[Dune] dune installation problem

[Arya Fallahi]

Hi Christoph,

Sorry for sending you the problems again and again. I could figure out a
command which was doing everything correctly, till it came to the
installation of my application. I am using the following line:

sudo CONFIGURE_FLAGS="MPICC='$HOME/extlib/openmpi-1.8/bin/mpicc'
--enable-parallel --prefix='$HOME/extlib/cyrus'
--with-metis='$HOME/extlib/metis-5.1'
--with-alugrid='$HOME/extlib/alugrid-1.52'" ./dune-common/bin/dunecontrol
--no-cmake all

It installs all the required modules and detects Alugrid and open mpi.
Howver, when it comes to the installation of my application, it behaves as
mpi is not found. Have a look at the following lines:

Now run ./configure to setup cyrus
--- calling configure for cyrus ---
----- using default flags $CONFIGURE_FLAGS from environment -----
./configure MPICC='/afs/desy.de/user/a/afallahi/extlib/openmpi-1.8/bin/mpicc'
--enable-parallel --prefix='/afs/desy.de/user/a/afallahi/extlib/cyrus'
--with-metis='/afs/desy.de/user/a/afallahi/extlib/metis-5.1'
--with-alugrid='/afs/desy.de/user/a/afallahi/extlib/alugrid-1.52'
"--with-dune-common=/afs/desy.de/user/a/afallahi/workspace/dune-common/"
"--with-dune-geometry=/afs/desy.de/user/a/afallahi/workspace/dune-geometry/"
"--with-dune-grid=/afs/desy.de/user/a/afallahi/workspace/dune-grid/"
ACLOCAL_AMFLAGS="-I . -I m4 -I /afs/
desy.de/user/a/afallahi/workspace/dune-common/m4 -I /afs/
desy.de/user/a/afallahi/workspace/dune-geometry/m4 -I /afs/
desy.de/user/a/afallahi/workspace/dune-grid/m4"
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking how to create a pax tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking how to create a pax tar archive... (cached) gnutar
checking for inkscape... no
checking for doxygen... no
checking for latex... latex
checking for bibtex... bibtex
checking for dvipdf... dvipdf
checking for dvips... dvips
checking for wml... no
checking for dot... no
checking for perl... perl
checking for convert... convert
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to
x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain
format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for ranlib... (cached) ranlib
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran...
-L/usr/lib/gcc/x86_64-linux-gnu/4.8
-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu
-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...
-L/usr/lib/gcc/x86_64-linux-gnu/4.8
-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu
-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no
extra underscore
checking whether compiler is officially supported by DUNE... yes
checking whether g++ accepts -std=c++11... yes
checking whether nullptr is supported... yes
checking for C++11 constexpr... yes
checking for C++11 noexcept specifier... yes
checking for C++11 range-based for... yes
checking whether compiling C++ code works... yes
checking whether linking C++ objects works... yes
checking for __attribute__((deprecated))... yes
checking for __attribute__((deprecated("message")))... yes
checking for C++11 keyword 'final'... yes
checking for __attribute__((unused))... yes
checking for C++11 std::declval()... yes
checking whether the compiler properly supports testing for operator[]...
yes
checking for abi::__cxa_demangle... yes
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for mpicc... /afs/
desy.de/user/a/afallahi/extlib/openmpi-1.8/bin/mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
configure: Trying to identify the version of MPI compiler /afs/
desy.de/user/a/afallahi/extlib/openmpi-1.8/bin/mpicc
checking for lam... no
checking for mpich... no
checking for OpenMPI... yes
checking whether compiling with OpenMPI works... yes
checking whether MPI is recent enough (MPI-2.1)... yes
configure: WARNING: Disabled test whether running with OpenMPI works.
checking for MPI_Finalized in -lm... yes
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... no
checking whether pthreads work with -Kthread... no
checking whether pthreads work with -kthread... no
checking for the pthreads library -llthread... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for cc_r... gcc
checking whether the linker needs -Wl,-no-as-needed... yes (Ubuntu)
checking libraries needed for std::thread...
checking linker flags needed for std::thread... -Wl,-no-as-needed -pthread
checking compiler flags needed for std::thread... -pthread
