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="$CPPFLAGS -I/usr/include"
#+end_SRC
then, configure runs well, but still picks up the =contrib/netcdf4=. I
think that I will live with this. I am sure that there is a silly
mistake. I hope that it is useful to others. If you want more debugging
information, let me know.
On 2019-12-30 00:21, ed...@openmail.cc wrote:
I attach a patch for netcdf.m4 which can help to use the system's
netcdf. Mind you, this is the first autoconf script that I prepare.
=make= is currently running. If there is a better solution, let me
know. You can also find the file here:
https://notabug.org/broncodev/libmesh-pkgbuild and you need to run
=autoconf= in the libmesh root directory
On 2019-12-25 13:40, ed...@openmail.cc wrote:
Hello,
Is there a way to use my system's netcdf instead of the one in the
contrib directory? Thanks!
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# Based on the AUR package, adapted to my PETSc
# (Metis, Hypre, OpenMPI, VTK, HDF5, ifem, nodeconstraint
# shared libraries; Methods: opt oprof dbg; x86_64)
pkgname=libmesh-petsc
realname=libmesh
pkgrel=1
pkgver=list.r22.g19706028f
pkgdesc="A C++ Finite Element Library"
arch=("x86_64")
url="http://libmesh.github.io/";
license=('LGPL')
provides=($realname "metaphysicl" "timpi")
conflicts=($realname)
depends=('eigen' 'hdf5' 'boost-libs' 'intel-tbb' 'vtk' 'glpk' 'netcdf' 'nlopt'
"petsc" "hypre" "openmpi" "metis")
makedepends=('bison')
# From tar.bz2
#
source=("https://github.com/libMesh/libmesh/releases/download/v${pkgver}/libmesh-${pkgver}.tar.bz2";)
#
sha256sums=('638cf30d05c249315760f16cbae4804964db8857a04d5e640f37617bef17ab0f')
source=(
"${realname}::git+https://github.com/libMesh/libmesh";
"netcdf.m4.patch"
)
sha256sums=('SKIP'
'18109f9d52b61498061101de92d4bcd783253472ae935c29a8f21ee37a72f1b7')
petsc_h=$(pacman -Ql petsc | grep -m 1 petsc.h | sed 's-^[[:alpha:]-]* --g')
petsc_dir=$(dirname "$petsc_h")
export PETSC_DIR=${petsc_dir%%/include}
#####################################################################
# From UPC: Building And Using Static And Shared "C" Libraries.html #
# #+begin_QUOTE #
# we need that all jump calls ("goto", in assembly speak) #
# and subroutine calls will use relative addresses, and not #
# absolute addresses. Thus, we need to use ... ~-fPIC~ or #
# ~-fpic~ #
# #+end_QUOTE #
#####################################################################
###############################################################################
# From makepkg.conf #
# -march (or -mcpu) builds exclusively for an architecture #
# -mtune optimizes for an architecture, but builds for whole processor family #
###############################################################################
# -O3 optimises
generic_flags="-fPIC -fopenmp -O3 -march=amdfam10 -mtune=generic"
# I used these for PETSc (from MOOSE)
# generic_flags="-fPIC -fopenmp -O3 -march=x86-64 -mtune=generic"
export COPTFLAGS=-O3
export CPPOPTFLAGS=-O3
export CXXOPTFLAGS=-O3
export CFLAGS="$generic_flags"
# Fortify is optional
export CPPFLAGS="$generic_flags -D_FORTIFY_SOURCE=2"
export CXXFLAGS="$generic_flags"
export FFLAGS="$generic_flags"
export FCFLAGS="$generic_flags"
export F90FLAGS="$generic_flags"
export F77FLAGS="$generic_flags"
# I used these for PETSc (from MOOSE)
export METHODS="opt"
