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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
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