[gmx-users] Installation problem
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Fri Dec 30 10:46:58 CET 2005
On Friday 30 December 2005 10:26, Dhananjay wrote:
> 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 ?
>
take a look at http://www.gromacs.org/installation/prerequisites.php
The configuration script will check this for you, and complain load
if your version is too old. GNU Binutils 2.12 and later are know to work,
but some earlier ones might also be OK - it is checked by the configuration
script, which will complain loud if there is a problem. If your version is too
old you can download and install from this source:
so should be ok and you can start with compiling gromacs
./configure ...
>
>
> 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
> >
> > -------------------------------------------------------------------------------
> > _______________________________________________
> > 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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