<br><br><div class="gmail_quote">On Fri, Feb 6, 2009 at 4:12 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;">
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Hi,<br><br>I always compile Gromacs with --enable_mpi --enable-mpi-environment=...<br>such that you can run a serial mdrun without using mpirun.</div></blockquote><div><br>Interesting. So what does that "..." (or VAR in the help of configure) means? I'm sorry, but I can't find any information about it anywhere. If it's just a variable we come up with, how or when do we set it (and what do we set it to) when running the MPI mdrun? It doesn't seem to work when I don't set it at all...<br>
<br>Regards,<br>Joćo<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: Fri, 6 Feb 2009 15:22:54 +0000<br>
Subject: Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2<div><div></div><div class="Wj3C7c"><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>
<br><div>On Mon, Jan 19, 2009 at 6:09 PM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br><blockquote style="padding-left: 1ex;">
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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 style="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><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><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>