[gmx-users] Installation problem
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Thu Dec 29 13:39:29 CET 2005
hi,
On Thursday 29 December 2005 13:19, Dhananjay wrote:
> Hi all,
>
> I have tried fresh installation on the node.
> I got following errors....
> What is wrong here please tell me ?
>
> Gromacs-3.3
>
> 1. lam-7.0.6 installed.
>
> 2. fftw-3.0.1 installed by downloading fftw-3.0.1.tar.gz
with downloading this it`s not installed ...
follow the howto on gromacs.org
>
> 2. binutils can not install. Errors are as follows..
>
> make[2]: *** [config.texi] Error 1
> make[2]: Leaving directory
> `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16
> /binutils/doc'
> make[1]: *** [install-recursive] Error 1
> make[1]: Leaving directory
> `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16/binutils'
> make: *** [install-binutils] Error 2
binutils should be installed on you basis system installation else update your
linux.
>
> 3. Gromacs installation tried with mpi option as follows
>
> ./configure --enable-mpi --enable-shared
>
> the error message:
>
> mpicc: No such file or directory
> make[4]: *** [libgmx_mpi.la] Error 1
> make[4]: Leaving directory
> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src/gmxlib'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory
> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory
> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory
> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src'
> make: *** [all-recursive] Error 1
>
> Waiting for reply...
seems you don`t have a proper mpich installation
try
which mpicc to see if you have installed
perhaps with (s)locate or find you can see if mpich is installed proper.
You also have to add then the directory to your path, if you use something
like (t)csh than: setenv $PATH foundedpath:$PATH
>
> On 12/29/05, Dhananjay <dhananjay.c.joshi at gmail.com> wrote:
> >
> > Hello David,
> >
> > Yes I am also now confused and according to my administrator I have 16
> > nodes having operating system linux and the master is SF440 which is
> > having Solaries 9.0 operating system and N1GE 6.0 Software.
> >
> > Well I will compile every thing on one of the node and let you know the
> > results.
> >
> > Still if you have any thing to say please reply me ...
> >
> > Thanks..
> >
> >
> > Dhananjay
> >
> >
> >
> > On 12/29/05, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> > >
> > > Dhananjay wrote:
> > > > Thanks for reply,
> > > >
> > > >
> > > > Well before that let me tell you about my system that just now I
> > > > discussed with administrator.
> > > >
> > > > I have 16 node grid. (In last mail I said that I have 8 nodes but now
> > > I
> > > > can use all 16 nodes)
> > > >
> > > > In details:
> > > >
> > > > Operating System is Redhat WS 3.0 and 16 nodes are excutation host
> > > which
> > > > are installed by N1Grid Engine 6.0 (i.e. N1GE 6.0 )
> > > >
> > > > Master N1GE is SF440 which is having Solaries 9.0 operating system
> > > and
> > > > N1GE 6.0 Software.
> > >
> > > This is confusing, you say you have Redhat WE 3.0 and the lines below
> > > show that you have Linux on your grid master, simultaneously you say
> > > that you have Solaris on the master node. It is very unlikely that it
> > > will work to mix operating systems.
> > > The easiest way is to install gromacs on the master node and use NFS to
> > > ount a disk on the client nodes. You can even do it in your home
> > > directory, provided it is called the same everywhere. Then the
> > > instructions on the gromacs site should be sufficient to install.
> > >
> > > If however the master runs solaris and the clients/nodes run Linux then
> > > you should compile everything on one of the nodes.
> > >
> > >
> > >
> > > >
> > > > Also when I typed "uname -a" on command line I got following
> > > information:
> > > >
> > > > Linux cdfd-grid-master 2.4.21-19.ELsmp #1 SMP Thu Aug 12 23:22:47 EDT
> > > > 2004 x86_64 x86_64 x86_64 GNU/Linux
> > > >
> > > > I want to install Gromacs parallel version. Will installation on
> > > > master N1GE is sufficient or I have to install it on all the nodes ?
> > > >
> > > > Second thing is master N1GE is having Solaries 9.0 operating System.
> > > So
> > > > will it be possible to install Gromacs-3.3 on Solaries 9.0 ?
> > > >
> > > > Let me tell you that I am not master of Computer Adminitration area
> > > but
> > > > still I wish to workout this installation. Therefore I am following
> > > > your instructions and suggestions...
> > > >
> > > >
> > > > On 12/28/05, *David van der Spoel* <spoel at xray.bmc.uu.se
> > > > <mailto: spoel at xray.bmc.uu.se>> wrote:
> > > >
> > > > Dhananjay wrote:
> > > >
> > > > > Hello all,
> > > > >
> > > > > I have tried and successfully installed Gromacs-3.3 on single
> > > node.
> > > > >
> > > > > Now I want to install parallel gromacs.
> > > >
> > > >
> > > > start (on the master node) with make distclean, then start from
> > > the
> > > > configure step again. It could be that the mpi library you have
> > > > installed is not in the proper binary format (i.e. 32 vs 64 bits).
> > > >
> > > > >
> > > > > when I tried it on the same node, I got error as follows:
> > > > >
> > > > >
> > > >
> > > /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../../lib64/libmpi.a:
> > > > > could not read symbols: Bad value
> > > > > collect2: ld returned 1 exit status
> > > > > mpicc: No such file or directory
> > > > > make[4]: *** [libgmx_mpi.la] Error 1
> > > > > make[4]: Leaving directory
> > > > >
> > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3
> > > /src/gmxlib'
> > > > > make[3]: *** [all-recursive] Error 1
> > > > > make[3]: Leaving directory
> > > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-
> > > > 3.3/src/gmxlib'
> > > > > make[2]: *** [all-recursive] Error 1
> > > > > make[2]: Leaving directory
> > > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3
> > > /src'
> > > > > make[1]: *** [all] Error 2
> > > > > make[1]: Leaving directory
> > > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-
> > > 3.3/src'
> > > > > make: *** [all-recursive] Error 1
> > > > >
> > > > >
> > > > > I could not understand the meaning of these erre. Will anybody
> > > please
> > > > > tell me ?
> > > > >
> > > > > Presently I can use 8 nodes. Is there any specific
> > > procedure/steps of
> > > > > installation on nodes/grid ?
> > > > > I mean to say should I start installation from master node ?
> > > > >
> > > > > 2 out og 8 nodes has gromacs-3.3 alrady installed.
> > > > >
> > > > > Dhananjay
> > > > >
> > > > >------------------------------------------------------------------------
> > >
> > > > >
> > > > >_______________________________________________
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> > > > >
> > > >
> > > >
> > > > --
> > > > David.
> > > >
> > > ________________________________________________________________________
> > > >
> > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
> > > group,
> > > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > > spoel at xray.bmc.uu.se
> > > > <mailto:spoel at xray.bmc.uu.se> spoel at gromacs.org
> > > > <mailto:spoel at gromacs.org> http://xray.bmc.uu.se/~spoel<http://xray.bmc.uu.se/%7Espoel>
> > > >
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > >
> > > >
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> > > >
> > > >
> > > ------------------------------------------------------------------------
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> > >
> > > --
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > > phone: 46 18 471 4205 fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se spoel at gromacs.org
> > > http://xray.bmc.uu.se/~spoel <http://xray.bmc.uu.se/%7Espoel>
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> >
>
Greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
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