[MINC-users] installation problem with N3 on Linux (red hat 9)

[Steve ROBBINS]

On Wed, Dec 10, 2003 at 09:08:07PM -0800, siamak Ardekani wrote:
> Dear Steve,
> 
> Thank you for the reply. I installed blas/lapack and now the
> configuration recognize the library. However, now it complains about
> netcdf library. I used the rpm file provided at
> http://www.bic.mni.mcgill.ca/software/distribution to install the netcdf
> and MINC.
> 
>  
> [root@localhost MNI_N3]# rpm -qpl netcdf-3.5.0-linux-2.4-intel.rpm
> /usr/local/mni/bin
> /usr/local/mni/bin/ncdump
> /usr/local/mni/bin/ncgen
> /usr/local/mni/include
> /usr/local/mni/include/netcdf.h
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

That's in /usr/local/mni/include, a path not normally searched by
the C compiler.  You need to tell the compiler to look there.

Re-run configure as follows

	./configure --with-build-path=/usr/local/mni --prefix=/usr/local/mni

Cheers,
-Steve





> /usr/local/mni/lib
> /usr/local/mni/lib/libnetcdf.a
> /usr/local/mni/man
> /usr/local/mni/man/man1
> /usr/local/mni/man/man1/ncdump.1
> /usr/local/mni/man/man1/ncgen.1
> /usr/local/mni/man/man3
> /usr/local/mni/man/man3/netcdf.3
> 
> 
> when I launch configure:
> 
> 
> [root@localhost N3]# ./configure --prefix=/usr/local/mni
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> 
> [....]
> 
> 
> 
> checking for sgemm_ in -lblas... (cached) yes
> checking for sgemm_ in -lessl... no
> checking for sgemm_ in -lblas... (cached) yes
> checking for cheev_... no
> checking for cheev_ in -llapack... yes
> checking for library EBTKS... yes
> checking for library m... yes
> checking for library netcdf... no
> configure: error: cannot find required library netcdf
> [root@localhost N3]#
> 
> 
> looking at config.log :
> 
> 
> 
> configure:6803: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG 
> conftest.c -lm
>  -lEBTKS -lm  >&5
> configure:6809: $? = 0
> configure:6812: test -z                          || test ! -s
> conftest.err
> configure:6815: $? = 0
> configure:6818: test -s conftest
> configure:6821: $? = 0
> configure:6832: result: yes
> configure:6841: checking for library netcdf
> configure:6868: /usr/bin/cc -o conftest -O -Df2cFortran -DNDEBUG 
> conftest.c -ln
> etcdf -lm -lEBTKS -lm  >&5
> conftest.c:16:20: netcdf.h: No such file or directory
> configure:6874: $? = 1
> configure: failed program was:
> | /* confdefs.h.  */
> |
> | #define PACKAGE_NAME ""
> | #define PACKAGE_TARNAME ""
> | #define PACKAGE_VERSION ""
> | #define PACKAGE_STRING ""
> | #define PACKAGE_BUGREPORT ""
> | #define PACKAGE "N3"
> | #define VERSION "1.07"
> | #ifdef __cplusplus
> | extern "C" void std::exit (int) throw (); using std::exit;
> | #endif
> | #define HAVE_BLAS 1
> | #define HAVE_LAPACK 1
> | /* end confdefs.h.  */
> | #include <netcdf.h>
> | #ifdef F77_DUMMY_MAIN
> |
> | #  ifdef __cplusplus
> |      extern "C"
> | #  endif
> |    int F77_DUMMY_MAIN() { return 1; }
> |
> | #endif
> | int
> | main ()
> | {
> | int i = ncopen("",0);
> |   ;
> |   return 0;
> | }
> configure:6897: result: no
> configure:6900: error: cannot find required library netcdf
> 
> 
> 
> I was wondering why it complains about netcdf.h where it is already
> installed in the correct location?
> 
> Thanks,
> 
> Siamak
> 
> 
> 
> 
> On Wed, 2003-12-10 at 09:32, Steve ROBBINS wrote:
> > On Tue, Dec 09, 2003 at 11:11:55PM -0800, siamak Ardekani wrote:
> > > Dear All,
> > > 
> > > I was checking the archive and noticed a message posted by one of the
> > > members describing a problem similar to mine. Basically, I am trying to
> > > install MNI_N3 version 1.07 on a Linux box running red hat 9. I got the
> > > following error while executing the configure:
> > >
> > > [root@localhost N3]# ./configure --prefix=/usr/local/MNI
> > 
> >   [...]
> > 
> > > checking for library F77... no
> > > configure: error: cannot find required library F77
> > > 
> > > I have already installed CLAPACK in /usr/local directory. Although, I am
> > > not sure if configure can recognize the library.
> > 
> > To diagnose this problem, you need to look through "config.log" for
> > the error messages.  
> > 
> > With regards to blas/lapack, you have two options.  
> > 
> > #1 Install vendor packages.  You need to have the "developer" package
> > installed.  For Debian, the package names are "blas-dev" and "lapack-dev".
> > I'm guessing that redhat has something similar.
> > 
> > 
> > #2 Install clapack as described in N3's INSTALL file.  In particular,
> > 
> >   N3 requires the the three libraries be named "libF77.a",
> >   "libblas.a", and "liblapack.a" and that their associated header files
> >   ("f2c.h" and "blaswrap.h") be installed on the system. You need to
> >   manually copy the libraries and header files to the appropriate
> >   pathnames on your system.
> > 
> > The three ".a" files should be in /usr/local/lib, and the ".h" files
> > should be in /usr/local/include.
> > 
> > Regards,
> > -Steve
> > 
> > 
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > 
> 
> _______________________________________________
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> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users