[Gmsh] Singular value decomposition requires LAPACK

David Colignon David.Colignon at ulg.ac.be
Tue Jun 2 11:11:12 CEST 2009


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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