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

[Amal Inge]

hi kevin, it was just a mistake because i tried many files.
i correct it but same error i get

Le lun. 3 déc. 2018 à 22:59, Kevin Hallock <hallock at ucar.edu> a écrit :

> Hello,
>
> I noticed something else in your dox.ncl script that could potentially
> cause problems:
>
>    a = addfile("dox_med_1.4-101.nc","r")
>    ...
>    diro = "./"                     ; Output directory
>    filo = "dox_med_1.4-101.nc"
>    system("/bin/rm -f " + diro + filo)    ; remove if exists
>    foutput  = addfile (diro + filo, "c")  ; open output file
>    ...
>    foutput->dox = (/dox_masked/)
>
> The possible issue I see with this is that the script reads from the file “
> dox_med_1.4-101.nc”, deletes the file, recreates the file, and then
> writes several variables back onto the file. If any errors occur before all
> of the desired variables are written to foutput, then you could end up with
> an incomplete input data file when you run this script in the future. If
> it’s absolutely necessary to use the same filename, you may want to instead
> use a temporary filename for “filo” and then rename the temporary file at
> the end of your script:
>
>    filo = "tmp_dox_med_1.4-101.nc"
>    foutput  = addfile (diro + filo, "c")  ; open output file
>    ...
>    foutput->dox = (/dox_masked/)
>    system("/bin/mv " + diro + filo + " " + diro + "dox_med_1.4-101.nc")
>
>
> I don’t think this is the cause of the memory allocation error, but I
> thought it might be worth mentioning anyway.
>
> I hope this helps,
> Kevin
>
>
> On Dec 3, 2018, at 2:28 PM, Rick Brownrigg <brownrig at ucar.edu> wrote:
>
> 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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