[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[netCDF #BFM-570963]: errors with HDF5 library check when running "make check"

This archive contains answers to questions sent to Unidata support through mid-2025. Note that the archive is no longer being updated. We provide the archive for reference; many of the answers presented here remain technically correct, even if somewhat outdated. For the most up-to-date information on the use of NSF Unidata software and data services, please consult the Software Documentation first.

  • Subject: [netCDF #BFM-570963]: errors with HDF5 library check when running "make check"
  • Date: Mon, 29 Mar 2010 16:12:12 -0600
Hi Mary,

> More information: I unsetenv LD_LIBRARY_PATH and this made my build
> use my copy of the HDF5 libraries. I've attached the config.log if
> you're interested.
> 
> 
> I ran make check again, and had some problems. I've included the
> output from this. Do I need to be worried about these?

I don't understand why a file included in the tar.gz distribution apparently
wasn't in the ncdump directory after you unpacked the tarball, as shown by
this part of the "make check" output:

> *** creating tst_ncml.nc from tst_ncml.cdl
> can't open file ./tst_ncml.cdl for reading: 
> No such file or directory
> FAIL: tst_output.sh

When I unpack the 4.1.1-rc2 distribution, that file is in the ncdump directory:
  $ ls -l ncdump/tst_ncml.cdl
  -rw-r--r--   1 russ     ustaff       209 Aug  9  2007 ncdump/tst_ncml.cdl

Is it possible you ran out of disk space while unpacking the sources?  There's 
another similar failure later on showing that the file ncdump/tst_calendars.cdl
is missing, but it's in the ncdump directory after I unpack it:
  $ ls -l ncdump/tst_calendars.cdl
  -rw-r--r--   1 russ     ustaff      3732 Oct 26  2008 ncdump/tst_calendars.cdl

You may want to check that your downloaded copy of the rc2 tarball has the same
size and MD5 signature as mine:

  $ ls -l netcdf-4.1.1-rc2.tar.gz; gmd5sum netcdf-4.1.1-rc2.tar.gz
  -rw-rw-r--   1 russ     ustaff   11256880 Mar 23 13:03 netcdf-4.1.1-rc2.tar.gz
  8869308b58de7a6c187ebf685cd8fb63  netcdf-4.1.1-rc2.tar.gz

--Russ

> --Mary
> 
> On Mar 28, 2010, at 11:32 AM, Mary Haley wrote:
> 
> > I think I see the issue with this.  I *am* getting some system HDF5
> > library, even though I have my own copy of it, and I specified the
> > path to it using
> >
> > ./configure --enable-netcdf-4 --enable-opendap --disable-f90 --
> > disable-shared --with-hdf5=/contrib/ncl-5.2.0/external --with-zlib=/
> > contrib/ncl-5.2.0/external --with-szlib=/contrib/ncl-5.2.0/external
> > --prefix=/contrib/ncl-5.2.0/external
> >
> > In the "make check" output, I see this kind of thing:
> >
> > libtool: link: gcc -fPIC -o tst_h_files tst_h_files.o  -L/contrib/
> > ncl-5.2.0/external/lib -L/usr/kerberos/lib ./.libs/libnetcdf.a /
> > contrib/ncl-5.2.0/external/lib/libcurl.a -lidn -lldap -lrt -lssl -
> > lcrypto -ldl /usr/local/hdf5-1.8.2/lib/libhdf5_hl.so /usr/local/
> > hdf5-1.8.2/lib/libhdf5.so /contrib/ncl-5.2.0/external/lib/
> > libhdf5_hl.a /contrib/ncl-5.2.0/external/lib/libhdf5.a /contrib/
> > ncl-5.2.0/external/lib/libsz.a -lm -lz -Wl,-rpath -Wl,/usr/local/
> > hdf5-1.8.2/lib -Wl,-rpath -Wl,/usr/local/hdf5-1.8.2/lib
> >
> > Note that "/usr/local/hdf5-1.8.2" somehow got in there, even though
> > I didn't point to this.
> >
> > I'm going to see if this is in my LD_LIBRARY_PATH. Perhaps this is
> > overriding my "--with-hdf5" setting?
> >
> > --Mary

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



Ticket Details
===================
Ticket ID: BFM-570963
Department: Support netCDF
Priority: Normal
Status: Closed