Hi <span class="gmail_quote">Florian Haberl ,<br>
<br>
Thanks for reply..<br>
<br>
Please go through the following...<br>
<br>
</span><br><div><span class="gmail_quote">On 12/29/05, <b class="gmail_sendername">Florian Haberl</b> <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de">Florian.Haberl@chemie.uni-erlangen.de</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">hi,<br><br>On Thursday 29 December 2005 13:19, Dhananjay wrote:<br>> Hi all,<br>><br>> I have tried fresh installation on the node.
<br>> I got following errors....<br>> What is wrong here please tell me ?<br>><br>> Gromacs-3.3<br>><br>> 1. lam-7.0.6 installed.<br>><br>> 2. fftw-3.0.1 installed by downloading fftw-3.0.1.tar.gz
<br>with downloading this it`s not installed ...<br>follow the howto on <a href="http://gromacs.org">gromacs.org</a></blockquote><div><br>
I have alrady installed according to the path suggested. I mean
to say that I have not used .rpm files but followed
following path:<br>
./configure<br>
make<br>
make install<br>
<br>
The installation is sussessfull.<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">><br>> 2. binutils can not install. Errors are as follows..<br>><br>> make[2]: *** [
config.texi] Error 1<br>> make[2]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16<br>> /binutils/doc'<br>> make[1]: *** [install-recursive] Error 1<br>> make[1]: Leaving directory
<br>> `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16/binutils'<br>> make: *** [install-binutils] Error 2<br><br>binutils should be installed on you basis system installation else update your<br>linux.
</blockquote><div><br>
Here I have tries again but of no use, still I am getting error message <br>
<br>
<br>
</div>make[4]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16/binutils/doc'<br>
make[3]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16/binutils/doc'<br>
rm -f config.texi<br>
echo '@set VERSION 2.16' > config.texi<br>
/bin/sh: line 1: config.texi: Permission denied<br>
make[2]: *** [config.texi] Error 1<br>
make[2]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16/binutils/doc'<br>
make[1]: *** [install-recursive] Error 1<br>
make[1]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16/binutils'<br>
make: *** [install-binutils] Error 2<br>
<br>
You said that " binutils should be installed on you basis system installation else update your<br>
linux " . What king of update I needed, whether advance version of Linux or upgradation of binutild in the system ?<br>
<br>
<br>
<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">><br>> 3. Gromacs installation tried with mpi option as follows<br>><br>> ./configure --enable-mpi --enable-shared
<br>><br>> the error message:<br>><br>> mpicc: No such file or directory<br>> make[4]: *** [libgmx_mpi.la] Error 1<br>> make[4]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-
3.3/src/gmxlib'<br>> make[3]: *** [all-recursive] Error 1<br>> make[3]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src/gmxlib'<br>> make[2]: *** [all-recursive] Error 1
<br>> make[2]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src'<br>> make[1]: *** [all] Error 2<br>> make[1]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-
3.3/src'<br>> make: *** [all-recursive] Error 1<br>><br>> Waiting for reply...<br><br>seems you don`t have a proper mpich installation<br>try<br>which mpicc to see if you have installed<br>perhaps with (s)locate or find you can see if mpich is installed proper.
<br>You also have to add then the directory to your path, if you use something<br>like (t)csh than: setenv $PATH foundedpath:$PATH</blockquote><div><br>
Using which and locate I found mpicc at /usr/bin/mpicc <br>
<br>
<br>
Now what should I do next ?<br>
<br>
<br>
Dhananjay<br>
<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">><br>> On 12/29/05, Dhananjay <<a href="mailto:dhananjay.c.joshi@gmail.com">
dhananjay.c.joshi@gmail.com</a>> wrote:<br>> ><br>> > Hello David,<br>> ><br>> > Yes I am also now confused and according to my administrator I have 16<br>> > nodes having operating system linux and the master is SF440 which is
<br>> > having Solaries 9.0 operating system and N1GE 6.0 Software.<br>> ><br>> > Well I will compile every thing on one of the node and let you know the<br>> > results.<br>> ><br>> > Still if you have any thing to say please reply me ...
