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Re: [netcdfgroup] help4Netcdf4.2

Hi Alex

You say:

> All these issues leads to 'libhdf5_hl.so.7 not found, but I find it in
> /usr/local/include dir.

Hmmm ...
Just to avoid confusion.
Is the libhdf5_hl.so.7 really installed in /usr/local/include,
or is it in /usr/local/lib or /usr/local/lib64 perhaps?
Libraries go to directories named lib or lib64, not to include.
Include/header files go to /usr/local/include.
Executables to to /usr/local/bin.
Sticking to this convention saves you a lot of headaches.

If the libraries were installed by mistake on /usr/local/include,
I'd suggest that you reinstall HDF5, and perhaps libz (if it is misplaced also) and direct them to /usr/local. 
[After cleaning up the previous installation, of course.]
I.e. during configure, use --prefix=/usr/local.
If the HDF5 and libz libraries are already in /usr/local/lib, or in /usr/local/lib64, maybe your linker/loader is not configured to search 
for things in /usr/local/lib or /usr/local/lib64?
In this case, you could set the LD_LIBRARY_PATH to point to where
the HDF5 library is, to force the linker to find it.
Something like this (please adjust to what you actually have):

[sh/bash syntax]
export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}

[csh/tcsh syntax]
setenv LD_LIBRARY_PATH  /usr/local/lib:${LD_LIBRARY_PATH}

If the problem persists, it may help if you send the configure
commands that you actually used to install libz, HDF5 and NetCDF (C and Fortran bindings). 

I hope this helps,
Gus Correa

On 05/15/2014 09:47 PM, alexalex43210@xxxxxxxxx wrote:

Thanks for your help, Gus Correa and Ekin.
But I installed zlib and hdf5 to /usr/local and they are both
distributed on the 'include' and 'lib' dir.
I cheked the test-suite.log in hdf5_test:
==========================================
netCDF 4.3.2: h5_test/test-suite.log
==========================================

# TOTAL: 26
# PASS: 0
# SKIP: 0
# XFAIL: 0
# FAIL: 26
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: tst_h_files
=================

./tst_h_files: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_files2
==================

./tst_h_files2: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_files4
==================

./tst_h_files4: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_atts
================

./tst_h_atts: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_atts3
=================

./tst_h_atts3: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_atts4
=================

./tst_h_atts4: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_vars
================

./tst_h_vars: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_vars2
=================

./tst_h_vars2: error while loading shared libraries: libhdf5_hl.so.7:
cannot open shared object file: No such file or directory

FAIL: tst_h_vars3
=================
All these issues leads to 'libhdf5_hl.so.7 not found, but I find it in
/usr/local/include dir.
hope your further help,


------------------------------------------------------------------------
/Best regards,/
/yours alex/
/----------------------------------------------------/
alexalex43210@xxxxxxxxx <mailto:alexalex43210@xxxxxxxxx>
---------------------------------------------

    *From:* Gus Correa <mailto:gus@xxxxxxxxxxxxxxxxx>
    *Date:* 2014-05-16 02:50
    *To:* netcdfgroup <mailto:netcdfgroup@xxxxxxxxxxxxxxxx>
    *Subject:* Re: [netcdfgroup] help4Netcdf4.2
    Also, your make check error report says:
    "See h5_test/test-suite.log"
    That file may shed some light on why the tests failed.
    It should be in /home/xjc/netcdf_src/netcdf-c-4.3.2/h5_test
    Somehow config.log seems to have found the hdf5 header files and
    libraries.
    If you installed hdf5 from the packages
    (I am not familiar to SUSE, maybe it uses yum?),
    make sure you have any hdf5 "devel" packages installed,
    besides the basic hdf5.
    Also, make sure they are compatible with your computer architecture
    (ie x86_64, not i386).
    Gus Correa
    On 05/15/2014 11:23 AM, Ekin Akoglu wrote:
     > According to this in your config.log:
     >
     > gcc -o conftest -g -O2  -L/usr/local/lib conftest.c -lhdf5dll
    -lm -lz  >&5
     >
    /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
     > cannot find -lhdf5dll
     > collect2: ld returned 1 exit status
     >
     > and according to the error report, it fails testing "h5_test", all of
     > which must be related to your installed HDF5 libraries. Hence, I
    suspect
     > that it cannot detect the location of your HDF5 libraries
    installed. I
     > suggest you try configuring by specifying the directory of your HDF5
     > installation with something like this:
     >
     > $ CPPFLAGS=-I<PATH_TO_HDF5>/include LDFLAGS=-L<PATH_TO_HDF5>/lib
     > ./configure --prefix=/usr/local --disable-dap
     >
     > I hope it works.
     >
     > Ekin
     >
     >
     > On 15 May 2014 16:56, alexalex43210@xxxxxxxxx
     > <mailto:alexalex43210@xxxxxxxxx> <alexalex43210@xxxxxxxxx
     > <mailto:alexalex43210@xxxxxxxxx>> wrote:
     >
     >     Dear all,
     >          Nobody can help about these issue?
     >              I wanna install 'netcdf-fortran-4.2' into my linux
     >     platform(LSB Version: n/a ;Distributor ID: SUSE LINUX ;
    Description:
     >     openSUSE 11.2 (x86_64) ;Release: 11.2;Codename: n/a ). But before
     >     that, I choose to  install netcdf-c-4.3.2 c library. I received
     >     errors report when I install the library. The enclosed are
    the error
     >     report and config.log, and I hope you can give me a hand.
     >
     >     thanks again
     >
     >
    ------------------------------------------------------------------------
     >     /Best regards,/
     >     /yours alex/
     >     /----------------------------------------------------/
     >     alexalex43210@xxxxxxxxx <mailto:alexalex43210@xxxxxxxxx>
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