Thank you Russ.
I've gone ahead and installed the HDF5 augmentation tool (called
aug_eos5<http://hdfeos.org/software/aug_hdfeos5.php>),
which also requires the HDF5 and HDF-EOS5 libraries, which I have
installed. Following from the readme that accompanies the aug_eos5
documentation, I attempted to run the default augmentation:
aug_eos5 some_MERRA_file.hdf
I received the errors:
HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0:
#000: EHapi.c line 1493 in HE5_EHopen(): File
"MERRA300.prod.assim.inst3_3d_asm_Cp.20120101.hdf" cannot be opened.
major: File accessability
minor: Unable to open file
#001: ../../src/H5F.c line 1582 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#002: ../../src/H5F.c line 1373 in H5F_open(): unable to read superblock
major: File accessability
minor: Read failed
#003: ../../src/H5Fsuper.c line 334 in H5F_super_read(): unable to find
file signature
major: File accessability
minor: Not an HDF5 file
#004: ../../src/H5Fsuper.c line 155 in H5F_locate_signature(): unable to
find a valid file signature
major: Low-level I/O
minor: Unable to initialize object
HDF5-DIAG: Error detected in HDF5 (1.8.10) thread 0:
#000: GDapi.c line 309 in HE5_GDopen(): Cannot open the file
"MERRA300.prod.assim.inst3_3d_asm_Cp.20120101.hdf". Check the file name.
major: File accessability
minor: Unable to open file
error(3) at read.c:730 | HE5_GDopen
error(3) at run.c:1253 | open hdfeos5 file
Since this was supposed to be a simple default test of the augmentation
tool, but it failed, I'm stuck as to where to go. I have tested on a few
MERRA hdf files, all produce the same result.
On Mon, Dec 17, 2012 at 1:18 PM, Russ Rew <russ@xxxxxxxxxxxxxxxx> wrote:
> Taylor,
>
> The netCDF-Java library can read HDF-EOS data, so if the data is
> available from a server that uses netCDF-Java, such as TDS, then your
> C++ program can access the HDF-EOS data using the OPeNDAP client
> that's available with a recent netCDF-C based library built with DAP
> protocol support enabled (the default if libcurl is available at build
> time).
>
> As Dan Packman pointed out, you could instead download and make use of
> one of the HDF-EOS tools available from
>
> http://hdfeos.org/software/tool.php
>
> which also includes
>
> HDF-EOS5 to netCDF-4 Converter -- converts HDF-EOS5 to netCDF-4
>
> Description: HDF-EOS5 to netCDF-4 Converter converts an HDF-EOS5 file
> to a netCDF-4 file that the netCDF-4 library can read. Unlike the
> HDF-EOS5 Augmentation Tool, this tool creates a new file that the
> HDF-EOS5 library cannot read.
>
> --Russ
>
> > Hi Taylor,
> >
> > it's been a few years since I analyzed HDF-EOS data, but in case it's
> > useful, I'll offer that at that time HDF-EOS was a specialized kind of
> > *HDF* file, not a specialized kind of netcdf file. You need a separate
> > HDF-EOS library to access those files, not the netcdf4 library.
> >
> > Maybe things have changed, but you might be better off first looking
> > for HDF-EOS specific libraries.
> >
> > Regards,
> >
> > --Dave
> >
> >
> > On Mon, Dec 17, 2012 at 9:35 AM, Taylor Binnington
> > <tbinnington@xxxxxxxxx> wrote:
> > > Thank you for the replies.
> > >
> > > I see. I'm still learning the differences between these file formats.
> It
> > > appears that MERRA climate data is stored in HDF-EOS format, which is a
> > > specialized kind of NetCDF-4... what are the chances that I will ever
> be
> > > able to read this, even with newest versions of NetCDF with some HDF5
> and
> > > HDF4 support?
> > >
> > > I am running netcdf-4.0.1-19.1, since that is what was available in the
> > > openSUSE geo repository as an rpm (therefore no, I did not make check
> befor
> > e
> > > installing). I will uninstall this and manually install the binaries
> to tes
> > t
> > > the most current version (with fingers crossed that HDF-EOS is
> supported).
> > >
> > >
> > > On Mon, Dec 17, 2012 at 11:56 AM, Russ Rew <russ@xxxxxxxxxxxxxxxx>
> wrote:
> > >>
> > >> Taylor,
> > >>
> > >> More recent versions of netCDF-4 can access HDF5 data (and even HDF4
> > >> data) that was not written by netCDF-4, but not arbitrary HDF5 files.
> > >> Interoperability with HDF5 is documented here:
> > >>
> > >>
> http://www.unidata.ucar.edu/netcdf/docs/interoperability_with_hdf5.html
> > >>
> > >> and in these FAQs:
> > >>
> > >> http://www.unidata.ucar.edu/netcdf/docs/faq.html#fv20
> > >> http://www.unidata.ucar.edu/netcdf/docs/faq.html#fv15
> > >>
> > >> If netCDF-4 gets a segfault opening an HDF5 file, that's either a bug
> in
> > >> the legacy C++ library you're using or a bug in the accessing program.
