[gmx-users] mpi enabled gromacs

[Rajiv Gandhi]

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