Your LD_LIBRARY_PATH variable also has to be set to correctly find your
library files, so you'll want to make sure that the order of GNU compilers
found in PATH is the same as the GNU compiler libraries found in
LD_LIBRARY_PATH. What's likely happening is it's trying to link the
compiler libraries from the /usr/bin installation to the /usr/local/bin
compilers. If this is a machine that you have root permissions for, you may
consider moving all of the /usr/bin/ compilers (which I'm assuming are older
versions?) to .bak files (i.e. sudo mv /usr/bin/gfortran
/usr/bin/gfortran.bak, etc.) and creating links in the /usr/bin that point
to the /usr/local/bin installations (but you have to do the same for the
libraries).
However, is there any reason to have two sets of gnu compilers? It seems a
bit strange to me that ld couldn't find gfortranbegin since
libgfortranbegin.a is present in both gcc/lib directories. What does "echo
$LD_LIBRARY_PATH" return?
Good luck!
Jason
On Tue, Nov 24, 2009 at 4:28 PM, Lachele Foley <lfoley.ccrc.uga.edu> wrote:
> I have an alternate gcc/gfortran installed on a system in /usr/local/bin
> (etc.). If I rearrange my PATH so that the system sees the original install
> (in /usr/bin), AT configures and compiles (testing now). If I leave my path
> so it finds the gcc/gfortran in /usr/local/bin first, the configure fails
> with complaints about gfortran and netcdf.
>
> If there's a way in the configure script to specify alternate library
> paths, I don't see it. I can alter the config.h file, of course, but not if
> the configure script never makes one.
>
> On this system:
>
> Linux shaw.nuigalway.ie 2.6.18-128.1.10.el5xen #1 SMP Wed Apr 29 14:24:51
> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
>
>
> ========================================================
> [installer.shaw src]$ ./configure gnu
> Setting AMBERHOME to /array2/programs/amber11_AT_20091124
>
>
> Obtaining the gnu suite version:
> gcc -v
> The version is 4.3.1
>
> Testing the gcc compiler:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Obtaining the C++ compiler version:
> g++ -v
> The version is 4.3.1
> OK
>
> Testing the gfortran compiler:
> gfortran -O0 -o testp testp.f
> /usr/bin/ld: cannot find -lgfortranbegin
> collect2: ld returned 1 exit status
> ./configure: line 744: ./testp: No such file or directory
> Unable to compile a Fortran program using gfortran -O0
> We will be unable to compile sqm
>
> Testing flex:
> OK
>
> Configuring NetCDF; (may be time-consuming)
>
> Error: NetCDF configure returned 1
> NetCDF configure failed! Check the netcdf_config.log file.
> ========================================================
>
>
>
> the netcdf log complains:
>
> checking if Fortran "byte" is C "signed char"... configure: error: Could
> not link conftestf.o
> and conftest.o
>
> [installer.shaw src]$ which gfortran
> /usr/local/bin/gfortran
> [installer.shaw src]$ which gcc
> /usr/local/bin/gcc
> [installer.shaw src]$ locate conftestf.o
> [installer.shaw src]$ locate conftest.o
> [installer.shaw src]$
>
> Regarding gfortran:
>
> [installer.shaw src]$ locate gfortranbegin
> /application_downloads/gcc-4.3.1/x86_64-unknown-linux-gnu/libgfortran/
> libgfortranbegin.la
>
> /application_downloads/gcc-4.3.1/x86_64-unknown-linux-gnu/libgfortran/.libs/libgfortranbegin.a
>
> /application_downloads/gcc-4.3.1/x86_64-unknown-linux-gnu/libgfortran/.libs/
> libgfortranbegin.la
>
> /application_downloads/gcc-4.3.1/x86_64-unknown-linux-gnu/libgfortran/.libs/libgfortranbegin.lai
> /usr/lib/gcc/x86_64-redhat-linux/4.1.1/libgfortranbegin.a
> /usr/lib/gcc/x86_64-redhat-linux/4.1.1/32/libgfortranbegin.a
> /usr/local/gcc/x86_64-unknown-linux-gnu/32/libgfortran/libgfortranbegin.la
>
> /usr/local/gcc/x86_64-unknown-linux-gnu/32/libgfortran/.libs/libgfortranbegin.a
> /usr/local/gcc/x86_64-unknown-linux-gnu/32/libgfortran/.libs/
> libgfortranbegin.la
>
> /usr/local/gcc/x86_64-unknown-linux-gnu/32/libgfortran/.libs/libgfortranbegin.lai
> /usr/local/gcc/x86_64-unknown-linux-gnu/libgfortran/libgfortranbegin.la
>
> /usr/local/gcc/x86_64-unknown-linux-gnu/libgfortran/.libs/libgfortranbegin.a
> /usr/local/gcc/x86_64-unknown-linux-gnu/libgfortran/.libs/
> libgfortranbegin.la
>
> /usr/local/gcc/x86_64-unknown-linux-gnu/libgfortran/.libs/libgfortranbegin.lai
>
>
>
> :-) Lachele
> --
> B. Lachele Foley, PhD '92,'02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263
> lfoley.ccrc.uga.edu
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Nov 24 2009 - 15:30:02 PST