<br>> ><br>> > Thanks..<br>> ><br>> ><br>> > Dhananjay<br>> ><br>> ><br>> ><br>> > On 12/29/05, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se
</a>> wrote:<br>> > ><br>> > > Dhananjay wrote:<br>> > > > Thanks for reply,<br>> > > ><br>> > > ><br>> > > > Well before that let me tell you about my system that just now I
<br>> > > > discussed with administrator.<br>> > > ><br>> > > > I have 16 node grid. (In last mail I said that I have 8 nodes but now<br>> > > I<br>> > > > can use all 16 nodes)
<br>> > > ><br>> > > > In details:<br>> > > ><br>> > > > Operating System is Redhat WS 3.0 and 16 nodes are excutation host<br>> > > which<br>> > > > are installed by N1Grid Engine
6.0 (i.e. N1GE 6.0 )<br>> > > ><br>> > > > Master N1GE is SF440 which is having Solaries 9.0 operating system<br>> > > and<br>> > > > N1GE 6.0 Software.<br>> > ><br>> > > This is confusing, you say you have Redhat WE
3.0 and the lines below<br>> > > show that you have Linux on your grid master, simultaneously you say<br>> > > that you have Solaris on the master node. It is very unlikely that it<br>> > > will work to mix operating systems.
<br>> > > The easiest way is to install gromacs on the master node and use NFS to<br>> > > ount a disk on the client nodes. You can even do it in your home<br>> > > directory, provided it is called the same everywhere. Then the
<br>> > > instructions on the gromacs site should be sufficient to install.<br>> > ><br>> > > If however the master runs solaris and the clients/nodes run Linux then<br>> > > you should compile everything on one of the nodes.
<br>> > ><br>> > ><br>> > ><br>> > > ><br>> > > > Also when I typed "uname -a" on command line I got following<br>> > > information:<br>> > > >
<br>> > > > Linux cdfd-grid-master 2.4.21-19.ELsmp #1 SMP Thu Aug 12 23:22:47 EDT<br>> > > > 2004 x86_64 x86_64 x86_64 GNU/Linux<br>> > > ><br>> > > > I want to install Gromacs parallel version. Will installation on
<br>> > > > master N1GE is sufficient or I have to install it on all the nodes ?<br>> > > ><br>> > > > Second thing is master N1GE is having Solaries 9.0 operating System.<br>> > > So
<br>> > > > will it be possible to install Gromacs-3.3 on Solaries 9.0 ?<br>> > > ><br>> > > > Let me tell you that I am not master of Computer Adminitration area<br>> > > but
<br>> > > > still I wish to workout this installation. Therefore I am following<br>> > > > your instructions and suggestions...<br>> > > ><br>> > > ><br>> > > > On 12/28/05, *David van der Spoel* <
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> > > > <mailto: <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>> > > ><br>> > > > Dhananjay wrote:
<br>> > > ><br>> > > > > Hello all,<br>> > > > ><br>> > > > > I have tried and successfully installed Gromacs-3.3 on single<br>> > > node.<br>
> > > > ><br>> > > > > Now I want to install parallel gromacs.<br>> > > ><br>> > > ><br>> > > > start (on the master node) with make distclean, then start from
<br>> > > the<br>> > > > configure step again. It could be that the mpi library you have<br>> > > > installed is not in the proper binary format (i.e. 32 vs 64 bits).<br>> > > >
<br>> > > > ><br>> > > > > when I tried it on the same node, I got error as follows:<br>> > > > ><br>> > > > ><br>> > > ><br>> > > /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../../lib64/libmpi.a:
<br>> > > > > could not read symbols: Bad value<br>> > > > > collect2: ld returned 1 exit status<br>> > > > > mpicc: No such file or directory<br>> > > > > make[4]: *** [libgmx_mpi.la] Error 1
<br>> > > > > make[4]: Leaving directory<br>> > > > ><br>> > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3<br>> > > /src/gmxlib'<br>> > > > > make[3]: *** [all-recursive] Error 1
<br>> > > > > make[3]: Leaving directory<br>> > > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-<br>> > > > 3.3/src/gmxlib'<br>> > > > > make[2]: *** [all-recursive] Error 1
<br>> > > > > make[2]: Leaving directory<br>> > > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3<br>> > > /src'<br>> > > > > make[1]: *** [all] Error 2
<br>> > > > > make[1]: Leaving directory<br>> > > > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-<br>> > > 3.3/src'<br>> > > > > make: *** [all-recursive] Error 1
<br>> > > > ><br>> > > > ><br>> > > > > I could not understand the meaning of these erre. Will anybody<br>> > > please<br>> > > > > tell me ?
