[ncl-talk] setfileoption("h5" ...

Wed May 23 12:51:54 MDT 2018

To confirm Dennis' suspicion that this file is invalid, h5dump also fails
on this file:

$ h5dump 3A-MO.GPM.DPR.V2-20170217.20151201-S000000-E235959.12.V05A.HDF5
h5dump error: unable to open file "3A-MO.GPM.DPR.V2-20170217.
20151201-S000000-E235959.12.V05A.HDF5"

The reason NCL gives a NetCDF library error message is that it first checks
to see whether the file is HDF5. When that fails it tries to open it as a
NetCDF file, which results in an error message from the NetCDF library.
 -dave

On Wed, May 23, 2018 at 11:12 AM, Dennis Shea <shea at ucar.edu> wrote:

> Hi Laura
>
> I may be wrong about NCL's standard variable & file structures but I am
> pretty sure it is based on the classic netCDF-3 file and variable models.
>
> [a]
> There is no concept of multiple levels of data. netCDF-3 files are 'flat.'
> To accommodate this 'flat' nature, all variable names must be unique.
>
> [b]
> HDF5/netCDF4 allow multiple levels [eg: 'groups'].  A variable [eg: FOO]
> can exist in several groups with the same name and refer to completely
> different quantities.
>
> ---
>
> From setfileoption
>
> "In version *6.1.1*, this option only has an effect for classic model
> NetCDF files (including NetCDF4 classic files). But other than the
> difference in print output, there should be no difference in the way
> classic model NetCDF is read or written, regardless of the file structure.
>
> However, beginning with version 6.2.0
> <http://www.ncl.ucar.edu/prev_releases.shtml#6.2.0>, this option will
> work for HDF-EOS5 and shapefiles. Choosing the *"Advanced"* file
> structure will allow the user to *view these file formats using a
> representation closer to the structure implied by the native format.*
> Conversely, the *"Standard"* structure will remain available to let you
> to view the contents as you alway have; in other words backwards
> compatibility is maintained. Eventually other supported formats that can
> make ues of the advanced features, including HDF4 and HDFEOS2, may also be
> enabled to use the *"Advanced"* file structure.
>
> [Further ...]
>
> Like full model NetCDF4, HDF5 will be implemented using the *"Advanced"*
> file structure only."
>
> The above should read:
>
> Like full model NetCDF4, HDF5 will be *automatically* implemented using
> the *"Advanced"* file structure only."
>
> &&&&&&&&&&&&&
>
> There is a GPM example at:
>
> https://www.ncl.ucar.edu/Applications/HiResPrc.shtml
>
> gpm_1.ncl <https://www.ncl.ucar.edu/Applications/Scripts/gpm_1.ncl>
>
> &&&&&&&&&&&&&
> I think there is something wrong with the file you ftp'd:
>
> %> ncl_filedump  3A-MO.GPM.DPR.V2-20170217.2015
> 1201-S000000-E235959.12.V05A.HDF5
>
>  Copyright (C) 1995-2017 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version 6.5.0 -29Mar2018_0148
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
> Assertion failed: (0), function NC4_open, file nc4file.c, line 2874.
> Abort
>
> -----
>
> %> ncdump -k* 3A*-MO.GPM.DPR.V2-20170217.20151201-S000000-E235959.12.V05A.
> HDF5
>
> Assertion failed: (0), function NC4_open, file nc4file.c, line 2874.
>
> -----
>
> To illustrate that 'ncdump -k'  works, I have used it on a  different GPM
> file:
>
> %> ncdump -k *3B-*MO.MS.MRG.3IMERG.20140312-S000000-E235959.03.V03D.HDF5
>
>
>
>
> *netCDF-4-----*
>
>
>
> *For NCL-core developres, the file is at:/glade/p/ncldev/data/gpm*
>
>
>
>
> On Tue, May 22, 2018 at 2:19 PM, Laura Fowler <laura at ucar.edu> wrote:
>
>> Hello:
>> Just a couple of quick questions:
>>
>>
>> 1. I am reading an HDF5 file containing GPM data and I was wondering
>> if there was a description of the command:
>> setfileoption("h5","FileStructure","Advanced")
>>
>> In the online documentation, I found that setfileoption is described
>> for netCDF and GRIB, but not for HDF5?
>>
>>
>> 2. I read the HDF5 file and define the group g2 as:
>>
>> g2 = f=>/Grids/G2
>> mean   = g2->precipRateNearSurfaceUnconditional
>> .
>> .
>> .
>>
>> After I plot the variable mean, I am trying to open an other group g2 as:
>> ichn = 3
>> g2 = f=>/Grids/G2/precipRateNearSurface
>> mean  = g2->mean(:,ichn,:,:)
>>
>> Then, I get the error message:
>> fatal:["Execute.c":132]:variable (mean) is not in file
>> (3A-MO.GPM.DPR.V2-20170217.20151201-S000000-E235959.12.V05A.HDF5)
>> fatal:["Execute.c":6316]:variable (mean) is not in file (g2)
>> fatal:["Execute.c":8575]:Execute: Error occurred at or near line 95 in
>> file read.ncl
>>
>>
>> If I add the 2 lines:
>> delete(mean)
>> delete(g2)
>>
>> then I get the following error:
>> fatal:file (g2) isn't defined
>>
>>
>> Is there a way to reuse g2 for the second group? I thought that
>> deleting it first would work but it does not?
>>
>> Thanks,
>> Laura
>>
>>
>>
>> --
>> !-----------------------------------------------------------
>> --------------------------------------------------
>> Laura D. Fowler
>> Mesoscale and Microscale Meteorology Division (MMM)
>> National Center for Atmospheric Research
>> P.O. Box 3000, Boulder CO 80307-3000
>>
>> e-mail: laura at ucar.edu
>> phone: 303-497-1628
>>
>> !-----------------------------------------------------------
>> --------------------------------------------------
>> _______________________________________________
>> ncl-talk mailing list
>> ncl-talk at ucar.edu
>> List instructions, subscriber options, unsubscribe:
>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>>
>
>
> _______________________________________________
> ncl-talk mailing list
> ncl-talk at ucar.edu
> List instructions, subscriber options, unsubscribe:
> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.ucar.edu/pipermail/ncl-talk/attachments/20180523/73cd07c3/attachment.html>