From owner-chemistry@ccl.net Tue Jun 3 05:48:00 2008 From: "Justin Finnerty justin.finnerty]-[uni-oldenburg.de" To: CCL Subject: CCL: computer for high-level QC calculations Message-Id: <-37082-080603052631-6070-2iWKLJTaer0/ttUZ/L/dVw*o*server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 03 Jun 2008 10:34:27 +0200 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty-,-uni-oldenburg.de] On Mon, 2008-06-02 at 10:58 +0200, Pablo Echenique echenique.p:gmail.com wrote: > Dear friends and colleagues, > > at my laboratory, we are about to buy a computer for performing > high-level QC calculations (e.g., coupled cluster) in biological > molecules (e.g., peptides). I write to kindly ask you for advice > regarding the "best" (in whatever sense you consider appropriate) > choice. My observations of coupled cluster calculations on our cluster are the following. Most of the the QC codes that I know cannot run totally in memory, and often require lots of disk space. We find that local scratch disk is a must; we have a 2TB NFS filesystem and have tried parallel filesystems but both are very significantly inferior to local scratch for these jobs. We have one 16cpu machine with 64Gb RAM and 2.5Tb SCSI RAID storage and find that coupled cluster calculations performance "improvement" degrades when more than 8 cpus are used and also when more than one job runs on a node. If I was in your situation my recommendation as best value for money would be a base node with: 4 or 8 cpus (eg 2 x Quadcore AMDs) 2Gb RAM/CPU (eg 16 Gb RAM) 1 system disk (only ~50 Gb is necessary) 3 x 350+ Gb sata disks as local scratch (linux soft RAID, best not to include the system disk) Set up your queue system to run only one job per node. Unless you know that the problem sizes are always the same, I would buy some nodes with smaller and some with larger scratch disk systems. This would allow you to cater to a wider range of job sizes possibly without extra cost. To upgrade the performance/capacity to this base system I would recommend first buying more nodes rather than upgrading nodes, then larger disks, then more RAM and lastly more CPUs/CPU speed. Ideally I would ask potential suppliers to provide a test machine and actually run test jobs of the size you are actually going to be doing. In particular monitor memory and disk activity. Cheers Justin -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg