Re: [Getfem-users] Problem building getfem++ 3.0.3

[Madhusudan Singh]

Thanks for the response. That clears up a few things. I set a --prefix directive, fixed the ineffective toolbox option (I was mistakenly typing in "directory" instead of "dir"), and then tried again (I do not rely on a make clean, I just delete the directory, recreate it from the tar archive and go from there - just wish to avoid any issues arising from any more undiscovered bugs) :

I checked config.log - you are right; it does ignore the --with-matlab-toolbox-dir and just attempts to create it under /usr/local/getfem (my chosen prefix). No problem - I will create a symlink to my matlab toolbox directory later.

However, compilation fails now with a new error (I have never seen such an error before, so don't even know what to guess) :

creating libgetfem.la
(cd .libs && rm -f 
libgetfem.la && ln -s ../libgetfem.la libgetfem.la)
make[2]: Entering directory `/usr/local/src/science/getfem/getfem++-3.0.3/src'
test -z "/usr/local/getfem/lib" || mkdir -p -- "/usr/local/getfem/lib"
 /bin/sh ../libtool --mode=install /usr/bin/install -c  'libgetfem.la' '/usr/local/getfem/lib/libgetfem.la'
/usr/bin/install -c .libs/libgetfem.lai /usr/local/getfem/lib/libgetfem.la
/usr/bin/install: setting permissions for `/usr/local/getfem/lib/libgetfem.la': No such file or directory
/usr/bin/install -c .libs/libgetfem.a /usr/local/getfem/lib/libgetfem.a
/usr/bin/install: setting permissions for `/usr/local/getfem/lib/libgetfem.a': No such file or directory
chmod 644 /usr/local/getfem/lib/libgetfem.a
ranlib /usr/local/getfem/lib/libgetfem.a
ranlib: could not create temporary file whilst writing archive: No more archived files
make[2]: *** [install-libLTLIBRARIES] Error 1
make[2]: Leaving directory `/usr/local/src/science/getfem/getfem++-3.0.3/src'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/usr/local/src/science/getfem/getfem++-3.0.3/src'
make: *** [install-recursive] Error 1

****  Installation failed. Aborting package creation.

Cleaning up...OK

Bye.

I used the following configure directive for this compilation :

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

The compilation of this package gets more and more interesting (and not in a good way) with each attempt :)

Any help will be appreciated.

With regards,

MS

On Dec 11, 2007 5:15 AM, Richard George < address@hidden> wrote:

Hello,

I think there is a small bug in the documentation of 3.0.3

If you run ./configure --help

 it mentions setting an option --with-matlab-toolbox-dir=

but this option is ignored.

>From line 23970 of ./configure
the script is expecting the argument to be --with-toolbox-dir


# Check whether --with-toolbox-dir was given.
if test "${with_toolbox_dir+set}" = set; then
 withval=$with_toolbox_dir; TOOLBOXDIR="$withval"
else
 TOOLBOXDIR="$prefix/getfem_toolbox"
fi

