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[netCDF #FRY-525370]: while compiling (make check), netcdf is not able to find hdf5 path for shared libraries even after setting it in ./configuration and LD_LIBRARY_PATH

Subject: [netCDF #FRY-525370]: while compiling (make check), netcdf is not able to find hdf5 path for shared libraries even after setting it in ./configuration and LD_LIBRARY_PATH
Date: Mon, 16 Dec 2013 16:34:34 -0700
Hi Bhupendra.

What is the output of the command

  $ ldd /home/bhupendra/Downloads/netcdf-4.3.0/h5_test/tst_h_files

Also, what is the output of

  $ file -L /usr/local/lib/libhdf5.so.8

and

  $ ls -lL /usr/local/lib/libhdf5.so.8

--Russ

> Package Version: netcdf-4.3.0
> Operating System: Linux Mint 64bit Kernel 3.11.0-12-generic dual boot with 
> Mac OSX
> Hardware: Apple Macbook Pro
> Description of problem: 1. Previously, I have installed netcdf on Mac OSX. 
> Now I am trying to install it on a Linux machine (Linux Mint-16 64bit).
> I have installed zlib-1.2.8.tar.gz and hdf5-1.8.12.tar.gz with gcc-4.8.1
> I set hdf5 path as follow and use make check after installation.
> $ ./configure --prefix=/usr/local/ --enable-fortran --enable-cxx 
> --with-szlib=/usr/local/lib
> 
> 2. 'ls' to my /usr/local lib looks like this
> libhdf5.a                 libhdf5_hl_cpp.la           libhdf5.la
> libhdf5_cpp.a             libhdf5_hl_cpp.so           libhdf5.settings
> libhdf5_cpp.la            libhdf5_hl_cpp.so.8         libhdf5.so
> libhdf5_cpp.so            libhdf5_hl_cpp.so.8.0.1     libhdf5.so.8
> libhdf5_cpp.so.8          libhdf5hl_fortran.a         libhdf5.so.8.0.1
> libhdf5_cpp.so.8.0.1      libhdf5hl_fortran.la        libz.a
> libhdf5_fortran.a         libhdf5hl_fortran.so        libz.so
> libhdf5_fortran.la        libhdf5hl_fortran.so.8      libz.so.1
> libhdf5_fortran.so        libhdf5hl_fortran.so.8.0.1  libz.so.1.2.8
> libhdf5_fortran.so.8      libhdf5_hl.la               pkgconfig
> libhdf5_fortran.so.8.0.1  libhdf5_hl.so               python2.7
> libhdf5_hl.a              libhdf5_hl.so.8             python3.3
> libhdf5_hl_cpp.a          libhdf5_hl.so.8.0.1         site_ruby
> So I believe all is good.
> 
> 3. Then I configured netcdf with
> $ CPPFLAGS=-I/usr/local/include/ LDFLAGS=-L/usr/local/lib/ ./configure 
> --prefix=/usr/local/
> So far so good.
> 
> 4. Then I used several variants of "make check" w/o 'sudo' and 'make check 
> install' but I am getting following output for all my attempts.
> ===Shell Output starts======================================
> bhupendra@earth ~/Downloads/netcdf-4.3.0 $ sudo make check
> Making check in include
> make[1]: Entering directory `/home/bhupendra/Downloads/netcdf-4.3.0/include'
> make[1]: Nothing to be done for `check'.
> make[1]: Leaving directory `/home/bhupendra/Downloads/netcdf-4.3.0/include'
> Making check in h5_test
> make[1]: Entering directory `/home/bhupendra/Downloads/netcdf-4.3.0/h5_test'
> make  tst_h_files tst_h_files2 tst_h_files4 tst_h_atts tst_h_atts3 
> tst_h_atts4 tst_h_vars tst_h_vars2 tst_h_vars3 tst_h_grps tst_h_compounds 
> tst_h_compounds2 tst_h_wrt_cmp tst_h_rd_cmp tst_h_vl tst_h_opaques 
> tst_h_strings tst_h_strings1 tst_h_strings2 tst_h_ints tst_h_dimscales 
> tst_h_dimscales1 tst_h_dimscales2 tst_h_dimscales3 tst_h_enums 
> tst_h_dimscales4
> make[2]: Entering directory `/home/bhupendra/Downloads/netcdf-4.3.0/h5_test'
> make[2]: `tst_h_files' is up to date.
> make[2]: `tst_h_files2' is up to date.
> make[2]: `tst_h_files4' is up to date.
> make[2]: `tst_h_atts' is up to date.
> make[2]: `tst_h_atts3' is up to date.
> make[2]: `tst_h_atts4' is up to date.
> make[2]: `tst_h_vars' is up to date.
> make[2]: `tst_h_vars2' is up to date.
> make[2]: `tst_h_vars3' is up to date.
> make[2]: `tst_h_grps' is up to date.
> make[2]: `tst_h_compounds' is up to date.
> make[2]: `tst_h_compounds2' is up to date.
> make[2]: `tst_h_wrt_cmp' is up to date.
> make[2]: `tst_h_rd_cmp' is up to date.
> make[2]: `tst_h_vl' is up to date.
> make[2]: `tst_h_opaques' is up to date.
> make[2]: `tst_h_strings' is up to date.
> make[2]: `tst_h_strings1' is up to date.
> make[2]: `tst_h_strings2' is up to date.
> make[2]: `tst_h_ints' is up to date.
> make[2]: `tst_h_dimscales' is up to date.
> make[2]: `tst_h_dimscales1' is up to date.
> make[2]: `tst_h_dimscales2' is up to date.
> make[2]: `tst_h_dimscales3' is up to date.
> make[2]: `tst_h_enums' is up to date.
