[gmx-users] Installation problem
Dhananjay
dhananjay.c.joshi at gmail.com
Thu Dec 29 13:19:50 CET 2005
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
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
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...
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>
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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
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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
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> >
>
>
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