[gmx-users] problem with mpi configuration.
mario ciappy
mariociap at yahoo.it
Wed Mar 12 20:05:36 CET 2008
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
> >
> >
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>
>
> --
> Diego Enry B. Gomes
> Laboratório de Modelagem e Dinamica Molecular
> Universidade Federal do Rio de Janeiro - Brasil.
> _______________________________________________
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>
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--
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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