[ncl-talk] problem with ncl_filedump *.nc ?

Sam McClatchie smcclatchie at fishocean.info
Mon Sep 17 02:03:01 MDT 2018


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" ;
         :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/>

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
-- 
email signature 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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