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[netCDF #XIS-909415]: Problem Installing netcdf-4.3.1

Vic,

My first diagnosis was correct, the old version of HDF5 is the problem.

There was a bug in HDF5-1.8.7 that we didn't test for in the corresponding
netCDF version 4.1.3 released a month later, so that version could be
built with HDF5-1.8.7.  The current netCDF version 4.3.1.1 detects the
HDF5 bug when built with HDF5-1.8.7, but builds fine with HDF5 versions
1.8.8 and later.  If you have to rebuild HDF5 from source anyway, I
would recommend just using the latest version 1.8.12, as that's what
we've done the most testing with.

--Russ

> Oops, sorry, I can now duplicate the problem you are seeing, so
> will follow up with a diagnosis and solution.  It has nothing to
> do with the compiler version!
> 
> I had been  inadvertantly running in an environment in which the
> LD_LIBRARY_PATH variable was set to a directory that caused me to
> be testing a current version of HDF5 rather than HDF5-1.8.7.
> 
> Sorry about the red herrings :-) ...
> 
> --Russ
> 
> > > I have included the config.log file for trying to install netcdf-4.3.1.
> > > I am trying to install on a CENTOS 5 LINUX system. I checked what I
> > > installed on the system that I am trying to do the install using yum.
> > > Below is what I have installed currently for the hdf5,curl and zlib via 
> > > yum.
> > >
> > > hdf5.x86_64           1.8.7-1.el5.rf        installed
> > > hdf5-devel            1.8.7-1.el5.rf        installed
> > > curl.x86_64           7.15.5-9.el5_6.2      installed
> > > curl-devel.x86_64     7.15.5-9.el5_6.2      installed
> > > zlib.x86_64           1.2.3-3               installed
> > > zlib-devel.x86_64     1.2.3-3               installed
> > >
> > > Did not know if I should have used the ones you have in your download
> > > site instead of installing them using yum via the Centos 5 system
> >
> > Installing via yum should be fine, if the problem isn't related
> > to the older versions of HDF5, libcurl, and zlib that you're
> > building with.  I tried to duplicate the bug with the same version
> > of HDF5 you are using, but it worked fine for me, and curl and zlib
> > don't appear to be involved.
> >
> > > After downloading the netcdf-4.3.1 tar file and untarring it, I did
> > > the simple ./connfigure prefix=/home/tisone/HELP/NETCDF/local
> > > and then did the make check install that generated the error I sent
> > > Will have the the netcdf command set that it generates when it works be
> > > placed on our main fileserver in a common directory that is mounted on
> > > all of LINUX systems running CENTOS 5 and CENTOS 6 . ...
> >
> > This is puzzling.  I don't have access to a CENTOS 5 platform, but my old
> > Fedora 14 x86_64 should be pretty close, and your config.log shows only a
> > few differences, but you get the "make check" failure that I don't see.
> >
> > The differences are
> >
> > - You're using an older curl library without CURLOPT_KEYPASSWD defined
> > in curl/curl.h, but the ncdump test that's failing has nothing to do
> > with libcurl or DAP.
> > - In your older math.h, there are no definitions for the macros isfinite
> > or signbit, but that shouldn't matter, as configure flags make sure
> > substitutes are defined when not provided.
> > - Your compiler version, gcc-4.1.2, is older than the gcc-4.5.1 I'm using.
> >
> > It's grasping at straws, but there might have been a bug in gcc-4.1.2
> > that was later fixed and gets past the test failure you're seeing in the
> > call to an HDF5 function in creating a test file, in
> > ncdump/tst_h_scalar.c:
> >
> > /* Create variable-length string datatype */
> > if ((vlstr_typeid = H5Tcreate(H5T_STRING, (size_t)H5T_VARIABLE)) < 0) ERR;
> >
> > that resulted in
> >
> > HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
> > #000: H5T.c line 1597 in H5Tcreate(): unable to create type
> > major: Datatype
> > minor: Unable to initialize object
> > #001: H5T.c line 2990 in H5T_create(): type class is not appropriate - use 
> > H5Tcopy()
> > major: Datatype
> > minor: Feature is unsupported
> >
> > If you have access to gcc-4.5.1 or later on your CENTOS platform, could you
> > try building and testing with that instead?
> >
> > If that doesn't work, all I can suggest is using a more current HDF5-1.8.12
> > release ...
> >
> > --Russ
> >
> > > Unidata netCDF Support wrote:
> > > > Hi Vic,
> > > >
> > > >> I have been trying to install netcdf-4.3.1 on one of our Centos 5
> > > >> Linux systems --I get the errors that are contained in the atached
> > > >> test-suite.log file--Not sure what I need to do about it.
> > > >
> > > > I thought the problem might be using a pretty old version of HDF5 from
> > > > 2011 with the latest version of netCDF. but I can't duplicate the 
> > > > problem
> > > > here.  NetCDF-4.3.1.1 built with HDF5-1.8.7 seems to work fine and 
> > > > passes
> > > > all tests on my RHEL 14 Linux system,
> > > >
> > > > Can you send the config.log file generated when you ran configure?
> > > >
> > > > Thanks!
> > > >
> > > > --Russ
> > > >
> > > > Russ Rew                                         UCAR Unidata Program
> > > > address@hidden                      http://www.unidata.ucar.edu
> > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: XIS-909415
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Closed
> > >
> > > --
> > > Vic
> > >
> > > Victor P. Tisone           Computer System Management Team (CSMT)
> > > address@hidden            voice: (303)497-1519  fax: (303)497-1589
> > > High Altitude Observatory  P.O. Box 3000 Boulder CO 80307  USA
> > >
> > >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> 
> Russ Rew                                         UCAR Unidata Program
> address@hidden                      http://www.unidata.ucar.edu
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: XIS-909415
Department: Support netCDF
Priority: Normal
Status: Closed