[gmx-users] problem with mpi configuration.

[Diego Enry]

/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333
<<= just zoom in the middle of the command

right here:

mpi_d--prefix=

 you forgot to put a space between "mpi_d" and "--prefix"

copy&paste the corrected version bellow.
./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332

have fun !


On Wed, Mar 12, 2008 at 4:05 PM, mario ciappy <mariociap at yahoo.it> wrote:
>
>  Thank you very much for help me.
>  I have try to install gromacs 3.3.3 on rhel 4.0.
>  I try to configure gromacs single with the command  "./configure
> --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when
> I try to install, I have this error:
>  usr/bin/install: cannot create regular file
> `/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333': No such
> file or directory
>  make[3]: *** [install-binPROGRAMS] Error 1
>  make[3]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
>  make[2]: *** [install-am] Error 2
>  make[2]: Leaving directory `/home/mario/gromacs-3.3.3/src/kernel'
>  make[1]: *** [install-recursive] Error 1
>  make[1]: Leaving directory `/home/mario/gromacs-3.3.3/src'
>  make: *** [install-recursive] Error 1
>  I have try to edit the end of the configure command "/usr/local/gromacs332"
> with"/usr/local/gromacs333" and "/usr/local/gromacs" but I have anlogue
> errors. Can you help me?
>
>  Thanks in advance.
>
>
>  Mario
> Diego Enry <diego.enry at gmail.com> ha scritto:
>  You should check the user guide.
> http://www.mcs.anl.gov/research/projects/mpich2/documentation/index.php?s=docs
>
> In a nutshell:
> 1) You need is to install mpich in all machines. Actually you can sync
> the mpich install directory (also gromacs).
> 2) You also need to have the same /etc/hosts on every machine. rsync that.
> 3) You need to grant ssh access without password by creating a rsa-key
> for every user
>
> Fell free to private message if you need any additional help.
>
> Ciao.
>
> On Tue, Mar 4, 2008 at 6:04 AM, mario ciappy wrote:
> > Thank's Diego,
> > I'm grateful to you. I have only one question. How can I configure mpi/lam
> > for relaize the comunication between nodes?
> > I have created an hostsfile with my ip addresses.
> > Thank's a lot in advance.
> >
> > Mario
> >
> > Diego Enry ha scritto:
>
>
> >
> > Since you didn't show us the problems you met.. try following this:
> >
> > #1) Download essential packages
> > #1.1) mpich
> > wget
> >
> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz
> >
> > #1.2) fftw
> > wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz
> >
> > #1.3) gromacs
> > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz
> >
> >
> > #2) compile packages:
> >
> > #2.1) mpich
> > tar xvfz mpich2-1.0.6p1.tar.gz
> > cd mpich2-1.0.6p1
> > make distclean
> > ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx
> > --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.2) fftw single
> > tar xvfz fftw-3.1.2.tar.gz
> > cd fftw-3.1.2
> > make distclean
> > ./configure --enable-float --enable-sse --enable-threads
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.3) gromacs single
> > tar xvfz gromacs-3.3.2.tar.gz
> > cd gromacs-3.3.2
> > ./configure --enable-mpi --program-suffix=_mpi
> > --prefix=/usr/local/gromacs332
> > make
> > make install
> > make links
> > make distclean
> > cd ..
> >
> > #2.4) fftw double
> > cd fftw-3.1.2
> > ./configure --enable-sse2 --enable-threads
> > make
> > make install
> > make distclean
> > cd ..
> >
> > #2.2) gromacs double
> > cd gromacs-3.3.2
> > ./configure --enable-mpi --program-suffix=_mpi_d
> > --prefix=/usr/local/gromacs332 --enable-double
> > make
> > make install
> > make links
> > make distclean
> > cd ..
> >
> >
> >
> >
> > On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy wrote:
> > > Dear all,
> > > I'm tried to configure gromacs in parallel but I have meet some
> problems.
> > > I don't understand if the problems are relative to mpi or gromacs
> > > configuration. For this reason I'd be grateful if you explained a
> detailed
> > > installation procedure of all that require to run gromacs in parallel,
> > > started by mpi/lam configuration. I now that is an hard and demanding
> > > request, but it is a big help for me because you are only resource.
> > >
> > > Thank's in advance
> > >
> > > Mario
> > >
> > >
> > > ________________________________
> > > ________________________________
> > >
> > > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> > >
> >
> >
> >
> > --
> > Diego Enry B. Gomes
> > Laboratório de Modelagem e Dinamica Molecular
> > Universidade Federal do Rio de Janeiro - Brasil.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> >
> >
> >
> >
> > ________________________________
> > ________________________________
> > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> >
>
>
>
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
>
>
>
>  ________________________________
>  Inviato da Yahoo! Mail.
>  Il servizio di posta con lo spazio illimitato.
> _______________________________________________
>  gmx-users mailing list    gmx-users at gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>



-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.