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...@openmail.cc 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...@openmail.cc 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...@openmail.cc 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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