[gmx-users] mpi enabled gromacs

[TH Chew]

Hi, I think you need to recompile your mpi library. See the "recompile with
-fPIC"? You need to recompile your mpi library with that option. At least
that is what I did last time when I install GROMACS.
On Oct 22, 2012 5:04 PM, "Rajiv Gandhi" <grajiv03 at gmail.com> wrote:

> Dear Gromacs users,
>
> I have been trying to install mpi enabled gromacs in my cluster. I have
> followed the exact procedure which is described in gromacs manual by
> giving following command line.
>
> ./configure --program-suffix=_mpi --enable-mpi
>
> I get only this following error after i command " make mdrun "
>
> usr/bin/ld: /home/rajiv/lam/lib/libmpi.a(csize.o): relocation R_X86_64_32
> against `lam_mpi_comm_world' can not be used when making a shared object;
> recompile with -fPIC
> /home/rajiv/lam/lib/libmpi.a: could not read symbols: Bad value
> collect2: error: ld returned 1 exit status
> mpicc: No such file or directory
> make[2]: *** [libgmx_mpi.la] Error 1
> make[2]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/gmxlib'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/gmxlib'
> (cd ./src/mdlib && make install ; exit 0)
> make[1]: Entering directory `/home/rajiv/gromacs-4.5.5/src/mdlib'
> make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by `
> libmd_mpi.la'.  Stop.
> make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/mdlib'
> (cd ./src/kernel && make install-libLTLIBRARIES ; exit 0)
> make[1]: Entering directory `/home/rajiv/gromacs-4.5.5/src/kernel'
> /bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
> -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined
> -version-info 6:0:0  -L/home/rajiv/fftw/lib   -o
> libgmxpreprocess_mpi.la-rpath /home/rajiv/gmx/lib add_par.lo
> compute_io.lo convparm.lo
> fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
> gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
> readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
> topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
> vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
> unhandled
> argument `../mdlib/libmd_mpi.la'
> make[1]: *** [libgmxpreprocess_mpi.la] Error 1
> make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/kernel'
> (cd ./src/kernel && make install-mdrun ; exit 0)
> make[1]: Entering directory `/home/rajiv/gromacs-4.5.5/src/kernel'
> /bin/sh ../../libtool --tag=CC   --mode=link mpicc  -O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
> -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined
> -version-info 6:0:0  -L/home/rajiv/fftw/lib   -o
> libgmxpreprocess_mpi.la-rpath /home/rajiv/gmx/lib add_par.lo
> compute_io.lo convparm.lo
> fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo
> gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo
> readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo
> topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo
> vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm
> libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or
> unhandled
> argument `../mdlib/libmd_mpi.la'
> make[1]: *** [libgmxpreprocess_mpi.la] Error 1
> make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/kernel'
> [root at masters gromacs-4.5.5]#
>
>
> Please advice me how do i install mpi based gromacs without having any
> error? Thanks in advance.
>
>
>
> Regards
>
> Rajiv
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