[Gmsh] Singular value decomposition requires LAPACK

Vadivelan C vc at tetrahedrix.com
Tue Jun 2 11:32:32 CEST 2009


Hi Dave,

Thank you very much for helping me. It works well now :D.
 - Ranjith

On Tue, Jun 2, 2009 at 2:41 PM, David Colignon <David.Colignon at ulg.ac.be>wrote:

>
> configure is not able to compile a test program with the blas library :
>
>
>
> configure:5544: checking for dgemm_ in -lblas
>
> configure:5579: g++ -o conftest -g -O2   -L/usr/lib/ -L/usr/lib//lib
> conftest.cpp -lblas -lgfortran -lm  >&5
>
> /usr/bin/ld: cannot find -lgfortran
>
> collect2: ld returned 1 exit status
>
> configure:5585: $? = 1
> configure: failed program was:
> | /* confdefs.h.  */
> | #define PACKAGE_NAME ""
> | #define PACKAGE_TARNAME ""
> | #define PACKAGE_VERSION ""
> | #define PACKAGE_STRING ""
> | #define PACKAGE_BUGREPORT ""
> | #define HAVE_FLTK 1
> | #define HAVE_TREE_BROWSER 1
> | #define HAVE_LIBJPEG 1
> | #define HAVE_LIBPNG 1
> | #define HAVE_LIBM 1
> | #define HAVE_ANN 1
> | #define HAVE_GMM 1
> | #define HAVE_CHACO 1
> | #define HAVE_METIS 1
> | #define HAVE_NETGEN 1
> | #define HAVE_MATH_EVAL 1
> | #define HAVE_LIBZ 1
> | /* end confdefs.h.  */
> |
> | /* Override any GCC internal prototype to avoid an error.
> |    Use char because int might match the return type of a GCC
> |    builtin and then its argument prototype would still apply.  */
> | #ifdef __cplusplus
> | extern "C"
> | #endif
> | char dgemm_ ();
> | int
> | main ()
> | {
> | return dgemm_ ();
> |   ;
> |   return 0;
> | }
> configure:5603: result: no
>
>
>
> the problem may perhaps comes from the ordrering of the directories in your
> $PATH. Configure detects GCC in
> /home/velan/OpenFOAM/ThirdParty/gcc-4.3.1/platforms/linux/bin/gcc , which is
> GCC version 4.3.1 , but detects gfortran in  /usr/bin/gfortran , which is
> version  4.3.2
>
> can you try to configure Gmsh with :
>
> ./configure --prefix=/home/soft/gmsh-2.3.1
> --with-blas-lapack-prefix=/usr/lib/ CC=/usr/bin/gcc CXX=/usr/bin/g++
> FC=/usr/bin/gfortran
>
> Cheers,
>
> Dave
>
>
> --
> David Colignon, Ph.D.
> Collaborateur Logistique du F.R.S.-FNRS
> CÉCI - Consortium des Équipements de Calcul Intensif
> ACE - Applied & Computational Electromagnetics
> Sart-Tilman B28
> Université de Liège
> 4000 Liège - BELGIQUE
> Tél: +32 (0)4 366 37 32
> Fax: +32 (0)4 366 29 10
> WWW:    http://hpc.montefiore.ulg.ac.be/
> Agenda:
> http://www.google.com/calendar/embed?src=david.colignon%40gmail.com
>
>
>
> Vadivelan C wrote:
>
>> I have attached the config.log file.
>>
>>  - Ranjith
>>
>> On Tue, Jun 2, 2009 at 1:44 PM, David Colignon <David.Colignon at ulg.ac.be<mailto:
>> David.Colignon at ulg.ac.be>> wrote:
>>
>>    Can you send us your  config.log  file ?
>>
>>
>>    Dave
>>
>>    --    David Colignon, Ph.D.
>>    Collaborateur Logistique du F.R.S.-FNRS
>>    CÉCI - Consortium des Équipements de Calcul Intensif
>>    ACE - Applied & Computational Electromagnetics
>>    Sart-Tilman B28
>>    Université de Liège
>>    4000 Liège - BELGIQUE
>>    Tél: +32 (0)4 366 37 32
>>    Fax: +32 (0)4 366 29 10
>>    WWW:    http://hpc.montefiore.ulg.ac.be/
>>    Agenda:
>>    http://www.google.com/calendar/embed?src=david.colignon%40gmail.com
>>
>>
>>
>>    Vadivelan C wrote:
>>
>>        Hi Dave,
>>
>>        Thanks for your quick reply. BTW, i have installed lapack, blas
>>        libraries using yum. I have checked
>>
>>        [velan at scram ~]$ ls /usr/lib/{*lapack*,*blas.*}
>>        -rw-r--r-- 1 root root 5.6M 2008-07-08 22:58 /usr/lib/liblapack.a
>>        -rw-r--r-- 1 root root 483K 2008-07-08 22:58 /usr/lib/libblas.a
>>        -rwxr-xr-x 1 root root 4.0M 2008-07-08 22:58
>>        /usr/lib/liblapack.so.3.1.1
>>        -rw-r--r-- 1 root root 6.1M 2008-07-08 22:58
>>        /usr/lib/liblapack_pic.a
>>        -rwxr-xr-x 1 root root 354K 2008-07-08 22:58
>>        /usr/lib/libblas.so.3.1.1
>>        -rwxr-xr-x 1 root root 221K 2008-09-16 13:25
>>        /usr/lib/libgslcblas.so.0.0.0
>>        lrwxrwxrwx 1 root root   20 2009-05-31 19:51
>>        /usr/lib/libgslcblas.so.0 -> libgslcblas.so.0.0.0
>>        lrwxrwxrwx 1 root root   16 2009-06-02 11:21
