Hi Alex
Your setup looks right to me.
The only thing that may have caused a problem is having a previous/older
installation of hdf5 and netcdf in the same /usr/local.
Did you clean up the older versions before you installed the new ones?
Also, is there anything in that h5_test/test-suite.log that indicates
*why* it didn't find libhdf5_hl.so.7?
What happens if you do "make" only, not "make check"?
Does it build the NetCDF libraries?
I haven't tried NetCDF 4.3.2 (currently I am using 4.3.0),
but I wonder if there is some mistake in the configure script or
in the Makefiles that do the testing that is not picking up your
environment correctly.
I hope this helps,
Gus Correa
On 05/17/2014 03:03 AM, alexalex43210@xxxxxxxxx wrote:
Dear Correa, I send you the specification of dir which is installed:
*in /usr/local/bin:* curl gif2h5 h5cc h5debug h5dump h5jam h5mkgrp
h5redeploy h5repart h5unjam ncgen perl curl-config h52gif h5copy
h5diff h5import h5ls h5perf_serial h5repack h5stat ncdump nf-config
sshpass *in /usr/local/lib:* libcurl.a libcurl.so.4 libhdf5.a
libhdf5_hl.so libhdf5.la libhdf5.so.7 libnetcdf_c++.a libnetcdff.so
libz.a libz.so.1.2.5 libcurl.la libcurl.so.4.1.1 libhdf5_hl.a
libhdf5_hl.so.7 libhdf5.settings libhdf5.so.7.0.3 libnetcdff.a
libnetcdff.so.5 libz.so libz.so.1.2.8 libcurl.so libcurl.so.4.3.0
libhdf5_hl.la libhdf5_hl.so.7.0.3 libhdf5.so libnetcdf.a
libnetcdff.la libnetcdff.so.5.3.1 libz.so.1 pkgconfig *in
/usr/local/include:* curl H5Cpublic.h H5Epublic.h H5FDlog.h
H5FDmulti.h H5Fpublic.h H5Lpublic.h H5overflow.h H5public.h
H5Tpublic.h hdf5_hl.h netcdf.hh zconf.h H5ACpublic.h H5Dpublic.h
H5FDcore.h H5FDmpi.h H5FDpublic.h H5Gpublic.h H5LTpublic.h
H5Ppublic.h H5Rpublic.h H5version.h ncvalues.h netcdf.inc zlib.h
H5api_adpt.h H5DSpublic.h H5FDdirect.h H5FDmpio.h H5FDsec2.h
H5IMpublic.h H5MMpublic.h H5PTpublic.h H5Spublic.h H5Zpublic.h
netcdfcpp.h netcdf.mod H5Apublic.h H5Epubgen.h H5FDfamily.h
H5FDmpiposix.h H5FDstdio.h H5Ipublic.h H5Opublic.h H5pubconf.h
H5TBpublic.h hdf5.h netcdf.h typesizes.mod
I installed hdf5 and zlib as the suggestions by netcdf: ***$
./configure --prefix=/usr/local* *$ make check install* * * ***$
./configure --with-zlib=/usr/local --prefix=/home/ed/local* *$ make
check install* then I did the following setting in my bashrc: *export
LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH* after those upper: I
did: ***$ CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib
./configure --prefix=/usr/local* *$ make check install* then issues
came out.
by the way, before I installed hdf5-1.8.9, there also existed another
version hdf5-1.8.6(I installed before) in the /usr/local dir: *hdf5
hdf5-1.8.6 include lib lib64 man netcdf netcdf4.13*
Thanks again.
------------------------------------------------------------------------
/Best regards,/
/yours alex/ /----------------------------------------------------/
alexalex43210@xxxxxxxxx <mailto:alexalex43210@xxxxxxxxx>
---------------------------------------------
*From:* Gus Correa <mailto:gus@xxxxxxxxxxxxxxxxx> *Date:* 2014-05-16
23:26 *To:* netcdfgroup <mailto:netcdfgroup@xxxxxxxxxxxxxxxx>
*Subject:* 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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