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[netCDF #FLE-841916]: Testsuite summary for netCDF 4.3.2

Ben,

> I do have the HDF5version 1.8.13,
> I took the steps you mentioned:
> 
> 1) H5DIR=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> 2) CPPFLAGS=-I${H5DIR}/include
> 3) LDFLAGS=-L${H5DIR}/lib
> 
> for
> 4) ./configure ...
> I did ./configure --prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/NETCDF
> 
> …yet the problem persists. are there any other things that need to be pointed 
> tot he H5DIR?

Maybe this is a simple problem with the Unix shell you are using
and setting environment variables that shell scripts like 
configure can access.

You don't have to worry about this if you set CPPFLAGS and 
LDFLAGS as part of the list of arguments to configure, as
in

  ./configure --prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/NETCDF 
CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib

In that case, the configure script sees the settings and uses
them.

Instead, you can precede the configure command with the 
environment variable settings if you are using bash, ksh, 
zsh, or a similar POSIX-standard command shell, as in:

  CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib ./configure 
--prefix=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/NETCDF

If you set the environment variables separately from the configure 
command line, they are local to that shell, so to make them 
accessible to subshells such as script files like configure, you
have to explicitly export them, as in

  H5DIR=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
  CPPFLAGS=-I${H5DIR}/include
  LDFLAGS=-L${H5DIR}/lib
  export CPPFLAGS LDFLAGS

If you are instead using a non-POSIX shell such as csh, you
need to instead use the setenv command, as in

  setenv H5DIR /mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
  setenv CPPFLAGS -I${H5DIR}/include
  setenv LDFLAGS -L${H5DIR}/lib

I hope one of those works ...

--Russ

> On Sep 11, 2014, at 8:12 PM, Unidata netCDF Support <address@hidden> wrote:
> 
> > Hi Ben,
> >
> >> sorry to bombard your with questions.
> >
> > No problem ...
> >
> >> have you had a minute to consider my last one?
> >> I have installed hdf5 into the directory:
> >>
> >> /mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >
> > OK, but are you sure that's HDF5 version 1.8.8 or later, preferably 1.8.13?
> > You can check by looking in the file
> >
> >  /mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5/lib/libhdf5.settings
> >
> > for a line like:
> >
> >                HDF5 Version: 1.8.13
> >
> > which identifies the installed version.  An error message you're getting 
> > when
> > trying to run the netCDF tests seems to indicate an older HDF5 version,
> > 1.8.4 (patch1), which is too old to pass the stringent tests in netCDF 
> > 4.3.2.
> >
> >>> =========================================
> >>>
> >>> netCDF 4.3.2: ncdump/test-suite.log
> >>>
> >>> =========================================
> >>>
> >>> # TOTAL: 39
> >>> # PASS:  37
> >>> # SKIP:  0
> >>> # XFAIL: 0
> >>> # FAIL:  2
> >>> # XPASS: 0
> >>> # ERROR: 0
> >>>
> >>> .. contents:: :depth: 2
> >>>
> >>> FAIL: tst_h_scalar
> >>>
> >>> ==================
> >>>
> >>> HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 47514256252672:
> >>> #000: ../../../src/H5T.c line 1595 in H5Tcreate(): unable to create type
> >
> > To build netCDF, you need to set CPPFLAGS and LDFLAGS to point to your HDF5
> > installation directories, something like
> >
> >  H5DIR=/mnt/data/bweinste/MEGAN/MEGANv2.10/local/hdf5
> >  CPPFLAGS=-I${H5DIR}/include  LDFLAGS=-L${H5DIR}/lib ./configure ...
> >  make check
> >  make install # (or sudo make install)
> >
> > --Russ
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: FLE-841916
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: FLE-841916
Department: Support netCDF
Priority: Normal
Status: Closed