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[netCDF #WEP-155858]: NetCDF 4.2 Fortran on Ubuntu 12.10 (Intended to be used with ROMS ocean model)

Hi Alexis,

I'm glad the Fortran build on Ubuntu worked.  It's been useful to see the 
problems
encountered due to unclear documentation of the process.  As a result, I've
added another step in the instructions about avoiding the use of "sudo" before
"sudo make install":

  http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html

Your persistence in getting the problems solved will make it easier for others 
to
build the netCDF Fortran library in the future.  And it appears that I don't 
have
to complicate the instructions with advice about the -fPIC option, which 
apparently wasn't needed after all ...

--Russ

> Finally I succeded. I'm ashamed with you because of using this sudo
> commands. It's just that I saw the sudo commands in the ROMS forum and i
> thought I may need them for the further installation of ROMS
> (http://www.myroms.org/).
> 
> But anyway, the good news is that I finally succeeded. And I'm ashamed
> because after you told me to set the LD_LIBRARY_PATH as in your
> instructions I noticed that I failed to read correctly that instruction
> and that I could use the commands without sudo if I start from the clean
> directories from the downloads as you said in your email.
> 
> So, I started from clean directories and followed your instruction steps
> without the CFLAGS and FCFLAGS=-fPIC, and it worked without problems!!
> Please forgive me!!
> 
> 0) Uninstall everything and extract New folders
> 
> 1) For the C installation:
> CPPFLAGS=-I/usr/local/include
> LDFLAGS=-L/usr/local/lib
> ./configure --prefix=/usr/local
> make
> make check
> sudo make install
> (everything went fine)
> 
> 2) For the fortran installation:
> export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
> CPPFLAGS=-I/usr/local/include
> LDFLAGS=-L/usr/local/lib
> ./configure --prefix=/usr/local
> make
> make check
> sudo make install
> (everything went fine !!!)
> 
> Thanks a lot!
> Alexis.
> 
> PD. For your instructions of step 3, I suggest to add a note about
> checking that $PATH contains /usr/local/lib, as I thought that as the
> installation default was at /usr/local, this step was not neccesary. But
> obviously you were talking about the existing PATH and clearly my PATH
> did not contain /usr/local/lib.
> 
> On 4/15/2013 11:50 PM, Unidata netCDF Support wrote:
> >> I did my best effort on this, but the installation is not succesful yet.
> >>
> >> I tried the following:
> >>
> >> 0) sudo make uninstall, sudo make clean twice for each C and Fortran
> >> libraries
> > Your C installation looks fine, and you shouldn't need to repeat it.
> >
> >> 1) Set flags, configure, make and install for the C libraries.
> >> Everything seemed to have gone fine. The output of the
> >> configure,make,check and install steps are attached with the "C2" suffix:
> >> CFLAGS=-fPIC
> >> CPPFLAGS=-I/usr/local/include
> >> LDFLAGS=-L/usr/local/lib
> >> sudo ./configure --prefix=/usr/local
> >> sudo make
> >> sudo make check
> >> sudo make install
> >> (log files have the suffix _C6)
> >>
> >> 2) Set flags, configure and make for the Fortran libraries. Now there is
> >> no error with the -fPIC option,
> >> as previously. Now the error is more weird as it is asking for
> >> libnetcdf.so, while it is there!! and I already set
> >> the LDFLAGS to the directory. These are the steps for the fortran:
> >> CFLAGS=-fPIC
> >> FCFLAGS=-fPIC
> >> CC=gcc
> >> FC=gfortran
> >> F77=gfortran
> >> CPPFLAGS=-I/usr/local/include
> >> LDFLAGS=-L/usr/local/lib
> >> sudo ./configure --prefix=/usr/local
> >> sudo make
> >> sudo make check
> >> (The install step was not done as the error appeared in the check)
> >> (log files have the suffix _F6)
> >>
> >> 3) Previously I tried not to run any command with sudo. I did that for
> >> the C and for the Fortran libraries (as suggested by Russ).
> >> No sudo logs have a _F4 prefix (the _C4 files are not included as they
> >> presented no problems)
> >> But then on the make of the Fortran library an error appeared of
> >> permission to access files and libraries (as shown in the log_make_F4).
> >> That is why I tried again with sudo but still not able to succeed.
