[ncl-talk] problem with ncl_filedump *.nc ?
Rick Brownrigg
brownrig at ucar.edu
Mon Sep 17 09:32:12 MDT 2018
This is odd -- I am able to dump all of these files, using my development
version (which is still very 6.5.0-ish) and a bonafide 6.5.0 as installed
via conda -- everything runs just fine.
I wondering if I could get someone who is experiencing this issue to run:
ldd `which ncl`
uname -a
gcc -v
and send the output directly to me?
Rick
On Mon, Sep 17, 2018 at 8:11 AM, James Russell <jorussel at ncsu.edu> wrote:
> 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
>>> <https://maps.google.com/?q=38+Upland+Rd,+Huia,+Auckland+0604,+New+Zealand&entry=gmail&source=g>
>>> 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)
>>>
>>> _______________________________________________
>>> ncl-talk mailing list
>>> ncl-talk at ucar.edu
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>>>
>>>
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