a test error when I use ElmerSolver

[zhang liangfu]

Hi Mr Anil
I try your suggestion,the answer as follows.
zlf@zlf-ThinkPad-T420:~/elmerfem/fem$ ./configure --prefix="$ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi-inc-dir=/usr/include/mpi --with-lhuti=$ELMER_HOME/lib/libhuti.a
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
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... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for ftello... yes
checking for fseeko... yes
checking for answer to meaning of life... 42
checking for default compilation flags... optimized
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for xlC... no
checking for pathCC... no
checking for icc... no
checking for CC... no
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 for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for ranlib... ranlib
checking for ar... ar
checking for ar flags... cru
checking whether we are using the Microsoft C compiler... no
checking for /lib/cpp... yes
checking for C++ linker flags... checking how to run the C preprocessor... /lib/cpp
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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 64 bit compilation flags... let's see what happens
checking for 64 bit CFLAGS... -m64 -fPIC
checking for 64 bit FCFLAGS... -m64 -fPIC
checking for 64 bit CXXFLAGS... -m64 -fPIC
checking for 64 bit FFLAGS... -m64 -fPIC
checking for void*... yes
checking size of void*... 8
checking to see if we got 64 bits... oh yes
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 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 for Fortran char* mangling scheme... char_ptr
checking if fortran implements CONTIGUOUS attribute... yes
checking if fortran implements allocatable character strings... yes
checking for fortran intrinsic etime... found
checking for fortran intrinsic flush... found
checking for shl_load in -ldld... no
checking for shl_load... no
checking for shl_findsym... no
checking for dlopen in -ldl... yes
checking for dlopen... yes
checking for dlsym... yes
checking for dlerror... yes
checking for dlclose... yes
checking for mpi-directory...
checking for mpi-lib-directory...
checking for mpi-inc-directory... /usr/include/mpi
checking for mpi-library...
checking for mpi-include...
checking for compilation of an MPI program... seems ok
checking for mpf90... no
checking for mpxlf90... no
checking for saxpy_... no
checking for ATL_xerbla in -latlas... no
checking for saxpy_ in -lblas... yes
checking for daxpy_ in -ldaxpy... no
checking for saxpy_ in -lcxml... no
checking for saxpy_ in -ldxml... no
checking for saxpy_ in -lscs... no
checking for saxpy_ in -lcomplib.sgimath... no
checking for saxpy_ in -lblas... (cached) yes
checking for saxpy_ in -lessl... no
checking for saxpy_ in -lessl... (cached) no
checking for saxpy_ in -lblas... (cached) yes
checking for cheev_... no
checking for cheev_ in -llapack... yes
checking for huti_d_gmres_ in -lhuti... yes
checking for eio_init_ in -leiof... yes
checking for dseupd_ in -larpack... yes
checking for pdneupd_ in -lparpack... no
configure: WARNING: No parallel arpack found.
checking for HYPRE_IJMatrixCreate in -lHYPRE_IJ_mv... yes
checking for dmumps_ in -ldmumps... no
checking for dmumps_ in -ldmumps... (cached) no
configure: WARNING: MUMPS not found, some functionaly will be disabled.
checking for umfpack_di_defaults in -lumfpack... yes
checking for mtc_init in -lmatc... yes
checking for main in -lm... yes
configure: error: The MPI version needs parpack. Disabling MPI.

[annier]

Hi Mr. Zhang,
Your ubuntu machine does not have the parpack libraries.
Try installing these libraries first and install the fem module of Elmer as normal.

