Hi
Can anybody please help me with this? Did the files libmesh_opt.la and
libnetcdf.la give any clues? I realized that without running the bootstrap
script, I get this warning right after I type "make"
WARNING: 'aclocal-1.12' is missing on your system. You should only need it
if
you modified 'acinclude.m4' or 'configure.ac'. You might want
to install the Automake and Perl packages. Grab them from
any GNU archive site.
cd ../Dropbox/libmesh && /bin/bash
/home/miguel/Dropbox/libmesh/build-aux/missing --run automake-1.12 --gnu
/home/miguel/Dropbox/libmesh/build-aux/missing: line 51: automake-1.12:
command not found
WARNING: 'automake-1.12' is missing on your system. You should only need
it if
you modified 'Makefile.am', 'acinclude.m4' or 'configure.ac'.
You might want to install the Automake and Perl packages.
Grab them from any GNU archive site.
This warning does not show up once I run bootstrap and I compile. My
automake and aclocal version is 1.13.3.
Thanks in advance.
Miguel
On Tue, Jul 29, 2014 at 1:12 PM, Miguel Angel Salazar de Troya <
[email protected]> wrote:
> I have tried configuring libmesh with the options --enable-netcdf=old
> --enable-exodus=old, but I got this error:
>
> unknown type name 'void_int'
>
> I have found that void_int is defined in the exodus 5.22b, but my exodus
> is v5.09, that might be the reason. My configuration options are:
>
> ./configure --enable-netcdf=old --enable-exodus=old --enable-mpi
> --enable-amr --enable-vsmoother --enable-dirichlet --enable-nodeconstraint
> --enable-parmesh --enable-pfem --enable-ifem --enable-second
> --enable-examples --enable-boost --enable-petsc --enable-periodic
> --enable-tetgen --enable-triangle --enable-vtk --with-boost=/usr/local
> --with-mpi=/home/miguel/petsc-3.5.0/arch-linux2-c-debug/externalpackages/openmpi-1.6.5
> --with-vtk-lib=/usr/local/lib/paraview-4.1 --disable-slepc --disable-eigen
> --disable-pthreads
> --with-cxx=/home/miguel/petsc-3.5.0/arch-linux2-c-debug/bin/mpicxx
> --with-cc=/home/miguel/petsc-3.5.0/arch-linux2-c-debug/bin/mpicc
> --with-fc=/home/miguel/petsc-3.5.0/arch-linux2-c-debug/bin/mpif90
> --disable-exodus-fortran
>
> This problem comes from the fact that I want to add a new class in the
> error_estimation. I add the source and header files and run the bootstrap
> script to add them to the compilation. Is there another way to do this?
> Because running bootstrap is what creates the problems that I have
> described on these emails.
>
> Thanks
> Miguel
>
>
> On Thu, Jul 10, 2014 at 5:39 PM, Miguel Angel Salazar de Troya <
> [email protected]> wrote:
>
>> I obtained the same error, although this time it can find the libnetcdf.so.7
>> in my libmesh build.
>>
>> /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to symbol
>> 'nc_close'
>> /home/miguel/libmeshbuild/contrib/netcdf/v4/liblib/.libs/libnetcdf.so.7:
>> error adding symbols: DSO missing from command line
>> collect2: error: ld returned 1 exit status
>>
>>
>>
>> On Thu, Jul 10, 2014 at 3:47 PM, Miguel Angel Salazar de Troya <
>> [email protected]> wrote:
>>
>>> Thanks a lot for your responses. I'll try uninstalling previous versions
>>> in the meantime.
>>>
>>> The libtool version I am using is 2.4.2. I'm attaching the files you
>>> mention.
>>>
>>>
>>> On Thu, Jul 10, 2014 at 2:48 PM, Kirk, Benjamin (JSC-EG311) <
>>> [email protected]> wrote:
>>>
>>>> An immediate workaround for you would be to fall back to the old
>>>> netcfd/exodus implementation that does not install such a substantial
>>>> netcdf:
>>>>
>>>> IIRC
>>>>
>>>> $ ./configure --prefix=... --enable-netcdf=old --enable-exodus=old ...
>>>>
>>>>
>>>>
>>>> On Jul 10, 2014, at 2:40 PM, Roy Stogner <[email protected]>
>>>> wrote:
>>>>
>>>> >
>>>> > On Mon, 7 Jul 2014, Miguel Angel Salazar de Troya wrote:
>>>> >
>>>> >> I ran the bootstrap script (just run it once) and it could detect
>>>> the new files, but I got an error during the compilation:
>>>> >> /usr/bin/ld: src/apps/meshid_opt-meshid.o: undefined reference to
>>>> symbol 'nc_close'
>>>> >> /usr/local/lib/libnetcdf.so.7: error adding symbols: DSO missing
>>>> from command line
>>>> >> collect2: error: ld returned 1 exit status
>>>> >>
>>>> >> I have netcdf enabled in the configuration. I didn't have this
>>>> problem before I ran the bootstrap script. I'm sorry not to provide more
>>>> details,
>>>> >> but I've no idea why this error happens because I know very little
>>>> about automake or autoconf tools and I could not find much on the internet.
>>>> i
>>>> >> think it's a problem of dependencies, but that's all.
>>>> >
>>>> > The bootstrap script seems to be a bit of a red herring: the real
>>>> > problems seems to be a conflict between the libnetcdf.so.7 that
>>>> > libMesh is trying to install and the one you've already got in
>>>> > /usr/lib/
>>>> >
>>>> > Usually when I see a conflict like that I throw up my hands and
>>>> > uninstall whatever outdated conflicting dependency version was in
>>>> > /usr. *Everything* and its dependencies tend to want /usr in your
>>>> > include/link paths, which is a big problem if there are outdated,
>>>> > conflicting libraries there.
>>>> >
>>>> > But this time... I'm not sure why I'm failing to replicate this (I've
>>>> > got /usr/lib/libnetcdf.so.7.1.1 on my system, which is likewise
>>>> > missing symbols that our libnetcdf.so.7.2.0 would have provided),
>>>> > and whatever is saving me might point to a better solution for you.
>>>> > Send me your libmesh_opt.la and contrib/netcdf/v4/liblib/libnetcdf.la
>>>> > files? What version of libtool are you using?
>>>> > ---
>>>> > Roy
>>>> >
>>>> >
>>>> ------------------------------------------------------------------------------
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>>>> > _______________________________________________
>>>> > Libmesh-users mailing list
>>>> > [email protected]
>>>> > https://lists.sourceforge.net/lists/listinfo/libmesh-users
>>>>
>>>>
>>>
>>>
>>> --
>>> *Miguel Angel Salazar de Troya*
>>>
>>> Graduate Research Assistant
>>> Department of Mechanical Science and Engineering
>>> University of Illinois at Urbana-Champaign
>>> (217) 550-2360
>>> [email protected]
>>>
>>>
>>
>>
>> --
>> *Miguel Angel Salazar de Troya*
>> Graduate Research Assistant
>> Department of Mechanical Science and Engineering
>> University of Illinois at Urbana-Champaign
>> (217) 550-2360
>> [email protected]
>>
>>
>
>
> --
> *Miguel Angel Salazar de Troya*
> Graduate Research Assistant
> Department of Mechanical Science and Engineering
> University of Illinois at Urbana-Champaign
> (217) 550-2360
> [email protected]
>
>
--
*Miguel Angel Salazar de Troya*
Graduate Research Assistant
Department of Mechanical Science and Engineering
University of Illinois at Urbana-Champaign
(217) 550-2360
[email protected]
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