I have just now tried <br>
<br>
which binutils <br>
<br>
The output is <br>
<br>
GNU which v2.14, Copyright (C) 1999 - 2001 Carlo Wood.<br>
GNU which comes with ABSOLUTELY NO WARRANTY;<br>
This program is free software; your freedom to use, change<br>
and distribute this program is protected by the GPL.<br>
<br>
<br>
Any suggestion please ?<br><br><br>
<br>
<div><span class="gmail_quote">On 12/30/05, <b class="gmail_sendername">Florian Haberl</b> <<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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 Friday 30 December 2005 08:34, Dhananjay wrote:<br>> Hi Florian Haberl ,<br>><br>> Thanks for reply..<br>><br>> Please go through the following...<br>><br>><br>> On 12/29/05, Florian Haberl <
<a href="mailto:Florian.Haberl@chemie.uni-erlangen.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">Florian.Haberl@chemie.uni-erlangen.de</a>> wrote:<br>> ><br>> > 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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gromacs.org</a><br>><br>><br>> I have alrady installed according to the path suggested. I mean to say<br>> 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>><br>> ><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<br>> > /binutils'<br>> > > make: *** [install-binutils] Error 2<br>> >
<br>> > binutils should be installed on you basis system installation else update<br>> > your<br>> > linux.<br>><br>><br>> Here I have tries again but of no use, still I am getting error message
<br>><br>><br>> make[4]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-2.16<br>> /binutils/doc'<br>> make[3]: Leaving directory<br>> `/usr/data/dhananjay/Dhananjay_installation/binutils/binutils-
2.16<br>> /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
<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>> You said that " binutils should be installed on you basis system<br>> installation else update your<br>> linux " . What king of update I needed, whether advance version of Linux
<br>> or upgradation of binutild in the system ?<br><br>try something like<br>which binutils<br>binutils ---version<br>to get version information of your installed binutils, normal distributions are up to date.<br><br>
Normally you don`t have to install a new binutils version, perhaps skip this step.<br><br>><br>><br>><br>> ><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<br>> > /src/gmxlib'<br>> > > make[3]: *** [all-recursive] Error 1<br>> > > make[3]: Leaving directory<br>> > > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-
3.3<br>> > /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<br>><br>><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>><br>><br>> ><br>> > > On 12/29/05, Dhananjay <<a href="mailto:dhananjay.c.joshi@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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<br>> > 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<br>> > 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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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<br>> > 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<br>> > system<br>> > > > > and<br>> > > > > > N1GE 6.0 Software.<br>> > > > ><br>> > > > > This is confusing, you say you have Redhat WE
3.0
and the lines<br>> > 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
<br>> > it<br>> > > > > will work to mix operating systems.<br>> > > > > The easiest way is to install gromacs on the master node and use NFS<br>> > 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
<br>> > 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<br>> > 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>> > > > > ><br>> > > > > > Second thing is master N1GE is having Solaries 9.0 operating<br>> > 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<br>> > area<br>> > > > > but<br>> > > > > > still I wish to workout this installation. Therefore I am
<br>> > 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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@xray.bmc.uu.se</a><br>> > > > > > <mailto: <a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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<br>> > 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<br>> > from<br>> > > > > the<br>> > > > > > configure step again. It could be that the mpi library you
<br>> > have<br>> > > > > > installed is not in the proper binary format (i.e. 32 vs 64<br>> > bits).<br>> > > > > ><br>> > > > > > ><br>> > > > > > > when I tried it on the same node, I got error as follows:
<br>> > > > > > ><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-
<br>> > 3.3<br>> > > > > /src/gmxlib'<br>> > > > > > > make[3]: *** [all-recursive] Error 1<br>> > > > > > > make[3]: Leaving directory<br>> > > > > > >
<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>> > > > > > ><br>> > `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3<br>> > > > > /src'<br>> > > > > > > make[1]: *** [all] Error 2
<br>> > > > > > > make[1]: Leaving directory<br>> > > > > > ><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
<br>> > 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<br>> > node ?<br>> > > > > > ><br>> > > > > > > 2 out og 8 nodes has gromacs-3.3 alrady installed.<br>> > > > > > >
<br>> > > > > > > Dhananjay<br>> > > > > > ><br>> > > > ><br>> > > >------------------------------------------------------------------------
<br>> > > > ><br>> > > > > > ><br>> > > > > > >_______________________________________________<br>> > > > > > >gmx-users mailing list
<br>> > > > > > ><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a> <mailto: <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org</a>><br>> > > > > > >
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> > > > > > >Please don't post (un)subscribe requests to the list. Use
<br>> > the
<br>> > > > > > >www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>
<br>> > > > > > <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-request@gromacs.org</a> >.<br>> > > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > > > --<br>> > > > > > David.
<br>> > > > > ><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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@xray.bmc.uu.se</a><br>>
> > > > >
<mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@xray.bmc.uu.se</a>> <a href="mailto:spoel@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@gromacs.org</a><br>>
> > > > >
<mailto:<a href="mailto:spoel@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@gromacs.org</a>>
<a href="http://xray.bmc.uu.se/%7Espoel" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://xray.bmc.uu.se/~spoel</a><<br>> > <a href="http://xray.bmc.uu.se/%7Espoel" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://xray.bmc.uu.se/%7Espoel</a>><br>> > > > > ><br>> > > > >
<br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> > > > > ><br>> > > > > ><br>> > > > > > _______________________________________________
<br>> > > > > > gmx-users mailing list<br>> > > > > > <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org
</a> <mailto: <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org
</a>><br>> > > > > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>> > > > > > < <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a><br>> > > > > > <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-request@gromacs.org</a>>.<br>> > > > > >
<br>> > > > > ><br>> > > > > ><br>> > > > > ><br>> > > > ><br>> > ------------------------------------------------------------------------<br>> > > > > >
<br>> > > > > > _______________________________________________<br>> > > > > > gmx-users mailing list<br>> > > > > > <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org
</a><br>> > > > > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a> .<br>> > > > >
<br>> > > > ><br>> > > > > --
<br>> > > > > David.<br>> > > > ><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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
spoel@gromacs.org</a><br>> > > > > <a href="http://xray.bmc.uu.se/%7Espoel" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://xray.bmc.uu.se/~spoel</a> <<a href="http://xray.bmc.uu.se/%7Espoel" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://xray.bmc.uu.se/%7Espoel</a>><br>> > > > ><br>> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
<br>> > > > > _______________________________________________<br>> > > > > gmx-users mailing list<br>> > > > > <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org</a><br>
> > > > > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.<br>> > > > >
<br>> > > ><br>> > > ><br>> > >
<br>> > Greetings,<br>> ><br>> > Florian<br>> ><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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
chemie.uni-erlangen.de</a><br>> ><br>> > -------------------------------------------------------------------------------<br>> > _______________________________________________<br>> > gmx-users mailing list
<br>> > <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.<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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
chemie.uni-erlangen.de</a>
<br>-------------------------------------------------------------------------------<br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org
</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users-request@gromacs.org</a>.<br></blockquote></div><br>