checking whether std::thread works... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for GMP... configure: searching for GMP in /usr...
checking gmpxx.h usability... no
checking gmpxx.h presence... no
checking for gmpxx.h... no
configure: WARNING: gmpxx.h not found in /usr
configure: searching for GMP in /usr/local...
checking for gmpxx.h... (cached) no
configure: WARNING: gmpxx.h not found in /usr/local
no
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for string.h... (cached) yes
checking for pow in -lm... yes
checking for sqrt... yes
checking for strchr... yes
configure: creating ./config.lt
config.lt: creating libtool
checking for dune-common installation or source tree... testing /afs/
desy.de/user/a/afallahi/workspace/dune-common/CMakeCache.txt
found in /afs/desy.de/user/a/afallahi/workspace/dune-common
checking dune/common/stdstreams.hh usability... yes
checking dune/common/stdstreams.hh presence... yes
checking for dune/common/stdstreams.hh... yes
checking for libdunecommon... yes
configure: Searching for dune-geometry...
checking for dune-geometry installation or source tree... testing /afs/
desy.de/user/a/afallahi/workspace/dune-geometry/CMakeCache.txt
found in /afs/desy.de/user/a/afallahi/workspace/dune-geometry
checking dune/geometry/quadraturerules.hh usability... yes
checking dune/geometry/quadraturerules.hh presence... yes
checking for dune/geometry/quadraturerules.hh... yes
checking for libdunegeometry... yes
checking for X... no
checking whether we are using the Microsoft C compiler... no
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for OpenGL library... no
configure: WARNING: X libraries were not found and therefore not Grape
check possible! See ./configure --help for X library options.
configure: PARMETIS: checking for /usr/local/include/parmetis
checking for METIS library... yes
checking for METIS_PartGraphKway in -lmetis... yes
checking for metis.h... yes
checking METIS in /afs/desy.de/user/a/afallahi/extlib/metis-5.1... ok
checking parmetis.h usability... no
checking parmetis.h presence... no
checking for parmetis.h... no
configure: WARNING: parmetis.h not found in  with  -I -I/afs/
desy.de/user/a/afallahi/extlib/metis-5.1/include -I/afs/
desy.de/user/a/afallahi/extlib/openmpi-1.8/include -pthread -DMPIPP_H
-DENABLE_MPI=1
checking ParMETIS in ... failed
configure: searching for ALBERTA in /usr...
configure: searching for ALBERTA in /usr/local...
configure: searching for ALBERTA in /usr/local/alberta...
configure: searching for ALBERTA in /opt/alberta...
checking alberta/alberta.h usability... no
checking alberta/alberta.h presence... no
checking for alberta/alberta.h... no
configure: WARNING: alberta/alberta.h not found in -I/include
-I/include/alberta
Package libug was not found in the pkg-config search path.
Perhaps you should add the directory containing `libug.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libug' found
Package libug was not found in the pkg-config search path.
Perhaps you should add the directory containing `libug.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libug' found
checking for UG... no
configure: WARNING: UG not found
checking for amiramesh/AmiraMesh.h... no
configure: WARNING: AmiraMesh.h not found in
/usr/local/amiramesh/include/amiramesh
checking for PSURFACE... no
configure: WARNING: PSurface >= 2.0 not found in /usr/local/psurface
checking psurface/PSurface.h usability... no
checking psurface/PSurface.h presence... no
checking for psurface/PSurface.h... no
configure: searching for ALUGrid in /afs/
desy.de/user/a/afallahi/extlib/alugrid-1.52...
checking ALUGrid version >= 1.52... yes (ALUGrid-1.52)
checking alugrid_serial.h usability... yes
checking alugrid_serial.h presence... yes
checking for alugrid_serial.h... yes
configure: WARNING: "ALUGRID was not built for parallel support!"
checking for library containing malloc... none required
checking for dune-grid installation or source tree... testing /afs/
desy.de/user/a/afallahi/workspace/dune-grid/CMakeCache.txt
found in /afs/desy.de/user/a/afallahi/workspace/dune-grid
checking dune/grid/onedgrid.hh usability... yes
checking dune/grid/onedgrid.hh presence... yes
checking for dune/grid/onedgrid.hh... yes
checking for libdunegrid... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating cyrus/Makefile
config.status: creating m4/Makefile
config.status: creating cyrus.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