> > >>
> > >> I just tried this example C++ program with the C++ library in netCDF
> > >> version 4.1.3:
> > >>
> > >>
> http://www.unidata.ucar.edu/netcdf/examples/programs/simple_xy_rd.cpp
> > >>
> > >> changing the test file to a file that doesn't exist, and
> > >> it seemed to behave correctly:
> > >>
> > >> $ ./simple_xy_rd
> > >> Couldn't open file!
> > >>
> > >> What version of the netCDF C++ library are you using? Did you run
> "make
> > >> check" before installing it?
> > >>
> > >> --Russ
> > >>
> > >> > Hi Taylor:
> > >> >
> > >> > The netcdf library can not open arbitrary HDF files, only ones built
> > >> > with the
> > >> > netcdf4 library. If this file was not built with the netcdf4
> library,
> > >> > then
> > >> > yes you will get an error.
> > >> >
> > >> > HTH,
> > >> >
> > >> > -Roy M.
> > >> > On Dec 17, 2012, at 8:14 AM, Taylor Binnington <
> tbinnington@xxxxxxxxx>
> > >> > wrote:
> > >> >
> > >> > > Hi all,
> > >> > >
> > >> > > This is my first time using the NetCDF C++ libraries, and I can't
> seem
> > >> > > to g
> > >> > et started. I would like to open an HDF file from a program using
> > >> > NcFile, usi
> > >> > ng the following:
> > >> > >
> > >> > > NcFile
> dataFile("MERRA300.prod.assim.inst3_3d_asm_Cp.20120101.hdf",
> > >> > > NcFile:
> > >> > :ReadOnly);
> > >> > >
> > >> > > However, gdb reveals a segfault at this line (yes, the file is
> stored
> > >> > > in th
> > >> > e same directory as the test script). Interestingly, I also receive
> the
> > >> > same
> > >> > error when I intentionally attempt to open a file that does not
> exist,
> > >> > which
> > >> > I find strange (I would have expected a 'file not found' type of
> error),
> > >> > and
> > >> > it makes me think that I simply can not open an HDF file with these
> > >> > libraries
> > >> > . Is this true? How would I proceed? Thank you in advance,
> > >> > >
> > >> > > Taylor Binnington
> > >> > >
> > >> > > --
> > >> > > Taylor Binnington
> > >> > > e. tbinnington@xxxxxxxxx
> > >> > > c. 647 926 4144
> > >> > >
> > >> > > _______________________________________________
> > >> > > netcdfgroup mailing list
> > >> > > netcdfgroup@xxxxxxxxxxxxxxxx
> > >> > > For list information or to unsubscribe, visit:
> > >> > > http://www.unidata.ucar.edu
> > >> > /mailing_lists/
> > >> >
> > >> > **********************
> > >> > "The contents of this message do not reflect any position of the
> U.S.
> > >> > Governm
> > >> > ent or NOAA."
> > >> > **********************
> > >> > Roy Mendelssohn
> > >> > Supervisory Operations Research Analyst
> > >> > NOAA/NMFS
> > >> > Environmental Research Division
> > >> > Southwest Fisheries Science Center
> > >> > 1352 Lighthouse Avenue
> > >> > Pacific Grove, CA 93950-2097
> > >> >
> > >> > e-mail: Roy.Mendelssohn@xxxxxxxx (Note new e-mail address)
> > >> > voice: (831)-648-9029
> > >> > fax: (831)-648-8440
> > >> > www: http://www.pfeg.noaa.gov/
> > >> >
> > >> > "Old age and treachery will overcome youth and skill."
> > >> > "From those who have been given much, much will be expected"
> > >> > "the arc of the moral universe is long, but it bends toward justice"
> > >> > -MLK Jr.
> > >> >
> > >> > _______________________________________________
> > >> > netcdfgroup mailing list
> > >> > netcdfgroup@xxxxxxxxxxxxxxxx
> > >> > For list information or to unsubscribe, visit:
> > >> > http://www.unidata.ucar.edu/m
> > >> > ailing_lists/
> > >
> > >
> > >
> > >
> > > --
> > > Taylor Binnington
> > > e. tbinnington@xxxxxxxxx
> > > c. 647 926 4144
> > >
> > >
> > > _______________________________________________
> > > netcdfgroup mailing list
> > > netcdfgroup@xxxxxxxxxxxxxxxx
> > > For list information or to unsubscribe, visit:
> > > http://www.unidata.ucar.edu/mailing_lists/
> >
> >
> >
> > --
> > David W. Pierce
> > Division of Climate, Atmospheric Science, and Physical Oceanography
> > Scripps Institution of Oceanography, La Jolla, California, USA
> > (858) 534-8276 (voice) / (858) 534-8561 (fax) dpierce@xxxxxxxx
>
--
Taylor Binnington
e. tbinnington@xxxxxxxxx
c. 647 926 4144
