[ncl-talk] problem with ncl_filedump *.nc ?
James Russell
jorussel at ncsu.edu
Mon Sep 17 08:11:20 MDT 2018
This is also an issue a colleague of mine has been having with a new
install of NCL 6.5.0. Here is his command and output:
ncl_filedump air.2017.nc
Segmentation fault (core dumped)
air.2017.nc was downloaded from
https://www.esrl.noaa.gov/psd/cgi-bin/db_search/DBListFiles.pl?did=192&tid=69856&vid=13.
To test it I ran ncl_filedump with version 6.4.0 and the output is as you'd
expect with no issues. He's running on a version of ubuntu (kubuntu). He's
tried multiple installations (the usual method and through conda) and
hasn't had any luck getting it to work. Here is the output of ncl -v:
Copyright (C) 1995-2018 - All Rights Reserved
University Corporation for Atmospheric Research
NCAR Command Language Version 6.5.0
The use of this software is governed by a License Agreement.
See http://www.ncl.ucar.edu/ for more details.
He says everything else (other than ncl_filedump) with this installation
works with no problem.
Thanks,
James
-----------------------------------------------------------------------------
Graduate Research & Teaching Assistant
PhD Candidate: Atmospheric Science
Department of Marine, Earth, and Atmospheric Sciences
North Carolina State University
http://go.ncsu.edu/james-russell
--------------------------------------------------------------------------
On Mon, Sep 17, 2018 at 9:21 AM Rick Brownrigg <brownrig at ucar.edu> wrote:
> 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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>>
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