export LANG=en_IE.UTF-8 LANGUAGE=en_IE.UTF-8 LC_ALL=en_IE.UTF-8
pkgver() {
cd $realname
git describe --long --tags | sed 's/\([^-]*-g\)/r\1/;s/-/./g'
}
prepare() {
# Replace contrib/netcdf with system netcdf if available
# (reminder -d: go to the right dir; by default the
# directories are removed from path)
patch -d "${srcdir}"/libmesh/m4 -i "${srcdir}"/netcdf.m4.patch
cd "${srcdir}/${realname}"
autoconf
# Go back
cd "${srcdir}"
# # Force NLOpt
# Directory for out of source build
[[ -d ../build ]] || mkdir ../build
# Update Git sub-modules
cd "${srcdir}/${realname}"
sed -i 's-=[[:space:]]*../../-=https://github.com/-g' .gitmodules
git submodule sync --recursive
git submodule update --init
##############################################################
# # I keep getting a very annoying error with an #
# # out-of-source build, saying that I need to run ~make #
# # distclean~, but if I do that, some make rules are not #
# # found. With this, I recreate whatever is needed for the #
# # out-of-source ~make distclean~ #
# ./configure \ #
# --prefix=/usr \ #
# $(for (( i=1; i<=${#CONFOPTS[@]}; i++)); do #
# echo "${CONFOPTS[$i]}"; #
# done) #
# make distclean #
##############################################################
}
build() {
cd ../build
# This happens in ${pkgdir} (out-of-source)
# Out of source build (recommended by Roy Stogner)
CONFOPTS=(
--enable-petsc-hypre-required # recommended by MOOSE
--with-metis=PETSc # use PETSCs' metis
--enable-cxx11-required # force C++11 standard
--enable-metaphysicl-required # recommended by MOOSE
--enable-vtk-required
--enable-curl
--enable-hdf5
--with-pic
--enable-mpi
--enable-complex # make sure to compile PETSc with complex too
--enable-netcdf # Does this work ?
--with-netcdf=/usr/include # Does this work ?
--with-netcdf-lib=/usr/lib # Does this work ?
--enable-fftw # Does this work ?
--with-nlopt=/usr/include # Does this work ?
--with-nlopt-lib=/usr/lib # Does this work ?
--enable-mumps # Does this work ?
--with-mumps=/usr/include # Does this work ?
--with-mumps-lib=/usr/lib # Does this work ?
--enable-superlu # Does this work ?
--enable-shared # shared libraries
--enable-unique-id # from libmesh GitHub wiki
--enable-march # get -march flag for this system
--enable-ifem # infinite elements
--enable-nodeconstraint # from libmesh GitHub wiki
)
"${srcdir}/${realname}"/configure \
--prefix=/usr \
$(for (( i=1; i<=${#CONFOPTS[@]}; i++)); do
echo "${CONFOPTS[$i]}";
done)
exit
make clean
make
}
check() {
cd ../build
mv examples/reduced_basis/reduced_basis_ex7/Makefile{,.bak}
echo -e "check:\ninstall:" > \
examples/reduced_basis/reduced_basis_ex7/Makefile
make check
}
package() {
# make DESTDIR=usr/share/doc/${realname}/examples examples_doc
make -C ../build DESTDIR="${pkgdir}"/usr/share/doc/${realname}/html doc
make -C ../build DESTDIR="${pkgdir}" install
mkdir -p "${pkgdir}/usr/share/doc/${realname}/"
cp -a ../build/doc/* "${pkgdir}/usr/share/doc/${realname}/"
install -d "${pkgdir}/etc/libmesh"
cp -a "${pkgdir}"/usr/Make.common "${pkgdir}/etc/libmesh"
mv "${pkgdir}"/usr/Make.common "${pkgdir}/usr/share/doc/libmesh/"
cp -a "${pkgdir}"/usr/examples "${pkgdir}/usr/share/doc/${realname}/"
rm -r "${pkgdir}"/usr/contrib || echo "removed "
rm "${pkgdir}"/usr/Make.common || echo "removed"
}
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