Your compiler setup is unable to link C and Fortran code, which
indicates an improper installation. Try upgrading your compilers - Gnu
4.3 is pretty old at this point.
-Dan
On Mon, Dec 24, 2018 at 8:17 PM Sundar <jubilantsundar.gmail.com> wrote:
>
> Thanks,
>
> I followed your instructions and ran following commands.
> cd $AMBERHOME/AmberTools/src
> ./configure_mpich gnu
>
> And successfully compiled mpich-3.3 within the folder after downloading it
> from http://www.mpich.org/.
> After that do I need to compile the parallel version using
> "cd $AMBERHOME
> ./configure -mpi gnu" and rest of the commands as listed in Amber User
> manual?
>
> If yes,
> "./configure -mpi gnu" gives me following errors.
>
> sundar.copper01:~/tools/amber18/amber18> ./configure -mpi gnu
> Checking for updates...
> Checking for available patches online. This may take a few seconds...
>
> Available AmberTools 18 patches:
>
> No patches available
>
> Available Amber 18 patches:
>
> No patches available
>
>
> AMBER_PREFIX=/u/sundar/tools/amber18/amber18
> AMBER_SOURCE=/u/sundar/tools/amber18/amber18
>
> Using the AmberTools miniconda installation in
> /u/sundar/tools/amber18/amber18/miniconda
> version 2.7.13
>
> Obtaining the gnu compiler suite versions, e.g.:
> gcc -v
> The C version is 4.3.4
> The Fortran version is 4.3.4
>
> Testing the gcc compiler:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Testing the CC compiler:
> CC -fPIC -o testp testp.cpp
> OK
>
> Testing the gfortran compiler:
> gfortran -fPIC -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c
> gfortran -fPIC -O0 -c -o testp.f.o testp.f
> gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> testp.c.o testp.f.o -lgfortran -w
> /usr/lib64/gcc/x86_64-suse-linux/4.3/libgfortran.a(fpu.o): In function
> `*_gfortrani_set_fpu':
> /usr/src/packages/BUILD/gcc-4.3.4-20091019/obj-x86_64-suse-linux/x86_64-suse-linux/libgfortran/./fpu-target.h:43:
> undefined reference to `fedisableexcept'
> /usr/src/packages/BUILD/gcc-4.3.4-20091019/obj-x86_64-suse-linux/x86_64-suse-linux/libgfortran/./fpu-target.h:80:
> undefined reference to `feenableexcept'
> /usr/src/packages/BUILD/gcc-4.3.4-20091019/obj-x86_64-suse-linux/x86_64-suse-linux/libgfortran/./fpu-target.h:72:
> undefined reference to `feenableexcept'
> /usr/src/packages/BUILD/gcc-4.3.4-20091019/obj-x86_64-suse-linux/x86_64-suse-linux/libgfortran/./fpu-target.h:64:
> undefined reference to `feenableexcept'
> /usr/src/packages/BUILD/gcc-4.3.4-20091019/obj-x86_64-suse-linux/x86_64-suse-linux/libgfortran/./fpu-target.h:47:
> undefined reference to `feenableexcept'
> /usr/src/packages/BUILD/gcc-4.3.4-20091019/obj-x86_64-suse-linux/x86_64-suse-linux/libgfortran/./fpu-target.h:88:
> undefined reference to `feenableexcept'
> collect2: ld returned 1 exit status
> ./configure2: line 2643: ./testp: No such file or directory
> Error: Unable to compile mixed C/Fortran code.
> Please check your compiler settings and configure flags.
> Configure failed due to the errors above!
>
> -Jubilant
>
>
>
> On Mon, Dec 24, 2018 at 9:32 AM David Case <david.case.rutgers.edu> wrote:
>
> > On Sun, Dec 23, 2018, Sundar wrote:
> >
> > >$ tail $AMBERHOME/AmberTools/src/fftw3_config.log
> > >
> > >checking for mpicc... no
> > >checking for hcc... no
> > >checking for mpcc... no
> > >checking for mpcc_r... no
> > >checking for mpxlc... no
> > >checking for cmpicc... no
> > >checking for MPI_Init... no
> > >checking for MPI_Init in -lmpi... no
> > >checking for MPI_Init in -lmpich... no
> > >configure: error: could not find mpi library for --enable-mpi
> >
> > It looks like your mpi installation is not correct, and this is the
> > first part of the installation script that catches this.
> >
> > What MPI are you using? What is the result of typing "which mpicc"?
> > (This executable, along with mpif90, needs to be in your PATH).
> >
> > The most straighforward method is to cd $AMBERHOME/AmberTools/src, and
> > run either configure_mpich or configure_openmpi there. This sets up the
> > correct executables and libraries, all inside the AMBERHOME folder.
> >
> > You can also install MPI via package managers; details vary depending on
> > which version of Linux or MacOS you have. But make sure that those
> > installations are using the same compilers as you use for compiling the
> > rest of Amber.
> >
> > ...good luck...dac
> >
> >
>
> --
> Thanks,
> Sundar Thangapandian
> _______________________________________________
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Received on Fri Dec 28 2018 - 06:30:03 PST
