Also, use the 'nice' command to run gmx at high priority, and switch off CPU frequency scaling. For me, cygwin performance is pretty much the same as that on linux, which is to be expected since most of the code isn't dependent on system calls. Apparently, the only difference you should be able to see is in disk I/O, but you don't want to I/O too frequently anyway.<br>
<br><div class="gmail_quote">On Fri, Jun 11, 2010 at 3:18 AM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br><br>----- Original Message -----<br>From: Nasim Biglari <<a href="mailto:nasimb88@yahoo.co.uk" target="_blank">nasimb88@yahoo.co.uk</a>><br>Date: Friday, June 11, 2010 2:51<br>Subject: [gmx-users] GROMACS on CYGWIN<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><br></div><span><p></p><table><tbody><tr><td><p></p><div style="font-family:garamond,new york,times,serif;font-size:12pt;color:rgb(0, 0, 0)">
<div><div class="im"><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>Dear all,<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font><br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font>I was wondering whether GROMACS on CYGWIN is less capable than GROMACS run on LINUX?<br><font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px">> </font> i.e. concerning its speed and its ability to simulate larger macromolecules. I assume that it is faster, but is it very much different?<br>
<font style="font-style:normal;font-weight:normal;background-color:rgb(245, 248, 240);font-size:14px"></font><br></div>GROMACS will run fine, and do approximately the same under either OS on comparable hardware with the same version of gcc, however for production simulation to be maximally effective you need to arrange for the simulation process not to be interrupted much. This is easier to arrange on Linux than Windows. You certainly don't want to be concurrently using either kind of machine as a desktop, and also you'd prefer not to be logged on to either machine.<br>
<br>Mark<br></div></div></td></tr></tbody></table><p></p></span>
<br>--<br>
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