> > I should have recommended running "sudo make distclean" rather than
> > "sudo make clean", because a file and directory that should have been
> > removed wasn't removed.  However, we haven't tested "sudo make
> > distclean" in the case of a failed build so it may not remove
> > everything needed in that case either.  At this point, I would
> > recommend just starting over with a new netcdf-fortran build
> > directory, unpacked from the netcdf-fortran-4.2 distribution without
> > using sudo.  Then don't use sudo in the Fortran build unless "make
> > check" works, after which you can use "sudo make install".
> >
> > The fact that you are no longer getting "-fPIC" error messages is
> > actually good progress, and I think the final problem is easier to
> > solve.  It may just be a matter of following step 3 in the
> > instructions at
> >
> >    
> > http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html
> >
> > by setting the environment variable LD_LIBRARY_PATH=/usr/local/lib
> > before running the netcdf-fortran configure script.  However, the
> > value of $LD_LIBRARY_PATH is often not inherited when you use sudo,
> > because of a security issue.
> >
> > Please ket us know if this works, because it will take some time to
> > try to duplicate this problem on our Ubntu virtual machine ...
> >
> > --Russ
> >
> >> I still need your help. Thank you very much for your interest and
> >> support on this issue. I hope yoo to be able to replicate the problem
> >> over there. I hope that you find the same problem. If not, then I will
> >> be lost! Remember, I'm trying to install in Ubuntu 12.10 (Quantal
> >> Quetzal) and in my first emal I indicated the list of dependencies
> >> utilities installed with apt-get up to now.
> >>
> >> Thank you very very VERY much.
> >>
> >> Alexis Espinosa
> >> University of Western Australia
> >>
> >>
> >> On 4/13/2013 1:21 AM, Unidata netCDF Support wrote:
> >>> Alexis,
> >>>
> >>>> Unfortunately, the FCFLAGS="-fPIC" did not modify the error message!
> >>> Hmm, that's unexpected.
> >>>
> >>>> This is what I did:
> >>>>
> >>>> 0) sudo make uninstall for both C and Fortran libraries.
> >>>>
> >>>> 1) Set flags, configure, make and install for the C libraries.
> >>>> Everything seemed to have gone fine. The output of the
> >>>> configure,make,check and install steps are attached with the "C2" suffix:
> >>>> CFLAGS=-fPIC
> >>>> CPPFLAGS=-I/usr/local/include
> >>>> LDFLAGS=-L/usr/local/lib
> >>>> sudo ./configure --prefix=/usr/local
> >>>> sudo make
> >>>> sudo make check
> >>>> sudo make install
> >>>>
> >>>> 2) Set flags, configure and make for the Fortran libraries, but the same
> >>>> error appeared as you can see from the log_make and log_check files for
> >>>> the fortran attempt:
> >>>> CFLAGS=-fPIC
> >>>> FCFLAGS=-fPIC
> >>>> CC=gcc
> >>>> FC=gfortran
> >>>> F77=gfortran
> >>>> CPPFLAGS=-I/usr/local/include
> >>>> LDFLAGS=-L/usr/local/lib
> >>>> sudo ./configure --prefix=/usr/local
> >>>> sudo make
> >>>> sudo make check
> >>>> (The install step was not done as the error appeared first)
> >>> I have two suggestions.  First, don't run "./configure", "make all",
> >>> or "make check" using sudo, because on some systems that prevents
> >>> inheritance of environment variable settings, as a security
> >>> precaution.  The only command you need to run with "sudo" is "make
> >>> install" (or possibly "make clean" if you've previously run as root).
> >>>
> >>> Second, make sure you run "make clean" before running "./configure",
> >>> to ensure the new FLAGS settings get applied to all the compile steps.
> >>> I noticed in the log_make_FORTRAN2 file you attached, some of the
> >>> objects were not recompiled, for example:
> >>>
> >>>     Making all in f90
> >>>     make[2]: Entering directory 
> >>> `/home/espinosa/ROMS/NetCDF/netcdf-fortran-4.2/f90'
> >>>     make  all-am
> >>>     make[3]: Entering directory 
> >>> `/home/espinosa/ROMS/NetCDF/netcdf-fortran-4.2/f90'
> >>>     make[3]: Nothing to be done for `all-am'.