<br>> > > > ><br>> > > > > Presently I can use 8 nodes. Is there any specific<br>> > > procedure/steps of<br>> > > > > installation on nodes/grid ?<br>>
> > > > I
mean to say should I start installation from master node ?<br>> > > > ><br>> > > > > 2 out og 8 nodes has gromacs-3.3 alrady installed.<br>> > > > ><br>> > > > > Dhananjay
<br>> > > > ><br>> > > > >------------------------------------------------------------------------<br>> > ><br>> > > > ><br>> > > > >_______________________________________________
<br>> > > > >gmx-users mailing list<br>> > > > ><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a>><br>> > > > ><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > > > >Please don't post (un)subscribe requests to the list. Use the
<br>> > > > >www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>> > > > <mailto:<a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a> >.<br>> > > > ><br>> > > ><br>> > > ><br>> > > > --<br>> > > > David.<br>> > > ><br>> > > ________________________________________________________________________
<br>> > > ><br>> > > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics<br>> > > group,<br>> > > > Dept. of Cell and Molecular Biology, Uppsala University.<br>
>
> > > Husargatan 3, Box
596, 75124
Uppsala, Sweden<br>> > > >
phone: 46 18 471
4205 fax: 46
18 511 755<br>> > > > <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> > > > <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> <a href="mailto:spoel@gromacs.org">
spoel@gromacs.org</a><br>>
> > >
<mailto:<a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a>>
<a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a><<a href="http://xray.bmc.uu.se/%7Espoel">http://xray.bmc.uu.se/%7Espoel</a>><br>> > > ><br>> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>> > > ><br>> > > ><br>> > > > _______________________________________________<br>> > > > gmx-users mailing list<br>> > > > <a href="mailto:gmx-users@gromacs.org">
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gmx-users-request@gromacs.org</a>>.<br>> > > ><br>> > > ><br>> > > ><br>> > > ><br>> > > ------------------------------------------------------------------------
<br>> > > ><br>> > > > _______________________________________________<br>> > > > gmx-users mailing list<br>> > > > <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
</a><br>> > > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > > > Please don't post (un)subscribe requests to the list. Use the
<br>> > > > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> .<br>> > ><br>> > ><br>> > > --<br>> > > David.<br>> > > ________________________________________________________________________
<br>> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> > > Dept. of Cell and Molecular Biology, Uppsala University.<br>> > > Husargatan 3, Box 596, 75124 Uppsala, Sweden
<br>> > > phone: 46 18 471 4205 fax: 46 18 511 755<br>> > > <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a><br>> > >
<a href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a> <<a href="http://xray.bmc.uu.se/%7Espoel">http://xray.bmc.uu.se/%7Espoel</a>><br>> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>> > > _______________________________________________<br>> > > gmx-users mailing list<br>> > > <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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gmx-users-request@gromacs.org</a>.<br>> > ><br>> ><br>> ><br>><br>Greetings,<br><br>Florian<br><br>--<br>-------------------------------------------------------------------------------<br> Florian Haberl
<br> Computer-Chemie-Centrum<br> Universitaet Erlangen/ Nuernberg<br> Naegelsbachstr 25<br> D-91052 Erlangen<br> Mailto: florian.haberl AT <a href="http://chemie.uni-erlangen.de">chemie.uni-erlangen.de</a><br>-------------------------------------------------------------------------------
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