[gmx-users] mpi enabled gromacs

[Rajiv Gandhi]

I have recomplied the -fPIC and its complied well. I have not used mpi
cluster before so have some few doubts on it.

Could you please tell me how can i check whether my gromacs installed with
enable_mpi. How do i check the cluster are connected in groamcs? Is that
same procedure of running simulation steps with normal PC such as pdb2gmx,
grompp, or should i need to specify the mpi like pdb2gmx_mpi, grompp_mpi ?


Thanks in advance.

On Mon, Oct 22, 2012 at 6:12 PM, TH Chew <teonghan at gmail.com> wrote:

> 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
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Kind regards

Rajiv