> >>>     make[3]: Leaving directory 
> >>> `/home/espinosa/ROMS/NetCDF/netcdf-fortran-4.2/f90'
> >>>
> >>> When the files in that directory get recompiled, you should expect to
> >>> see:
> >>>
> >>>     /bin/sh ../libtool --tag=FC   --mode=compile gfortran  -fPIC -c -o 
> >>> netcdf4.lo  netcdf4.f90
> >>>     libtool: compile:  gfortran -fPIC -c netcdf4.f90  -fPIC -o 
> >>> .libs/netcdf4.o
> >>>
> >>> with "-fPIC" used.  That is the specific object that the error message
> >>> is about in
> >>>
> >>>     /usr/bin/ld: ../f90/.libs/libnetcdff90.a(netcdf.o): relocation 
> >>> R_X86_64_32 against   `.rodata.str1.8' can not be used when making a 
> >>> shared object; recompile with -fPIC
> >>>
> >>> so it's important that it gets recompiled with -fPIC.
> >>>
> >>>> The log_make_FORTRAN2 shows that the -fPIC option is being used for a
> >>>> lot of intermediate compiling steps, but that is still not enought for
> >>>> solving the problem.
> >>>>
> >>>> Any suggestions?
> >>> If the suggestions above don't work, I don't know why it's failing.  Next 
> >>> week a
> >>> staff member who has been at the EGU meeting in Vienna will return, and 
> >>> he might
> >>> be able to duplicate and debug the problem on an Ubuntu virtual machine 
> >>> to which
> >>> he has access ...
> >>>
> >>> --Russ
> >>>
> >>>> Thank you very much for your help and interest,
> >>>> Alexis Espinosa
> >>>>
> >>>> On 4/12/2013 1:02 AM, Unidata netCDF Support wrote:
> >>>>> Hi Alexis,
> >>>>>
> >>>>>> I'm trying to install netcdf-4.2 (fortran version) in my Ubuntu 12.10
> >>>>>> (Quantal) system. I have tried some suggestions available on the ROMS
> >>>>>> forum but those explanations were for Ubuntu 12.04 and for cygwin and a
> >>>>>> subtle difference may be creating the problem I'm finding: I can't pass
> >>>>>> the check correctly.
> >>>>>>
> >>>>>> So, I went directly to your page and found the "Building the netCDF-4.2
> >>>>>> and later Fortran libraries" explanation and followed it carefully, but
> >>>>>> it is still not working.
> >>>>>>
> >>>>>> 0. The first thing I found is that you suggest to install first the C
> >>>>>> library in shared mode. So I "make uninstall" the failed fortran and C
> >>>>>> succesful installations (which were first tried to be installed in
> >>>>>> --disable-shared mode)
> >>>>>>
> >>>>>> 1. Then I installed the C version again like this:
> >>>>>> sudo ./configure --prefix=/usr/local --enable-netcdf-4 --enable-dap
> >>>>>> (I kept the ROMS' forum suggestions except the --disable-shared option)
> >>>>>> sudo make
> >>>>>> sudo make check
> >>>>>> sudo make install
> >>>>>> (everything went fine. I'm attaching you the output of the
> >>>>>> sudo make check > log_check_C 2>&1
> >>>>>> command)
> >>>>>>
> >>>>>> 2. Then I tried the installation of the Fortran library
> >>>>>> CC=gcc
> >>>>>> FC=gfortran
> >>>>>> CPPFLAGS=-I/usr/local/include
> >>>>>> LDFLAGS=-L/usr/local/include/lib
> >>>>>> sudo ./configure --prefix=/usr/local
> >>>>>> sudo make
> >>>>>> sudo make check
> >>>>>> (But the make and make check failed. I'm attaching you the output of:
> >>>>>> sudo make > log_make_FORTRAN 2>&1
> >>>>>> and
> >>>>>> sudo make check > log_check_FORTRAN 2>&1
> >>>>>> commands)
> >>>>>>
> >>>>>> QUESTION: What should I do in order to install the fortran library
> >>>>>> correctly?
> >>>>> The error message you are getting
> >>>>>
> >>>>>      /usr/bin/ld: ../f90/.libs/libnetcdff90.a(netcdf.o): relocation 
> >>>>> R_X86_64_32 against `.rodata.str1.8' can not be used when making a 
> >>>>> shared object; recompile with -fPIC
> >>>>>
> >>>>> indicates that you need to add "-fPIC" the the compiler options for 
> >>>>> gfortran when configuring
> >>>>> the netCDF Fortran library.  It may also be necessary to add -fPIC to 
> >>>>> the gcc options when
> >>>>> configuring the netCDF C library.
