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>
<br>
2. binutils can not install. Errors are as follows..<br>
<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>
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 `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src/gmxlib'<br>
make[3]: *** [all-recursive] Error 1<br>
make[3]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src/gmxlib'<br>
make[2]: *** [all-recursive] Error 1<br>
make[2]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src'<br>
make[1]: *** [all] Error 2<br>
make[1]: Leaving directory `/usr/data/dhananjay/Dhananjay_installation/Gromacs/gromacs-3.3/src'<br>
make: *** [all-recursive] Error 1<br>
<br>
Waiting for reply... <br>
<br><div><span class="gmail_quote">On 12/29/05, <b class="gmail_sendername">Dhananjay</b> <<a href="mailto:dhananjay.c.joshi@gmail.com">dhananjay.c.joshi@gmail.com</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;">
Hello David,<br>
<br>
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. <br>
<br>
Well I will compile every thing on one of the node and let you know the results.<br>
<br>
Still if you have any thing to say please reply me ...<br>
<br>
Thanks..<br><span class="sg">
<br>
<br>
Dhananjay</span><div><span class="e" id="q_1087642fa8ddd2c7_2"><br>
<br>
<br><br><div><span class="gmail_quote">On 12/29/05, <b class="gmail_sendername">David van der Spoel</b> <<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:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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 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 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 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 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. 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 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" 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 single node.<br>
> ><br>> > Now I want to install parallel gromacs.<br>><br>><br>> start (on the master node) with make distclean, then start from 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>
> /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/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/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>> ><br>> > I could not understand the meaning of these erre. Will anybody please<br>> > tell me ?<br>> >
<br>> > Presently I can use 8 nodes. Is there any specific 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>> >gmx-users mailing list<br>> ><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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</a>>.<br>> ><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><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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</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" 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> <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>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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</span></div></blockquote></div><br>