>>        /usr/lib/libblas.so.3.1 -> libblas.so.3.1.1
>>        lrwxrwxrwx 1 root root   16 2009-06-02 11:21
>>        /usr/lib/libblas.so.3 -> libblas.so.3.1.1
>>        lrwxrwxrwx 1 root root   18 2009-06-02 11:21
>>        /usr/lib/liblapack.so.3.1 -> liblapack.so.3.1.1
>>        lrwxrwxrwx 1 root root   18 2009-06-02 11:21
>>        /usr/lib/liblapack.so.3 -> liblapack.so.3.1.1
>>        lrwxrwxrwx 1 root root   18 2009-06-02 11:21
>>        /usr/lib/liblapack.so -> liblapack.so.3.1.1
>>        lrwxrwxrwx 1 root root   16 2009-06-02 11:21 /usr/lib/libblas.so
>>        -> libblas.so.3.1.1
>>
>>        Which shows, lapack library was installed. During gmsh
>>        installation i have done following steps
>>
>>        ./configure --prefix=/home/soft/gmsh-2.3.1
>>        --with-blas-lapack-prefix=/usr/lib/
>>
>>        But still i am getting those errors. Can you tell me how to find
>>        whether lapack/blas libraries was configured during gmsh
>>        installation. I couldnt find anything on config.status files.
>>
>>        Thanks
>>         - Ranjith
>>
>>        On Tue, Jun 2, 2009 at 12:56 PM, David Colignon
>>        <David.Colignon at ulg.ac.be <mailto:David.Colignon at ulg.ac.be>
>>        <mailto:David.Colignon at ulg.ac.be
>>        <mailto:David.Colignon at ulg.ac.be>>> wrote:
>>
>>           Hi,
>>
>>           it just means that you have to install the lapack library or
>> that
>>           the library was not found at the ./configure step when you
>>        compiled
>>           gmsh.
>>
>>           Cheers,
>>
>>           Dave
>>
>>           --    David Colignon, Ph.D.
>>           Collaborateur Logistique du F.R.S.-FNRS
>>           CÉCI - Consortium des Équipements de Calcul Intensif
>>           ACE - Applied & Computational Electromagnetics
>>           Sart-Tilman B28
>>           Université de Liège
>>           4000 Liège - BELGIQUE
>>           Tél: +32 (0)4 366 37 32
>>           Fax: +32 (0)4 366 29 10
>>           WWW:    http://hpc.montefiore.ulg.ac.be/
>>           Agenda:
>>
>> http://www.google.com/calendar/embed?src=david.colignon%40gmail.com
>>
>>
>>
>>           Vadivelan C wrote:
>>
>>               Hi
>>
>>               I'm newbie to gmsh package. I installed gmsh without any
>>               problem. I tried to work on tutorials. I got the error
>>        message
>>               when i load tutorial/t5.geo
>>
>>
>>               Info    :
>>        -------------------------------------------------------
>>               Info    : Gmsh version   : 2.3.1
>>               Info    : Build OS       : Linux
>>               Info    : Build options  : Fltk TreeBrowser Jpeg Png Ann Gmm
>>               Chaco Metis Netgen MathEval Libz
>>               Info    : Build date     : Tue Jun  2 11:23:42 IST 2009
>>               Info    : Build host     : scram
>>               Info    : Packager       : root
>>               Info    : Home directory : /home/velan/
>>               Info    : Launch date    : Tue Jun  2 11:33:18 2009
>>               Info    : Command line   : gmsh
>>               Info    :
>>        -------------------------------------------------------
>>               Info    : Reading
>>               '/home/velan/Download/PACKAGE/gmsh-2.3.1/tutorial/t5.geo'
>>               Hole 1 (center = {0.166,0.75,0.166}, radius = 0.09) has
>>        number 69!
>>               Hole 2 (center = {0.332,0.75,0.332}, radius = 0.09) has
>>        number 99!
>>               Hole 3 (center = {0.498,0.75,0.498}, radius = 0.09) has
>>        number 129!
>>               Hole 4 (center = {0.664,0.75,0.664}, radius = 0.09) has
>>        number 159!
>>               Hole 5 (center = {0.83,0.75,0.83}, radius = 0.09) has
>>        number 189!
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>               Error   : Singular value decomposition requires LAPACK
>>
>>
>>               Please let me know if you have any idea about this error
>>        message.
>>
>>                - Ranjith
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
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>>
>>
>>
>>
>>
>>
>
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