[ncl-talk] problem with ncl_filedump *.nc ?
Rick Brownrigg
brownrig at ucar.edu
Mon Sep 17 07:21:12 MDT 2018
Hi Sam,
I am able to open/read that sst.nc file with ncl_dump just fine (?) Are
you able to send me your file so that I can check it out?
Rick
On Mon, Sep 17, 2018 at 2:03 AM, Sam McClatchie <smcclatchie at fishocean.info>
wrote:
> Hello
>
> I have an install of ncl 6.5.0 that is working fine. However i am
> beginning to suspect a problem with the ncl_filedump . The usage command
> works:
>
> smcc at jaguar:/data/dynamic_data/datasets/currents_Copernicus_CMEMS_model_satellite$
> ncl_filedump -h
>
> ncl_filedump [-c] [-v var1[,...]] [-sed sed1[,...]] [-itime] [-ftime]
> [-tps] [-h] file
> [-c] coordinate variable and header information
> [-v var1[,...]] data for variable(s) <var1>,...
> [-sed sed1[,...]] GRIB files only; set single element dimensions
> [default: none]
> choices are initial_time, forecast_time, level,
> ensemble,
> probability, all, none
> [-itime] GRIB files only; set initial time as a single
> element dimension
> (same as -sed initial_time)
> [-ftime] GRIB files only; set forecast time as a single
> element dimension
> (same as -sed forecast_time)
> [-tps] GRIB files only; remove suffix representing a time
> period (e.g. 2h)
> from statistically processed variables, leaving
> only type of
> processing as a suffix (e.g. _acc, _avg)
> [-h] this usage message
>
> but doing ncl_filedump on a supported file type (netCDF) failed.
>
> smcc at jaguar:/data/dynamic_data/datasets/currents_Copernicus_CMEMS_model_satellite$
> ncl_filedump dataset-uv-rep-monthly_1536962814624.nc
> Segmentation fault
>
> An ncdump of the file headers works:
>
> smcc at jaguar:/data/dynamic_data/datasets/currents_Copernicus_CMEMS_model_satellite$
> ncdump -h dataset-uv-rep-monthly_1536962814624.nc
> netcdf dataset-uv-rep-monthly_1536962814624 {
> dimensions:
> longitude = 241 ;
> latitude = 121 ;
> depth = 1 ;
> time = UNLIMITED ; // (264 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" ;
> double 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" ;
> float time(time) ;
> time:standard_name = "time" ;
> time:long_name = "Time" ;
> time:units = "hours since 1950-01-01 00:00:00 UTC" ;
> time:calendar = "standard" ;
> time:axis = "T" ;
> float vo(time, depth, latitude, longitude) ;
> vo:standard_name = "northward_sea_water_velocity" ;
> vo:long_name = "Absolute geostrophic velocity + depth Ekman
> velocity: meridian component" ;
> vo:units = "m/s" ;
> vo:_FillValue = 1.844674e+19f ;
> vo:missing_value = 1.844674e+19f ;
> vo:_ChunkSizes = 1, 1, 720, 1440 ;
> float uo(time, depth, latitude, longitude) ;
> uo:standard_name = "eastward_sea_water_velocity" ;
> uo:long_name = "Absolute geostrophic velocity + depth Ekman
> velocity: zonal component" ;
> uo:units = "m/s" ;
> uo:_FillValue = 1.844674e+19f ;
> uo:missing_value = 1.844674e+19f ;
> uo:_ChunkSizes = 1, 1, 720, 1440 ;
>
> // global attributes:
> :CDI = "Climate Data Interface version 1.8.1 (
> http://mpimet.mpg.de/cdi)" ;
> :Conventions = "CF-1.6" ;
> :institution = "CLS" ;
> :geospatial_lon_units = "degrees_east" ;
> :geospatial_vertical_max = 0. ;
> :product_version = "1.0" ;
> :geospatial_lat_units = "degrees_north" ;
> :creation_date = "2018-04-04 00:00:00" ;
> :contact = "servicedesk.cmems at mercator-ocean.eu"
> <servicedesk.cmems at mercator-ocean.eu> ;