Found the following Dune-components:

----------------------------------------

dune-common.............: version 2.4-git
dune-geometry...........: version 2.4-git
dune-grid...............: version 2.4-git
ALBERTA.................: no
ALUGrid.................: version 1.52 (serial)
AmiraMesh...............: no
GMP.....................: no
Grape...................: no
METIS...................: yes
MPI.....................: yes (OpenMPI)
OpenGL..................: no
ParMETIS................: no
UG......................: no
psurface................: no

----------------------------------------

See ./configure --help and config.log for reasons why a component wasn't
found

--- calling make for cyrus ---
build directory:
make
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /afs/
desy.de/user/a/afallahi/workspace/cyrus/missing autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[1]: Entering directory `/afs/desy.de/user/a/afallahi/workspace/cyrus'
Making all in cyrus
make[2]: Entering directory `/afs/
desy.de/user/a/afallahi/workspace/cyrus/cyrus'
make[3]: Entering directory `/afs/
desy.de/user/a/afallahi/workspace/cyrus/cyrus'
g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -pthread -I/afs/
desy.de/user/a/afallahi/workspace/dune-common -I/afs/
desy.de/user/a/afallahi/workspace/dune-common -I/afs/
desy.de/user/a/afallahi/workspace/dune-geometry -I/afs/
desy.de/user/a/afallahi/workspace/dune-geometry -I/afs/
desy.de/user/a/afallahi/workspace/dune-grid -I/afs/
desy.de/user/a/afallahi/workspace/dune-grid  -I/afs/
desy.de/user/a/afallahi/extlib/alugrid-1.52/include -I/afs/
desy.de/user/a/afallahi/extlib/alugrid-1.52/include/serial -I/afs/
desy.de/user/a/afallahi/extlib/alugrid-1.52/include/duneinterface
-DENABLE_ALUGRID -DWITH_INDEX_SETS -g -O2 -Wall -MT dgtd-dgtd.o -MD -MP -MF
.deps/dgtd-dgtd.Tpo -c -o dgtd-dgtd.o `test -f 'dgtd.cc' || echo
'./'`dgtd.cc
In file included from dgtd.cc:6:0:
../cyrus/dgtd.hh:26:17: fatal error: mpi.h: No such file or directory
 #include <mpi.h>
                 ^
compilation terminated.
make[3]: *** [dgtd-dgtd.o] Error 1
make[3]: Leaving directory `/afs/
desy.de/user/a/afallahi/workspace/cyrus/cyrus'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/afs/
desy.de/user/a/afallahi/workspace/cyrus/cyrus'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/afs/desy.de/user/a/afallahi/workspace/cyrus'
make: *** [all] Error 2
--- Failed to build cyrus ---
Terminating dunecontrol due to previous errors!

I have also attached the config.log. I will be thankful if you share me any
ideas which may solve the problem.

Thank you very much for your helps,
Arya

On Wed, Jun 3, 2015 at 1:19 PM, Christoph Grüninger <
christoph.grueninger at iws.uni-stuttgart.de> wrote:

> Hi Arya,
> difficult to tell. You might have a look in to the configure script at
> line 6982
>
> > configure:6863: checking whether gfortran-4.7 accepts -g
> > configure:6874: gfortran-4.7 -c -g  conftest.f >&5
> > configure:6874: $? = 0
> > configure:6882: result: yes
> > configure:6971: checking build system type
> > configure:6982: error: /bin/sh ./config.sub
> >  failed
>
> Your opts file does the line breaks the wrong way. Within the string you
> have to indicate a line break with a backslash \ without trailing
> whitespace.
>
> When you try without the opts file, you have to pass the necessary flags
> like that in a single line:
> CC=/usr/bin/whatever CONFIGURE_FLAGS="--prefix=/home/myself/dune
> --enable-parallel" dunecontroll all
>
> Bye
> Christoph
>
> --
> A mathematician is a scientist who can figure out anything, except
> such simple things as squaring the circle and trisecting an angle.
> [Evan Esar (1899-1995), Esar's Comic Dictionary]
>
>
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