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



Vic,

> 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



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


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