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-- B. Lachele Foley, PhD '92,'02 Assistant Research Scientist Complex Carbohydrate Research Center, UGA 706-542-0263 lfoley.ccrc.uga.edu ----- Original Message ----- From: Jason Swails [mailto:jason.swails.gmail.com] To: AMBER Developers Mailing List [mailto:amber-developers.ambermd.org] Sent: Tue, 24 Nov 2009 18:27:28 -0500 Subject: Re: [AMBER-Developers] AT 1.3 config fails for alternate gnu location > 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 > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers > _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Tue Nov 24 2009 - 17:00:03 PST