> >>>>>
> >>>>> Sometimes -fPIC is needed for 64-bit shared libraries but not for 
> >>>>> 32-bit shared libraries.  I
> >>>>> thought libtool was supposed to figure this out and provide the 
> >>>>> Position Independent Code
> >>>>> option automatically when needed, but it doesn't seem always do that 
> >>>>> when needed.
> >>>>>
> >>>>> Please try configuring and building the netCDF C library with 
> >>>>> CFLAGS="-fPIC" and then
> >>>>> installing it again.  Then try configuring and building the netCDF 
> >>>>> Fortran library
> >>>>> with FCFLAGS="-fPIC".  If "make check" doesn't work after that, please 
> >>>>> let us know.
> >>>>> We don't have an Ubuntu platform configured on which to test the netCDF 
> >>>>> Fortran build,
> >>>>> so we'd also like to know if this succeeds, in which case we'll add to 
> >>>>> the instructions.
> >>>>>
> >>>>> Thanks for reporting the problem!
> >>>>>
> >>>>> --Russ
> >>>>>
> >>>>>> Thanks a lot,
> >>>>>> Alexis Espinosa
> >>>>>> PD I previously installed a lot of supposed dependencies:
> >>>>>> sudo apt-get install -y cdbs debhelper gcc gfortran libcunit1-dev
> >>>>>> libcurl4-gnutls-dev libdap-dev libhdf5-dev texinfo texlive-base
> >>>>>> texlive-latex-base zlib1g-dev make build-essential bison doxygen curl
> >>>>>> g++ libmpich2-dev subversion
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> Alexis Espinosa Gayosso
> >>>>>> PhD Candidate
> >>>>>> School of Environmental Systems Engineering and The UWA Oceans 
> >>>>>> Institute
> >>>>>> The University of Western Australia
> >>>>>> MO15, 35 Stirling Highway
> >>>>>> Crawley, WA 6009
> >>>>>> Australia
> >>>>>>
> >>>>>> Tel: (+618) 6488-7359
> >>>>>> Fax: (+618) 6488-1015
> >>>>>> Email: address@hidden
> >>>>>> Web: www2.sese.uwa.edu.au/~espinosa/
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> Russ Rew                                         UCAR Unidata Program
> >>>>> address@hidden                      http://www.unidata.ucar.edu
> >>>>>
> >>>>>
> >>>>>
> >>>>> Ticket Details
> >>>>> ===================
> >>>>> Ticket ID: WEP-155858
> >>>>> Department: Support netCDF
> >>>>> Priority: Normal
> >>>>> Status: Closed
> >>>>>
> >>>>>
> >>>> --
> >>>> Alexis Espinosa Gayosso
> >>>> PhD Candidate
> >>>> School of Environmental Systems Engineering and The UWA Oceans Institute
> >>>> The University of Western Australia
> >>>> MO15, 35 Stirling Highway
> >>>> Crawley, WA 6009
> >>>> Australia
> >>>>
> >>>> Tel: (+618) 6488-7359
> >>>> Fax: (+618) 6488-1015
> >>>> Email: address@hidden
> >>>> Web: www2.sese.uwa.edu.au/~espinosa/
> >>>>
> >>>>
> >>>>
> >>> Russ Rew                                         UCAR Unidata Program
> >>> address@hidden                      http://www.unidata.ucar.edu
> >>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: WEP-155858
> >>> Department: Support netCDF
> >>> Priority: Normal
> >>> Status: Closed
> >>>
> >>>
> >>
> >> --
> >> Alexis Espinosa Gayosso
> >> PhD Candidate
> >> School of Environmental Systems Engineering and The UWA Oceans Institute
> >> The University of Western Australia
> >> MO15, 35 Stirling Highway
> >> Crawley, WA 6009
> >> Australia
> >>
> >> Tel: (+618) 6488-7359
> >> Fax: (+618) 6488-1015
> >> Email: address@hidden
> >> Web: www2.sese.uwa.edu.au/~espinosa/
> >>
> >>
> >>
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: WEP-155858
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 
> --
> Alexis Espinosa Gayosso
> PhD Candidate
> School of Environmental Systems Engineering and The UWA Oceans Institute
> The University of Western Australia
> MO15, 35 Stirling Highway
> Crawley, WA 6009
> Australia
> 
> Tel: (+618) 6488-7359
> Fax: (+618) 6488-1015
> Email: address@hidden
> Web: www2.sese.uwa.edu.au/~espinosa/
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: WEP-155858
Department: Support netCDF
Priority: Normal
Status: Closed