On Mon, 2007-12-10 at 19:50 -0700, Madhusudan Singh wrote:
> A follow-up to my own response.
>
> I had configured the package using :
>
> ./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
>
> Upon installation, I find that the specified folder above
> - /usr/local/matlab/toolbox/getfem is empty. No matlab files have
> apparently been installed.
>
> After running updatedb, locate gf_plot.m yields :
>
> locate gf_plot.m
> /usr/local/src/science/getfem/getfem
> ++-3.0.3/interface/src/matlab/gf_plot.m
> /usr/local/src/science/getfem/getfem
> ++-3.0.3/interface/src/matlab/NONE/getfem_toolbox/gf_plot.m
>
> Which is just the files in the installation directory, not the
> installed files, which should have been
> in /usr/local/matlab/toolbox/getfem.
>
> To confirm that this is not simply some wierd checkinstall issue, I
> manually ran make install. No change.
>
> I then ran make check.
>
> make  check-TESTS
> make[3]: Entering directory `/usr/local/src/science/getfem/getfem++-
> 3.0.3/tests'
> PASS: ../tests/dynamic_array.pl
> PASS: ../tests/dynamic_tas.pl
> PASS: ../tests/test_int_set.pl
> PASS: ../tests/test_tree_sorted.pl
> PASS: ../tests/poly.pl
> FAIL: ../tests/test_small_vector.pl
> PASS: ../tests/test_kdtree.pl
> PASS: ../tests/test_rtree.pl
> FAIL: ../tests/geo_trans_inv.pl
> PASS: ../tests/test_norm.pl
> PASS: ../tests/test_mesh.pl
> FAIL: ../tests/test_interpolation.pl
> .............
> PASS: ../tests/test_mat_elem.pl
> FAIL: ../tests/test_slice.pl
> FAIL: ../tests/integration.pl
> FAIL: ../tests/test_assembly.pl
> PASS: ../tests/test_interpolated_fem.pl
> ./laplacian /tmp/laplacian.param_592  2>&1 failed
> FAIL: ../tests/laplacian.pl
> ./elastostatic /tmp/elas.param_456  2>&1 failed
> FAIL: ../tests/elastostatic.pl
> FAIL: ../tests/stokes.pl
> FAIL: ../tests/plate.pl
> FAIL: ../tests/test_mesh_im_level_set.pl
> FAIL: ../tests/crack.pl
> ./xfem_dirichlet_demo /tmp/xfem.param_471  2>&1 failed
> FAIL: ../tests/xfem_dirichlet_demo.pl
> FAIL: ../tests/nonlinear_elastostatic.pl
> FAIL: ../tests/dynamic_friction.pl
> FAIL: ../tests/plasticity.pl
> FAIL: ../tests/helmholtz.pl
> PASS: ../tests/schwarz_additive.pl
> ./bilaplacian /tmp/elas.param_861  2>&1 failed
> FAIL: ../tests/bilaplacian.pl
> Gmm tests : Making 1 execution of each test
> Testing  ./gmm_torture01_lusolve.cc
> Testing  ./gmm_torture05_mult.cc
> Testing  ./gmm_torture06_mat_mult.cc
> Testing  ./gmm_torture10_qr.cc
> Testing  ./gmm_torture15_sub.cc
> Testing  ./gmm_torture20_iterative_solvers.cc
> ..................................................
>
> 50 effective experiments with no fault, size = 13 base type :
> St7complexIfE
> solver least square cg  : 50 exp. with no fault, ratio = 0, average nb
> iter = 16.3
> solver bicgstab : 251 exp. with no fault, ratio = 0, average nb iter =
> 52.2
> solver gmres    : 251 exp. with no fault, ratio = 0, average nb iter =
> 8.73
> solver qmr      : 250 exp. with no fault, ratio = 0, average nb iter =
> 10.8
> solver cg       : 200 exp. with no fault, ratio = 0, average nb iter =
> 8.31
> no precond      : 250 exp. with no fault, ratio = 0, average nb iter =
> 31.5
> diag precond    : 200 exp. with no fault, ratio = 0, average nb iter =
> 38.1
> mr precond      : 2 exp. with no fault, ratio = 0, average nb iter =
> 25.5
> ilu precond     : 150 exp. with no fault, ratio = 0, average nb iter =
> 22.4
> ilut precond    : 150 exp. with no fault, ratio = 0, average nb iter =
> 9.03
> ilutp precond   : 150 exp. with no fault, ratio = 0, average nb iter =
> 0.72
> ildlt precond   : 50 exp. with no fault, ratio = 0, average nb iter =
> 1
> ildltt precond  : 50 exp. with no fault, ratio = 0, average nb iter =
> 1.16
> PASS: ../tests/make_gmm_test.pl
> =====================
> 18 of 31 tests failed
> =====================
> make[3]: *** [check-TESTS] Error 1
> make[3]: Leaving directory `/usr/local/src/science/getfem/getfem
> ++-3.0.3/tests'
> make[2]: *** [check-am] Error 2
> make[2]: Leaving directory `/usr/local/src/science/getfem/getfem++-
> 3.0.3/tests'
> make[1]: *** [check-recursive] Error 1
> make[1]: Leaving directory `/usr/local/src/science/getfem/getfem
