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

[netCDF #LKB-522731]: netcdf4 isntall

Hi Edin,

Your latest email from last night did not get sent to our support system, for
some reason.
even though I assume you sent it to "address@hidden".

I got your email sent to me this afternoon, but you should continue sending
responses
to the support-netcdf address instead, if possible, because that way they get
into
our support tracking system and someone else will see them in case I'm away
from my
email.  We are also trying to develop software, so sometimes it may takes
several days
to respond to support questions.

From the output you sent, it appears that you are sometimes giving up on the
configure
followed by make steps and instead manually editing a Makefile.  In general
this is
a bad way to proceed, as the automake system requires the Makefiles to be
generated by
the configure script, never manually edited.  If you make a change to a
Makefile, it
doesn't show up in the shell output you attach, so we have no way of knowing
whether
the change was consistent with the rest of the Makefile.

In general, you will have better luck specifying all the configuration
information
you need on the command line to configure or in environment variables.  If that
doesn't work, just send in the output indicating the problem rather than
modifying
a Makefile.

> *** Checking HDF5 variable with unlimited dimension...ok.
> HDF5-DIAG: Error detected in HDF5 (1.8.1) thread 0:
>   #000: H5Z.c line 1268 in H5Zget_filter_info(): Filter not defined
>     major: Invalid arguments to routine
>     minor: Bad value
>   #001: H5Z.c line 918 in H5Z_find(): required filter is not registered
>     major: Data filters
>     minor: Object not found
> *** Checking HDF5 deflate filter setting and getting...Sorry! Unexpected
> result, tst_h_vars.c, line: 228
> 1 failures

This is an HDF5 failure, having nothing to do with netCDF-4, and indicates
the zlib compression library, libz, is not being found.  From your
configure line:

dhcp-235:netcdf-4.0 edo$ ./configure --enable-netcdf-4 --with-hdf5=/usr/local/
--with-zlib=/usr/local/ --prefix=/usr/local/ CFLAGS=-m64 CXXFLAGS=-m64 CC=gcc

you are saying that zlib is installed in /usr/local/, which means the following
library and include files must exist:

  /usr/local/lib/libz.a
  /usr/local/include/zlib.h

Looking at your shell log, I see:

> dhcp-235:zlib-1.2.3 edo$ ./configure --prefix=/usr/local CC=gcc CFLAGS=-m64
> unknown option: CC=gcc
> ./configure --help for help
> dhcp-235:zlib-1.2.3 edo$ emacs Makefile
> dhcp-235:zlib-1.2.3 edo$ emacs Makefile
> dhcp-235:zlib-1.2.3 edo$ ./configure --prefix=/usr/local

so I have no idea how you edited the Makefile that configure should have
generated.

In the HDF5 make check output, I see:

> Testing  zip_perf
> Finished testing zip_perf
> ============================
>  zip_perf  Test Log
> ============================
> No compression IO performance because zlib was not configured
>         0.00 real         0.00 user         0.00 sys

so that confirms that the HDF5 installation won't be able to do compression
using zlib.

In one of the attempts to build netcdf-4, I see:

> configure: error: Can't find the hdf5 header and/or library, or can't link a
program       to it. HDF5 must be built with zlib; the location of zlib must be
specified for netCDF-4 with the       --with-zlib option. If HDF5 was also
built with szlib, then the location of szlib must also be       specified with
the --with-slib option.
> dhcp-235:netcdf-4.0 edo$ emacs Makefile
> dhcp-235:netcdf-4.0 edo$ sudo  ./configure --enable-netcdf-4
--with-hdf5=/usr/local/  --with-zlib=/usr/local/include --prefix=/usr/local/
CFLAGS=-m64

indicating an error finding zlib, probably because it was installed in
/usr/local/
but the configure option --with-zlib=/usr/local/include is indicating the wrong
location.  Editing the Makefile may appear to fix this problem, but may cause
other
problems if it doesn't match what configure would generate when the correct
location
is specified.

Sorry, but that's about all I can tell from the output you sent.  Be careful
with
extra spaces, as they aren't allowed in configure arguments.  Attempts to set
the
CXXFLAGS to "-m64" for configure should leave out the spaces.  you must use
   CXXFLAGS=-m64
not
   CXXFLAGS= -m64
and not
   CXXFLAGS = -m64

Also be careful to specify the configure flags you intend:

> dhcp-235:netcdf-4.0 edo$ sudo  ./configure --enable-netcdf-4
--with-hdf5=/usr/local/  --with-zlib=/usr/local/include --prefix=/usr/local/
CFLAGS=-m64 CXX=-m64

fails because it attempts to set C++ compiler flags using
   CXX=-m64
but ends up setting the C++ compiler to "-m64".  You must instead use
   CXXFLAGS=-m64

Finally, when specifying library paths, with the --with-hdf5 or --with-zlib
options,
you should specify a directory that contains lib/ and include/ subdirectories
with
the needed library and header files.  At one point you had installed HDF5 under
/usr/local/hdf5/ but were trying --with-hdf5=/usr/local/ or
--with-hdf5=/usr/local/include/, when you needed --with-hdf5=/usr/local/hdf5/.
Now it appears you have installed HDF5 under /usr/local/ and you're giving the
correct location --with-hdf5=/usr/local/.

--Russ



--Russ



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



Ticket Details
===================
Ticket ID: LKB-522731
Department: Support netCDF
Priority: Normal
Status: Closed