[gmx-users] Installation problem
Dhananjay
dhananjay.c.joshi at gmail.com
Fri Dec 30 10:26:34 CET 2005
I have just now tried
which binutils
The output is
GNU which v2.14, Copyright (C) 1999 - 2001 Carlo Wood.
GNU which comes with ABSOLUTELY NO WARRANTY;
This program is free software; your freedom to use, change
and distribute this program is protected by the GPL.
Any suggestion please ?
On 12/30/05, Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de> wrote:
>
> hi
>
> On Friday 30 December 2005 08:34, Dhananjay wrote:
> > Hi Florian Haberl ,
> >
> > Thanks for reply..
> >
> > Please go through the following...
> >
> >
> > On 12/29/05, Florian Haberl < Florian.Haberl at chemie.uni-erlangen.de>
> wrote:
> > >
> > > 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
> >
> >
> > I have alrady installed according to the path suggested. I mean to say
> > that I have not used .rpm files but followed following path:
> > ./configure
> > make
> > make install
> >
> > The installation is sussessfull.
> >
> > >
> > > > 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.
> >
> >
> > Here I have tries again but of no use, still I am getting error
> message
> >
> >
> > make[4]: Leaving directory
> > `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16
> > /binutils/doc'
> > make[3]: Leaving directory
> > `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils- 2.16
> > /binutils/doc'
> > rm -f config.texi
> > echo '@set VERSION 2.16' > config.texi
> > /bin/sh: line 1: config.texi: Permission denied
> > 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
> >
> > You said that " binutils should be installed on you basis system
> > installation else update your
> > linux " . What king of update I needed, whether advance version of
> Linux
> > or upgradation of binutild in the system ?
>
> try something like
> which binutils
> binutils ---version
> to get version information of your installed binutils, normal
> distributions are up to date.
>
> Normally you don`t have to install a new binutils version, perhaps skip
> this step.
>
> >
> >
> >
> > >
> > > > 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
> >
> >
> > Using which and locate I found mpicc at /usr/bin/mpicc
> >
> >
> > Now what should I do next ?
> >
> >
> > Dhananjay
> >
> >
> >
> > >
> > > > 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
> > > > > > > >
> > > > > >
> > >
> > >------------------------------------------------------------------------
>
> > > > > >
> > > > > > > >
> > > > > > > >_______________________________________________
> > > > > > > >gmx-users mailing list
> > > > > > > >gmx-users at gromacs.org <mailto: gmx-users at gromacs.org>
> > > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > > >Please don't post (un)subscribe requests to the list.
> Use
> > > the
> > > > > > > >www interface or send it to
> gmx-users-request at gromacs.org
> > > > > > > <mailto: gmx-users-request at gromacs.org >.
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > 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>
> <
> > > http://xray.bmc.uu.se/%7Espoel>
> > > > > > >
> > > > > >
> > >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > >
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > gmx-users mailing list
> > > > > > > gmx-users at gromacs.org <mailto: gmx-users at gromacs.org >
> > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > > < http://www.gromacs.org/mailman/listinfo/gmx-users>
> > > > > > > Please don't post (un)subscribe requests to the list. Use
> the
> > > > > > > www interface or send it to gmx-users-request at gromacs.org
> > > > > > > <mailto:gmx-users-request at gromacs.org>.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > >
> ------------------------------------------------------------------------
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > gmx-users mailing list
> > > > > > > gmx-users at gromacs.org
> > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > > www interface or send it to gmx-users-request at gromacs.org .
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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> <
> http://xray.bmc.uu.se/%7Espoel>
> > > > > >
> > >
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list
> > > > > > gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > >
> > > Greetings,
> > >
> > > Florian
> > >
> > > --
> > >
> > >
> -------------------------------------------------------------------------------
> > > Florian Haberl
> > > Computer-Chemie-Centrum
> > > Universitaet Erlangen/ Nuernberg
> > > Naegelsbachstr 25
> > > D-91052 Erlangen
> > > Mailto: florian.haberl AT chemie.uni-erlangen.de
> > >
> > >
> -------------------------------------------------------------------------------
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> >
>
> 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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