But one thing as i did make links so definitely there are links of those executables in /usr/local/bin.How can i easily remove them..??<br><br><div class="gmail_quote">On Sun, Dec 21, 2008 at 10:15 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d"><br>
<br>
Chitrita Dutta Roy wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
tar -zxvf openmpi-1.2.8.tar.bz2<br>
cd openmpi-1.2.8<br>
./configure<br>
make<br>
make install<br>
<br>
i had my fftw library installed.<br>
<br>
untarred gromacs went to its directory..<br>
./configure --enable-mpi --program_suffix="_mpi"<br>
make<br>
make install<br>
<br>
grompp -f pr2.mdp -c em.gro -r em.gro -p scr8.top -n em.ndx -o pr.tpr<br>
mpirun -np 4 /usr/local/gromacs/bin/mdrun -v -s pr.tpr -deffnm pr<br>
<br>
</blockquote>
<br></div>
Well, that can't be right; all of your programs should have the _mpi suffix, if you followed the steps above.<br>
<br>
What you've done isn't entirely necessary, although I don't know if it will have any adverse effects. Follow the exact instructions posted here, they are given line-by-line and are perfectly clear:<br>
<br>
<a href="http://www.gromacs.org/content/view/20/34/" target="_blank">http://www.gromacs.org/content/view/20/34/</a><div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
i tried like these besides i also tried with mdrun_mpi but the same occured rather showed more time requirement to complete.And i would also liked to know one thing if i want to do a fresh install removing the earlier one.How would i remove the earlier one.As i tried doing it from yum remove and rpm -e but all went in vain although they can show that these things are installed.<br>
<br>
</blockquote>
<br></div>
Just remove the Gromacs directory and try again, as long as any previous attempts haven't installed in other locations (i.e., /usr/local/bin, etc.)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="Ih2E3d">
Thanks again for your help.Plz instruct me to get one complete set of steps to succefully install the Gromacs with mpi and to utilize the power of four cores.<br>
<br>
<br></div><div class="Ih2E3d">
On Sun, Dec 21, 2008 at 9:52 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Chitrita Dutta Roy wrote:<br>
<br>
I tried that way it basically creates 4 jobs and takes hold of 4<br>
cpus but the problem is that it shows to take more time than it<br>
would normally without mpirun..and not only that a weird thing<br>
starts happening.Once being progressed to some steps it retreats<br>
back again to an older one and sometimes it just loops around in<br>
that fashion calculating practically the same set of steps over<br>
and over again.<br>
<br>
I somehow feel that the tpr file which is needed for the mdrun<br>
was not built properly to run on 4 separate cores<br>
simultaneously.ANd that is why maybe actually the 4 cores are<br>
running the same copy of the program and so the same steps.And<br>
what i see is kinda race condition.I guess i compiled it<br>
properly with mpi so..now i am helpless.<br>
<br>
Thanks for your help.Waiting for some more.<br>
<br>
<br>
Please post the following information:<br>
<br>
1. The exact series of commands you gave when installing Gromacs.<br>
2. The exact commands you are issuing to create your job (grompp and<br>
mdrun).<br>
<br>
-Justin<br>
<br>
<br>
On Sun, Dec 21, 2008 at 7:56 PM, Manik Mayur<br>
<<a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a> <mailto:<a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a>><br></div>
<mailto:<a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a> <mailto:<a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a>>>><div class="Ih2E3d">
<br>
wrote:<br>
<br>
On Sun, Dec 21, 2008 at 5:04 PM, Chitrita Dutta Roy<br>
<<a href="http://chitrita.md" target="_blank">chitrita.md</a> <<a href="http://chitrita.md" target="_blank">http://chitrita.md</a>><br>
<<a href="http://chitrita.md" target="_blank">http://chitrita.md</a>>@<a href="http://gmail.com" target="_blank">gmail.com</a> <<a href="http://gmail.com" target="_blank">http://gmail.com</a>><br>
<<a href="http://gmail.com" target="_blank">http://gmail.com</a>>> wrote:<br>
<br>
Thanks to all for helping me previously.<br>
Now i am unable to arrange the .tpr file for position<br>
restraint<br>
mdrun on a quad core as in version 4.0.2 grompp -np is not a<br>
valid comand can anybody help me in building a tpr file for<br>
parallel run on 4 cores of a quad core machine .I have<br>
installed<br>
gromacs using Open MPI Library and my files are suffixed<br>
as _mpi.<br>
<br>
try running: mpirun -np 4 mdrun_mpi options<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="Ih2E3d"><br>
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-- <br><div><div></div><div class="Wj3C7c">
========================================<br>
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Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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