Re: [Libmesh-users] how to compile with installed netcdf?

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I think that I found a way to use my system's netcdf with libMesh (make 
check gave no errors).

- System: Parabola GNU/Linux x86_64 AMD Ryzen 2500
- PETSc from Git commit 5f77d1e0e5
- libMesh from Git commit 19706028f
- a bunch of packagees from repositories (cgns 3.4.0-2, hdf5-openmpi 
1.10.5-1, hdf5-openmpi 1.10.5-1, netcdf-openmpi 4.7.1-2, paraview 
5.7.0-3, pnetcdf-openmpi 1.12.0-1, python-h5py-openmpi 2.10.0-1, vtk 
8.2.0-9, hwloc 2.1.0-2, metis 5.1.0.p7-1, openmp 9.0.0-2, openmpi 
4.0.2-3, suitesparse 5.6.0-1, scotch 6.0.6-1)
- some from AUR's user-contributed packages (fftw-mpi 3.3.8-1, hypre-sm 
2.14.0-1, mumps 5.2.1-3, superlu 5.2.1-9)

If you want to try, my recipe is here:
https://notabug.org/broncodev/libmesh-pkgbuild.git (commit e3d46fc)
https://notabug.org/broncodev/petsc-pkgbuild.git (commit 3e9d679)

MUMPS is still not detected by libMesh :( .
Let me know if I did something unwise. Thanks!

On 2019-12-30 10:40, ed...@op... wrote:
> I can still not compile with my system's netcdf. With this code, I can
> compile and run a test:
> 
>   #+begin_SRC cpp
>     #include "netcdf.h"
> 
>     int main(void){
>              static int ncid;
>              nc_create("test.nc", NC_NETCDF4|NC_CLOBBER, &ncid);}
>   #+end_SRC
> 
>   #+begin_SRC bash
>     gcc -Wall -lnetcdf -L/usr/lib -I/usr/include -o run-test test.cpp
>     ./run-test
>     ls test.nc
>   #+end_SRC
> 
>   #+RESULTS:
>   : test.nc
> 
> I added what I thought would be the same to netcdf.m4, but it seems
> that it cannot compile. I show the relevant portions of the attached
> file
> 
>   #+begin_SRC autoconf
>     m4_define([_AX_CXX_COMPILE_NETCDF_preamble],
>     [[
>     @%:@include "netcdf.h"
>     ]])
> 
>     m4_define([_AX_CXX_COMPILE_NETCDF_body],
>     [[
>     static int ncid;
>     nc_create("test.nc", NC_NETCDF4|NC_CLOBBER, &ncid);
>     ]])
>   #+END_SRC
> 
> This message does not show up in the log
> 
>   #+begin_SRC autoconf
>     AS_IF([test "$netcdfincFound" = "no"],
>     [
>     AC_MSG_RESULT(NETCDF header files not found!)
>     enablenetcdf=no;
>     ])
>   #+end_SRC
> 
> So I think that this should work
> 
>   #+BEGIN_SRC autoconf
>     NETCDF_INCLUDE="-I$NETCDF_INC"
>   #+END_SRC
> ---8<--- snip
>   #+begin_SRC autoconf
>     AS_IF([test "x$RPATHFLAG" != "x" && test -d $NETCDF_LIB],
>           [NETCDF_RPATH_FLAGS="${RPATHFLAG}${NETCDF_LIB}"
>            NETCDF_LIBRARY="${RPATHFLAG}${NETCDF_LIB} $NETCDF_LIBRARY"
>           ],
>           [NETCDF_LIBRARY="-L${NETCDF_LIB} -lnetcdf $NETCDF_LIBRARY"])
>     LIBS="$LIBS $NETCDF_LIBRARY"
>     CPPFLAGS="$CPPFLAGS $NETCDF_INCLUDE"
>   #+end_SRC
> 
> But I get the error from here
> 
>   #+begin_SRC autoconf
> 
> AC_LINK_IFELSE([AC_LANG_PROGRAM([_AX_CXX_COMPILE_NETCDF_preamble],[_AX_CXX_COMPILE_NETCDF_body])],
>     [AC_DEFINE(HAVE_NETCDF, 1, [Flag indicating whether the library
> will be compiled with Netcdf support])],
>     [AC_MSG_ERROR(*** Linking a test program against the NETCDF
> libraries failed)])
>   #+end_SRC
> 
> What I find funny is that if I force
> 
>   #+begin_SRC autoconf
>     LIBS="$LIBS -lnetcdf -L/usr/lib"
>     CPPFLAGS="$CPPFLAGS -I/usr/include"
>   #+end_SRC
> 
> then, configure runs well, but still picks up the =contrib/netcdf4=. I
> think that I will live with this. I am sure that there is a silly
> mistake. I hope that it is useful to others. If you want more
> debugging information, let me know.
> 
> On 2019-12-30 00:21, ed...@op... wrote:
>> I attach a patch for netcdf.m4 which can help to use the system's
>> netcdf. Mind you, this is the first autoconf script that I prepare.
>> =make= is currently running. If there is a better solution, let me
>> know. You can also find the file here:
>> https://notabug.org/broncodev/libmesh-pkgbuild and you need to run
>> =autoconf= in the libmesh root directory
>> 
>> On 2019-12-25 13:40, ed...@op... wrote:
>>> Hello,
>>> 
>>> Is there a way to use my system's netcdf instead of the one in the
>>> contrib directory? Thanks!
>> 
>> 
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> 
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