> ++-3.0.3/tests'
> make: *** [check-recursive] Error 1
>
> Clearly, something is seriously wrong.
>
>
> On Dec 10, 2007 4:46 PM, Madhusudan Singh < address@hidden>
> wrote:
>         Thanks for your suggestions.
>
>         Feeling a little emboldened by your plausible suggested
>         solution, I made a small change to the configure directive
>         after setting the shell variable :
>
>         ./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 --enable-matlab-rpc
>
>         (enabling matlab-rpc)
>
>         and tried again. Now the compilation quits with :
>
>         creating libgetfemint.la
>         (cd .libs && rm -f libgetfemint.la && ln -s ../libgetfemint.la
>         libgetfemint.la )
>         if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../src -I../../src
>         -DGMM_USES_BLAS -I/usr/local/include  -O3 -MT gfi_rpc_server.o
>         -MD -MP -MF ".deps/gfi_rpc_server.Tpo" -c -o gfi_rpc_server.o
>         gfi_rpc_server.c; \
>                 then mv -f ".deps/gfi_rpc_server.Tpo"
>         ".deps/gfi_rpc_server.Po"; else rm -f
>         ".deps/gfi_rpc_server.Tpo"; exit 1; fi
>         if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../src -I../../src
>         -DGMM_USES_BLAS -I/usr/local/include  -O3 -MT gfi_rpc_svc.o
>         -MD -MP -MF ".deps/gfi_rpc_svc.Tpo" -c -o gfi_rpc_svc.o
>         gfi_rpc_svc.c; \
>                 then mv -f ".deps/gfi_rpc_svc.Tpo"
>         ".deps/gfi_rpc_svc.Po"; else rm -f ".deps/gfi_rpc_svc.Tpo";
>         exit 1; fi
>         if gcc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../src -I../../src
>         -DGMM_USES_BLAS -I/usr/local/include  -O3 -MT gfi_rpc_xdr.o
>         -MD -MP -MF ".deps/gfi_rpc_xdr.Tpo" -c -o gfi_rpc_xdr.o
>         gfi_rpc_xdr.c; \
>                 then mv -f ".deps/gfi_rpc_xdr.Tpo"
>         ".deps/gfi_rpc_xdr.Po"; else rm -f ".deps/gfi_rpc_xdr.Tpo";
>         exit 1; fi
>         make[3]: *** No rule to make target
>         `../src/getfem/libgetfem.la', needed by `getfem_server'.
>         Stop.
>         make[3]: Leaving directory
>         `/usr/local/src/science/getfem/getfem++- 3.0.3/interface/src'
>
>         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.
>
>
>         I then removed the rpc option and ran make. It compiled
>         without any problems.
>
>         Any ideas ?
>
>         Thanks,
>
>         MS
>
>
>
>
>         On Dec 10, 2007 11:49 AM, Richard George < address@hidden>
>         wrote:
>                 I think this could be a missing shell variable.
>                 if you type on the command line:
>
>                 echo $MATLAB
>
>                 it should report:
>                 /usr/local/matlab
>
>                 but I think the lines
>
>                 >
>                 >            Here
>                 >
>                 >                MATLAB = /
>                 >
>                 >            Please contact:
>                 >
>
>                 mean this variable is unset and you will see just a
>                 blank line.
>                 try typing:
>
>                 export MATLAB=/usr/local/matlab
>
>                 (or the equivalent) and then 'make' again
>
>                 You should also put that command in your shell
>                 configuration file so you
>                 don't have to type it each time.
>
>                 Best wishes
>
>                 Richard
>
>
>
>                 PS. You might have to run 'make clean' and then
>                 './configure ----'
>                 I'm not sure if the $MATLAB variable is expanded
>                 when ./configure is
>                 run, or when make is run
>
>
>
>
>
>
>                 On Mon, 2007-12-10 at 10:46 -0700, Madhusudan Singh
>                 wrote:
>                 > 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
>
>                 > _______________________________________________
>                 > Getfem-users mailing list
>                 > address@hidden
>                 > https://mail.gna.org/listinfo/getfem-users
>
>
>
>


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