cmems at mercator-ocean.eu" ;
>         :bulletin_date = "2017-12-01" ;
>         :bulletin_type = "analysis" ;
>         :field_type = "monthly_mean_beginning_at_time_field" ;
>         :title = "Net Primary Production and Dissolved Oxygen (3D) -
> Monthly Mean" ;
>         :History = "Translated to CF-1.0 Conventions by Netcdf-Java CDM
> (CFGridWriter2)\n",
>             "Original Dataset = sv03-med-ogs-bio-rean-m; Translation Date
> = 2018-12-03T14:34:09.553Z" ;
>         :geospatial_lat_min = 30.1875 ;
>         :geospatial_lat_max = 45.9375 ;
>         :geospatial_lon_min = -5.5625 ;
>         :geospatial_lon_max = 36.25 ;
>         :CDO = "Climate Data Operators version 1.8.1 (
> http://mpimet.mpg.de/cdo)" ;
>
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