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

[siamak ardekani]

Dear Steve,

Thanks again for the comment. Finally, I was able install N3 and make it
run. To test the performance I tried to run nu_correct on one of the data
files located in the N3/testing folder named block.mnc. However, I didn't
see any difference before and after correction. I also ran the program on a
real MRI brain data without any success (using different combinations
of -stop, -distance, -iteration and -fwhm). Is there any appropriate way to
check the algorithm and make sure that installation has been done ok.

Thanks,

Siamak


----- Original Message ----- 
From: "Steve ROBBINS" <stever@bic.mni.mcgill.ca>
To: <minc-users@bic.mni.mcgill.ca>
Sent: Thursday, December 11, 2003 6:29 AM
Subject: Re: [MINC-users] installation problem with N3 on Linux (red hat 9)


> 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
> >
> >
> >
> >