[gmx-users] problem with mpi configuration.
Dr. Niharendu Choudhury
nihcho at barc.gov.in
Thu Mar 13 12:27:45 CET 2008
Dear Pohl,
I think your prefix directory /usr/local/gromacs332 is not accesible for
writting. Try to creat new directories with other names and use those in
prefix.
Have you setenv for the include and lib of the fftw files?
(For instance, assume we have installed FFTW with --prefix=/home/joe/fftw.
If your shell is tcsh, you set
setenv CPPFLAGS -I/home/joe/fftw/include
setenv LDFLAGS -L/home/joe/fftw/lib
or, if you are using a bash shell:
export CPPFLAGS=-I/home/joe/fftw/include
export LDFLAGS=-L/home/joe/fftw/lib )
If not do that.
Nihar
Quoting Jens Pohl <Pohl.Jens at web.de>:
>
> > -----Ursprüngliche Nachricht-----
> > Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Gesendet: 12.03.08 20:06:55
> > An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Betreff: Re: [gmx-users] problem with mpi configuration.
>
>
> > 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.
>
> Hallo Mario!
> (Maybe) you have to install as root. When I tried to install gromacs as user,
> I had similar problems.
> Jens
>
> >
> > 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.
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
> >
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*************************************************************************
* *
* Dr. Niharendu Choudhury Tel: 91-22-2559 5089 *
* Theoretical Chemistry Section, Fax: 91-22-2550 5151 *
* RC & CD Division, Chemistry Group, 91-22-2551-9613 *
* Mod. Lab, Email: nihcho at barc.gov.in *
* Trombay, Mumbai-400 085 *
* INDIA *
* *
* Residence Tel. No. 91-22-2552 7832 *
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