[Getfem-users] Problem building getfem++ 3.0.3

[Madhusudan Singh]

Hello,

I wish to use Getfem++'s matlab interface to solve Poisson's equation in 3 dimensions. I have gmsh installed for providing the initial mesh to getfem++. I am new to finite elements (but am well versed in electromagnetics), but hope to learn enough to start using this tool quickly.

I would like to report a problem and seek its solution.

Build system :

Linux / Ubuntu 7.10 (Gutsy).
hostname = nanak
uname -m = i686
uname -r = 2.6.22-14-generic
uname -s = Linux
uname -v = #1 SMP Sun Oct 14 23:05:12 GMT 2007
QD and qhull libraries installed.
Matlab 7.4.0.336 (R2007a)
g++ (GCC) 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Next, I created a directory - /usr/local/matlab/toolbox/getfem (my matlab installation is under /usr/local/matlab) and issued the following configure directive :

./configure --enable-dd --enable-qd --enable-qhull --enable-matlab --enable-python --with-matlab-toolbox-directory=/usr/local/matlab/toolbox/getfem --with-qd-lib-dir=/usr/lib

Some messages from the configure process :

...

checking for mex... mex
checking for matlab path...  /usr/local/matlab
checking for mex extension...  .mexglx
Matlab release is : R14

...

configure: creating ./config.status
config.status


: creating Makefile
config.status: creating m4/Makefile
config.status: creating cubature/Makefile
config.status: creating superlu/Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating tests/meshes/Makefile
config.status: creating tests-2.0/Makefile
config.status: creating contrib/Makefile
config.status: creating contrib/icare/Makefile
config.status: creating contrib/delaminated_crack/Makefile
config.status: creating contrib/static_friction/Makefile
config.status: creating contrib/bimaterial_crack_test/Makefile
config.status: creating contrib/bimat_contact_crack_test/Makefile
config.status: creating contrib/mixed_elastostatic/Makefile
config.status: creating contrib/xfem_contact/Makefile
config.status: creating contrib/crack_plate/Makefile
config.status: creating contrib/inter_element_test/Makefile
config.status: creating contrib/aposteriori/Makefile
config.status: creating bin/Makefile
config.status: creating interface/Makefile
config.status: creating interface/bin/Makefile
config.status: creating interface/src/Makefile
config.status: creating interface/src/matlab/Makefile
config.status: creating interface/src/matlab/@gfCvStruct/Makefile
config.status: creating interface/src/matlab/@gfEltm/Makefile
config.status: creating interface/src/matlab/@gfFem/Makefile
config.status: creating 
interface/src/matlab/@gfGeoTrans/Makefile
config.status: creating interface/src/matlab/@gfInteg/Makefile
config.status: creating interface/src/matlab/@gfMesh/Makefile
config.status: creating interface/src/matlab/@gfMeshFem


/Makefile
config.status: creating interface/src/matlab/@gfSlice/Makefile
config.status: creating interface/src/matlab/@gfMeshIm/Makefile
config.status: creating interface/src/matlab/@gfSpmat/Makefile
config.status


: creating interface/src/matlab/@gfPrecond/Makefile
config.status: creating interface/src/matlab/@gfMdBrick/Makefile
config.status: creating interface/src/matlab/@gfMdState/Makefile
config.status: creating interface/src/matlab/@gfLevelSet


/Makefile
config.status: creating interface/src/matlab/@gfMeshLevelSet/Makefile
config.status: creating interface/src/matlab/private/Makefile
config.status: creating interface/src/python/Makefile
config.status


: creating interface/src/python/setup.py
config.status: creating interface/tests/Makefile
config.status: creating interface/tests/meshes/Makefile
config.status: creating interface/tests/matlab/Makefile
config.status


: creating interface/tests/matlab/private/Makefile
config.status: creating interface/tests/python/Makefile
config.status: creating getfem-config
config.status: WARNING:  

getfem-config.in
 seems to ignore the --datarootdir setting
config.status: creating getfem-config-notinstalled
config.status: creating gmm-config
config.status: WARNING:  gmm-config.in
 seems to ignore the --datarootdir setting
config.status: creating config.h
config.status: executing src/getfem/getfem_arch_config.h commands
config.status: creating src/getfem/getfem_arch_config.h - prefix GETFEM for config.h defines
config.status: executing depfiles commands

------------------------------------------------------------------------------
If you want to build the shared library of getfem++, use --enable-shared
(by default, only the static one will be built)
Using the QD library:
   high precision (quad-double precision) polynomials and integration methods are enabled
Using the qhull library for delaunay triangulations.

Link options for the BLAS library: -lblas -lg2c
You can give the location of your prefered blas library with either
the --with-blas=<lib> option, or the BLAS_LIBS environment variable
for example: ./configure BLAS_LIBS="-L/usr/lib/atlas/sse2 -lblas"

---------------------------------------
Ready to build getfem++
  building MATLAB interface: YES
  building PYTHON interface: YES (requires numarray)
---------------------------------------


I next use checkinstall to create a debian/ubuntu package (this just calls make and creates a convenient deb package).


Compilation runs for a long time and then stops at :

mex -output gf_matlab -g CDEBUGFLAGS="-O3" LD="g++" \
        -I. -I./.. -DMATLAB_RELEASE=14 \
        ./gfm_mex.c ./gfm_common.c ./../gfi_array.c \
        ../.libs/libgetfemint.a ../../../src/.libs/libgetfem.a -lqhull  -lblas -lg2c /usr/lib/libqd.a -lm  || (rm gf_matlab.mexglx; false)
/bin/pwd: couldn't find directory entry in `..' with matching i-node
/bin/pwd: couldn't find directory entry in `../../..' with matching i-node

    Sorry! No options file was found for mex.
           The mex script must be able to source
           an options file to define compiler flags
           and other settings.  This options file
           is normally found in MATLAB/bin/mexopts.sh.
           Please check to make sure that your installation
           is complete and includes this file.

           Here

               MATLAB = /

           Please contact:

               MathWorks Technical Support

           for further assistance.

rm: cannot remove `gf_matlab.mexglx': No such file or directory
make[4]: *** [gf_matlab.mexglx] Error 1
make[4]: Leaving directory `/usr/local/src/science/getfem/getfem++-3.0.3/interface/src/matlab'
make[3]: *** [install-recursive] Error 1
make[3]: Leaving directory `/usr/local/src/science/getfem/getfem++-
3.0.3/interface/src/matlab'
make[2]: *** [install-recursive] Error 1
make[2]: Leaving directory `/usr/local/src/science/getfem/getfem++-3.0.3/interface/src'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/usr/local/src/science/getfem/getfem++-
3.0.3/interface'
make: *** [install-recursive] Error 1

****  Installation failed. Aborting package creation.

Cleaning up...OK

Bye.

Its strange that the process above is using the matlab root directory as '/' above after discovering it (correctly) in the configure process to be /usr/local/matlab. 
The detected matlab release is also wrong.

Could you please advise as to how these bugs are to be handled ?

I am attaching the config.log file to this email for your convenience.

With regards,


MS

config.log
Description: Text Data