So you are saying that also in the Desktop (because I not use "mpirun") it is working with only one cpu??<br><br>Beniamino<br><br><div><span class="gmail_quote">2006/6/6, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Beniamino Sciacca wrote:<br><br>two points:<br><br>you can not do constraints in parallel in
3.3<br>you can not run in parallel without mpirun<br><br>ergo you are comparing apples and oranges.<br><br><br><br><br><br>> Also the machine (where now I've the problem) before worked as the other<br>> machine... I don't know before "what".
<br>> However...I start from a file .gro where is my system ready for<br>> constraint forces; I use grompp:<br>> "grompp_d -f MD_Eq.mdp -c DNA5x3_min.gro -p DNAx3.top -o DNA6x3_MD.tpr<br>> -n indexAcqua.ndx
-po mdout.mdp"<br>> "lamboot"<br>> and later mdrun:<br>> "mdrun_d -nice 0 -v -s DNA6x3_MD.tpr -pi pull.ppa -po pullout.ppa -pdo<br>> pull.pdo -o mdEq_traj.trr -c DNA6x3_MD.gro -e mdEq_ener.edr -pn
<br>> indexAcqua.ndx -x mdEq_traj.xtc -g EqD.log"<br>><br>> I don't use mpirun.<br>> There is no differences between the way to prepare calculations.<br>> one machine is a notebook (centrino duo)<br>> the other machine is a Desktop (AMD64 X2)
<br>> the kernel is the same (2.6) debian.<br>><br>> with the code written above notebook uses only one processor, Desktop<br>> uses both the cpu.<br>> I repeat...I also worked in this manner, and also the notebook has ever
<br>> worked until some week ago.<br>> Now for use both the cpu I must use mpirun.<br>><br>> Desktop kernel is non smp<br>> Laptop kernel has both smp and non-smp.<br>><br>> Beniamino<br>><br>> Mark Abraham ha scritto:
<br>>> Beniamino Sciacca wrote:<br>>>> Ok... the problem is certainly that I made two processes.<br>>>> But if I made only one process mdrun uses only one cpu...<br>>>> I want one process (and so I can use constraint forces) that use both
<br>>>> cpus.<br>>>> I know it's possible because I' ve another pc that is working in this<br>>>> manner.<br>>><br>>> So work out what is different between the two machines, their<br>
>> configurations and how you're preparing the calculations. If you can't<br>>> identify a difference, then tell us what you have done and maybe we<br>>> can suggest something you haven't tried.<br>>>
<br>>> Mark<br>>> _______________________________________________<br>>> gmx-users mailing list <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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</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
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