> make[2]: `tst_h_dimscales4' is up to date.
> make[2]: Leaving directory `/home/bhupendra/Downloads/netcdf-4.3.0/h5_test'
> make  check-TESTS
> make[2]: Entering directory `/home/bhupendra/Downloads/netcdf-4.3.0/h5_test'
> ./tst_h_files: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_files
> ./tst_h_files2: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_files2
> ./tst_h_files4: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_files4
> ./tst_h_atts: error while loading shared libraries: libhdf5_hl.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_atts
> 
> *** Checking HDF5 attribute functions some more.
> *** Tests successful!
> PASS: tst_h_atts3
> 
> *** Checking HDF5 attribute functions for memory leaks.
> *** Tests successful!
> PASS: tst_h_atts4
> ./tst_h_vars: error while loading shared libraries: libhdf5.so.8: cannot open 
> shared object file: No such file or directory
> FAIL: tst_h_vars
> ./tst_h_vars2: error while loading shared libraries: libhdf5_hl.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_vars2
> ./tst_h_vars3: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_vars3
> ./tst_h_grps: error while loading shared libraries: libhdf5.so.8: cannot open 
> shared object file: No such file or directory
> FAIL: tst_h_grps
> ./tst_h_compounds: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_compounds
> ./tst_h_compounds2: error while loading shared libraries: libhdf5.so.8: 
> cannot open shared object file: No such file or directory
> FAIL: tst_h_compounds2
> ./tst_h_wrt_cmp: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_wrt_cmp
> ./tst_h_rd_cmp: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_rd_cmp
> ./tst_h_vl: error while loading shared libraries: libhdf5.so.8: cannot open 
> shared object file: No such file or directory
> FAIL: tst_h_vl
> ./tst_h_opaques: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_opaques
> ./tst_h_strings: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_strings
> ./tst_h_strings1: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_strings1
> ./tst_h_strings2: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_strings2
> ./tst_h_ints: error while loading shared libraries: libhdf5.so.8: cannot open 
> shared object file: No such file or directory
> FAIL: tst_h_ints
> ./tst_h_dimscales: error while loading shared libraries: libhdf5_hl.so.8: 
> cannot open shared object file: No such file or directory
> FAIL: tst_h_dimscales
> ./tst_h_dimscales1: error while loading shared libraries: libhdf5_hl.so.8: 
> cannot open shared object file: No such file or directory
> FAIL: tst_h_dimscales1
> ./tst_h_dimscales2: error while loading shared libraries: libhdf5_hl.so.8: 
> cannot open shared object file: No such file or directory
> FAIL: tst_h_dimscales2
> ./tst_h_dimscales3: error while loading shared libraries: libhdf5_hl.so.8: 
> cannot open shared object file: No such file or directory
> FAIL: tst_h_dimscales3
> ./tst_h_enums: error while loading shared libraries: libhdf5.so.8: cannot 
> open shared object file: No such file or directory
> FAIL: tst_h_enums
> ./tst_h_dimscales4: error while loading shared libraries: libhdf5_hl.so.8: 
> cannot open shared object file: No such file or directory
> FAIL: tst_h_dimscales4
> ================================================
> 24 of 26 tests failed
> Please report to address@hidden
> ================================================
> make[2]: *** [check-TESTS] Error 1
> make[2]: Leaving directory `/home/bhupendra/Downloads/netcdf-4.3.0/h5_test'
> make[1]: *** [check-am] Error 2
> make[1]: Leaving directory `/home/bhupendra/Downloads/netcdf-4.3.0/h5_test'
> make: *** [check-recursive] Error 1
> ===========Shell output Ends=============================
> 
> 5. It looks like netcdf is not looking in /usr/local/lib/ for the hdf5 
> libraries.
> I have /usr/local/lib/ in my $LD_LIBRARY_PATH.
> I have also read and try following fixes on the unidata support forum without 
> any luck. :(
> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10943.html
> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11044.html
> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10958.html
> http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11607.html
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: FRY-525370
Department: Support netCDF
Priority: Normal
Status: Closed
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