Scalability of CHARMM on various architectures
jim at ks.uiuc.edu
Mon Jun 12 15:06:45 PDT 2000
Depending on the features you require, NAMD is compatible with CHARMM and
should scale better, especially on clusters. New version out soon.
On Wed, 7 Jun 2000 axelsen at axe1.med.upenn.edu wrote:
> We are designing a cluster for which the most important code will be the
> computational chemistry program, CHARMM. In our preliminary tests on
> an existing cluster, we have confirmed our expectation that interthread
> communications will be our first bottleneck. A test run on a typical
> problem did not scale beyond 4 nodes on a cluster composed of P2-450
> processors and fast ethernet interconnections. In contrast, the same
> code scales almost perfectly up to at least 12 processors on an SGI-Unix
> SMP machine. CHARMM uses PVM.
> I would appreciate contact from anyone who has run CHARMM on a cluster
> and has considered the best way to make this code scale better. From
> anyone, I would appreciate general guidance on several issues:
> * If we go with pentium II/III processors, how far is Myrinet likely to
> permit us to scale these calculations?
> * With Myrinet, would alpha nodes tend to scale any better than pentium nodes?
> (a single 500 MHz alpha processor is about 1.6-fold faster than a
> single 450 MHz P2 on a typical problem, but it is about 3-fold the
> cost. With this question, I am looking for any additional advantages
> of alpha to justify this cost)
> * Are there differences between different pentium chip sets that will impact
> this problem?
> * Is there any advantage to buying dual-processor machines, either alpha
> or pentium, with respect to scaling? Any advantage to dedicating one
> processor in each dual-box to communications? If we dedicate processors
> in this way, would both processors have to have the same clock speed?
> ------------- axe at pharm.med.upenn.edu -----------------
> Paul H. Axelsen .... .... . . . .
> Department of Pharmacology . . . .. . .. .
> University of Pennsylvania .... ... . . . . . .
> 3620 Hamilton Walk . . . .. . ..
> Philadelphia, PA 19104-6084 . .... . . . .
> Beowulf mailing list
> Beowulf at beowulf.org
More information about the Beowulf