<div class="gmail_quote">On Mon, Jan 19, 2009 at 6:09 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</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>
Hi,<br><br>When running in parallel on a cluster through a queuing system<br>one usually does not (or can not) see or check the nice level<br>of the mdrun processes. But the nice level can have a significant<br>impact on performance, especially when running in parallel,<br>
since all processes have to wait for the slowest one.<br>Therefore I set the nicelevel to 0 when running in parallel.<br><br>Note that if you configure mdrun with --enable_mpi --enable-mpi-environment,<br>running an MPI mdrun binary without mpirun will still give nice 19.</div>
</blockquote><div><br>Hi Berk,<br><br>Thanks for the answer and for the tip. It worked out
fine. But still, I was intrigued when you said "running an MPI mdrun
binary without mpirun". What do you mean with that? Do you mean that
you don't need to launch the mpirun before the MPI mdrun?<br>
<br>Regards,<br>Joćo <br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><br><br>Berk<br><br><hr>Date: Mon, 19 Jan 2009 16:29:16 +0000<br>
From: <a href="mailto:jmdamas@itqb.unl.pt" target="_blank">jmdamas@itqb.unl.pt</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>Subject: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2<div>
<div></div><div class="Wj3C7c"><br><br>Hello,<br><br>I would like to know if there is any reason for mdrun_mpi to have a nicelevel default of zero in Gromacs 4.0.2 instead of the default 19 of mdrun of every version or mdrun_mpi of the other versions. I searched the mailing list for any discussion related to this but I haven't found anything.<br>
<br>Thanks in advance,<br>Joćo<br clear="all"><br>-- <br>Joćo M. Damas<br>PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:+351-214469613<br><br></div></div><div class="WgoR0d"><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a></div>
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Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:+351-214469613<br>