[gmx-users] Installation problem
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Fri Dec 30 09:07:13 CET 2005
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
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> > the
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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>
> > > > > >
> > > > >
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list
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> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > ------------------------------------------------------------------------
> > > > > >
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list
> > > > > > gmx-users at gromacs.org
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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>
> > > > >
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > _______________________________________________
> > > > > gmx-users mailing list
> > > > > gmx-users at gromacs.org
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> > > > > 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
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> > 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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