> :references = "Rio, M.-H., S. Mulet, and N. Picot (2014),Beyond
> GOCE for the ocean circulation estimate: Synergetic use of altimetry,
> gravimetry, and in situ data provides new insight into geostrophic and
> Ekman currents, Geophys. Res. Lett., 41, doi:10.1002/2014GL061773" ;
> :geospatial_vertical_min = -15. ;
> :lon_min = -180. ;
> :lon_max = 179.75 ;
> :lon_res = 0.25f ;
> :lat_min = -90. ;
> :lat_max = 89.75 ;
> :lat_res = 0.25f ;
> :title = "Monthly mean total surface and 15m velocities" ;
> :description = "This product has been initiated in the frame of
> CNES/CLS projects and then consolidated during the Globcurrent project
> (funded by the ESA User Element Program)" ;
> :History = "Translated to CF-1.0 Conventions by Netcdf-Java CDM
> (CFGridWriter2)\n",
> "Original Dataset = dataset-uv-rep-monthly; Translation Date =
> 2018-09-14T22:06:54.704Z" ;
> :geospatial_lat_min = 20.125 ;
> :geospatial_lat_max = 50.125 ;
> :geospatial_lon_min = -149.875 ;
> :geospatial_lon_max = -89.875 ;
> :CDO = "Climate Data Operators version 1.8.1 (
> http://mpimet.mpg.de/cdo)" ;
> =====================
>
> To check, I repeated the test with an example netCDF file from
> <https://www.ncl.ucar.edu/Applications/Data/>
> <https://www.ncl.ucar.edu/Applications/Data/>
>
> I obtained the same result:
>
> smcc at jaguar:/data/dynamic_data/scratch$ ls *.nc
> sst.nc
>
> smcc at jaguar:/data/dynamic_data/scratch$ ncl_filedump sst.nc
> Segmentation fault
>
> smcc at jaguar:/data/dynamic_data/scratch$ ncdump -h sst.nc
> netcdf sst {
> dimensions:
> DEPTH = 1 ;
> DEPTHedges = 16 ;
> LAT = 64 ;
> LATedges = 65 ;
> LON = 181 ;
> TIME = UNLIMITED ; // (1 currently)
> variables:
> double DEPTH(DEPTH) ;
> DEPTH:units = "meters" ;
> DEPTH:positive = "down" ;
> DEPTH:point_spacing = "uneven" ;
> DEPTH:edges = "DEPTHedges" ;
> double DEPTHedges(DEPTHedges) ;
> DEPTHedges:edges = " " ;
> double LAT(LAT) ;
> LAT:units = "degrees_north" ;
> LAT:point_spacing = "uneven" ;
> LAT:edges = "LATedges" ;
> double LATedges(LATedges) ;
> LATedges:edges = " " ;
> double LON(LON) ;
> LON:units = "degrees_east" ;
> LON:point_spacing = "even" ;
> float TEMP(TIME, DEPTH, LAT, LON) ;
> TEMP:missing_value = -9.99e+33f ;
> TEMP:_FillValue = -9.99e+33f ;
> TEMP:long_name = "TEMPERATURE" ;
> TEMP:history = "From ncep_sd_corrected_monthly_means" ;
> TEMP:units = "deg. C" ;
> double TIME(TIME) ;
> TIME:units = "days since 1947-12-15 00:00:00" ;
> TIME:time_origin = "15-DEC-1947:00:00:00" ;
>
> // global attributes:
> :history = "Thu Oct 26 09:03:55 2000: ncks -d TIME,0,0 -d
> DEPTH,0,0 tamu.temps.nc sst.nc\n",
> "FERRET V5.00 (V500beta1.1) 25-Oct-00" ;
> }
> smcc at jaguar:/data/dynamic_data/scratch$
>
> ==================
> It seems either there is a problem with the ncl_filedump tool on my
> installation (which seems doubtful given that other things are working just
> fine), or the may be a problem with the tool?
>
> Best fishes
> Sam
> --
> Sam McClatchie (fisheries oceanographer)
> & Elena Turin (accounting & auditing)
> FishOcean Enterprises
> 38 Upland Rd, Huia, Auckland 0604, New Zealand
> cell: 027 752 8495
> Internet <http://www.fishocean.info>
>
>
> "The time has come", the tui said,
> "to talk of many things:
> Of songs - and ferns - and flowering flax,
> of Pukekos and dreams ..."
>
> (not Lewis Carroll)
>
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