[gmx-users] RE: Gromacs benchmark --poor performance on XEONmachine

Shejith P.P shejithp at hclinsys.com
Tue Oct 21 05:26:02 CEST 2003

I had installed gromacs on a dual XEON( 2.4GHz ) machine +RedHat 9.0 and I was using np=4( I had enabled hyperthreading).  But I was getting Gfloaps 1.5 and Mnb/f when I was running D.DPPC  -benchmark. This is very low value when we are comparing with the results posted in web site..
   I had installed fftw -foating point and enabled mpi and I am using LAM/MPI 7.0 .
I am not able to find out where I am making mistake. Can anyone tell me any hints.


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of David van der Spoel
Sent: Monday, October 20, 2003 5:09 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] RE: Gromacs benchmark --poor performance on

On Mon, 2003-10-20 at 13:28, Shejith P.P wrote:
> Hi,
>  Can anyone  give me the detailed installtion procedure for gromacs for parallel environment.
it's the same as te normal installation (see website)

> Regards
> Shejith 
>  -----Original Message-----
> From: 	Shejith P.P [mailto:shejithp at hclinsys.com] 
> Sent:	Monday, October 20, 2003 11:01 AM
> To:	'gmx-users at gromacs.org'
> Subject:	Gromacs benchmark --poor performance on XEON machine
> Hi,
>     I am running gromacs on P4 Xeon machine 2.4GHz. ( 1GB memeory ) - I am using a dual CPU machine.
> I have installed fftw(2.1.3) and gromacs (3.1.4 ) on my machine and I am running benchmarking using D.DPPC 
>    I have enabled hyperthreading and I was running 4 LAM on my machine.
>  And I hav erun gromacs for 4 CPUS and executed the mdrun command for 4 nodes. 
> But I am getting a very low value compared to the one I have seen in gromacs site.   I got Mnbf/s of 45 where in website It was 286 for dula xeon 2.2GHz.
>    I am afraid whether I am making any mistakes in installton itself....can enyone send me the detailed installtion procedure for gromacs  for  parallel environment.
> Regards
> Shejth
> ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿà›î±ê왨¥Šx%ŠË`›î±êìþ
> 虧,þŠà†ÛiÿÿðÃஉšrÏè®æj)fjåŠËbú?‚lÿºÇ«°ù^jǝ¢í¦‹-þéÿ²æìr¸›z·ª¹ë-²Ú-
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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