[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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