Code: Select all

  $sudo apt-get install  libblas-dev liblapack-dev libatlas-dev libarpack2-dev \
    libparpack2-dev libmpich2-dev libhypre-dev mpi-default-dev mpi-default-bin

Yours
Anil Kunwar

[zhang liangfu]

Hi Mr Anil
I do it before ,the error is always encounter, should I set some other valuable things? I use the ./configure --help .but I don't know how to do it .I am unfamiliar to teh coumputer.thankyou for your kindness.
yours sincerely
zhang liangfu

[annier]

Hi Mr. Zhang,
What compilers are you using in compile.sh

Code: Select all

export CC="mpicc"
export CXX="mpicxx"
export FC="mpif90"
export F77="mpif90"

or,

Code: Select all

export CC=gcc
export CXX=g++
export FC=gfortran
export F77=gfortran

The first one is for Elmer in parallel whereas the second one is for a general installation of Elmer. I am assuming that you are installing using the latter one compilers.

Yours
Anil Kunwar

[annier]

Hi Mr. Zhang,
As one of the warning is this:

Code: Select all

configure: WARNING: MUMPS not found, some functionaly will be disabled.

I guess you might be using mpi compilers and this is an advanced compiling.
It needs to be done in accordance to
viewtopic.php?f=2&t=2706&p=9354&hilit=i ... 598e#p9354

You can install elmer using general compilers.

So, at the beginning of compilation replace

Code: Select all

export CC="mpicc"
export CXX="mpicxx"
export FC="mpif90"
export F77="mpif90"

with

Code: Select all

export CC=gcc
export CXX=g++
export FC=gfortran
export F77=gfortran

and begin with all the modules of Elmer since other modules are also compiled with mpi compilers.

Yours
Anil Kunwar

[zhang liangfu]

Hi Mr Anil,
you are right .and how should I do ,I just don't know what should I do to solve my error.I compile it one by one from umfpack.......fem,but the fem runs wrong.
Thank you very very much.
yours sincerely
zhang liangfu

[annier]

Hi Mr. Zhang,
Delete the previuosly created directories and then restart the installation.
Please go step by step in accordace to this post.
viewtopic.php?f=2&t=3653&sid=3c5d90f787 ... 74af2c598e

And see till the final.
Yours
Anil Kunwar

[zhang liangfu]

Hi Mr Anil
can you give me some sugesstion on my script as follows,
#!/bin/sh -f
#Compile Elmer modules and install it
#
#The Elmer path is in home directory
export ELMER_HOME=$HOME/elmer-inst
export TCLTK_INCPATH="/usr/include/tcl8.4"

#replace these with your compilers:
export CC="mpicc"
export CXX="mpic++"
export FC="mpif90"
export F77="mpif90"

modules="matc umfpack mathlibs elmergrid meshgen2d eio hutiter"

for m in $modules; do
cd $m
./configure --prefix="ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi=yes --with-mpi-inc-dir=/usr/include/mpi
make clean
make
make install
cd ..
cd fem
./configure --prefix="ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi=yes --with-mpi-inc-dir=/usr/include/mpi --with-lhuti=$ELMER_HOME/lib/libhuti.a
make clean
make
make install
cd ..
done

[annier]

Hi Mr. Zhang,
I guess that the other modules except fem , do not require mpi. Also, i have replaced the compilers for simple installation of Elmer.

Code: Select all

#!/bin/sh -f
#Compile Elmer modules and install it
#
#The Elmer path is in home directory
export ELMER_HOME=$HOME/elmer-inst
export TCLTK_INCPATH="/usr/include/tcl8.4"

#replace these with your compilers:
export CC="gcc"
export CXX="g++"
export FC="gfortran"
export F77="gfortran"

modules="matc umfpack mathlibs elmergrid meshgen2d eio hutiter"

for m in $modules; do
cd $m
./configure --prefix="ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4"
make clean
make
make install
cd ..
cd fem
./configure --prefix="ELMER_HOME" --with-tcltk="-ltcl8.4 -ltk8.4" --with-mpi-inc-dir="/usr/include/mpi" 
make clean
make
make install
cd ..
done

Yours
Anil Kunwar

[annier]

Also, if your computer does not have these compilers previously installed, you can install them as:

Code: Select all

$sudo apt-get install gfortran gcc g++

Yours
Anil Kunwar