<FONT size=2> <div>Dear gmx users,</div> <div>I have some problem regarding scalling factor of cluster. Here I have given cluster specifications, installation procedure, i request you go through query and suggest me. </div> <div> </div> <div>Here is the system specifications:</div> <div>Master node: Intel Pentium 4, 3.0 GHz with 64HT 800 MHz FSB/2 MB L2</div> <div>Slave Nodes: Intel Xeon, 3.0 Ghz with HT 800 MHz FSB/2 MB L2</div> <div>OS : Redhat Linux Enterprizes 4.0, 64 bit</div> <div> </div> <div>I downloaded fftw-3.0.1.tar.gz. and gromacs-3.3.1tar.gz from gromacs website.</div> <div>For parallel installation, I used the fallowing commands(in master node, in root),</div> <div> </div> <div>For fftw instalation..</div> <div>./configure --enable-float --enable-sse --enable-mpi</div> <div>make</div> <div>make install</div> <div> </div> <div>For gromacs installation..</div> <div>./configure --enable-mpi</div> <div>make</div> <div>make
mdrun</div> <div>make install</div> <div>make install-mdrun</div> <div>make links</div> <div>It was installed in /opt/gromacs/</div> <div>I didn't get any error messages</div> <div> </div> <div>To the gromacs in parallel, I have used the fallowing commands...</div> <div>grompp -f equilibrium.mdp -n index.ndx -p dopc.top -c dopc.pdb -np 5 -o dopc-eq.tpr</div> <div>mpirun -np 5 -machinefile gmxguest -nolocal /opt/gromacs/bin/mdrunmpi -s dopc-eq.tpr -c dopc-eq.pdb -o dopc-eq.trr</div> <div>(Note: gmxguest file contains five node names) I checked in 5 nodes, job is going in all nodes.</div> <div> </div> <div>The cluster took 22 hours to finish the job but same job with same time scale in with one Intel Pentium 4, 3.0 GHz , 64bit, rehat linux OS, it took 26 hours.</div> <div>My question is why it is happening, is there any problem in installing or gromacs not support this type of clusters.</div> <div>To improve scalling factor of cluster, what i
have to do?</div> <div>Any suggestion is appreciated.</div> <div>Thank you in advance.</div> <div> with regards,</div> <div> Nagaraju Mulpuri. </div> <div> </div></FONT><p> 
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