[gmx-users] Installation problem
David van der Spoel
spoel at xray.bmc.uu.se
Thu Dec 29 10:30:59 CET 2005
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
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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
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