AMBER Archive (2008)

Subject: Re: AMBER: gigabit ethernet cards and switches

From: Alessandro Nascimento (
Date: Thu Nov 06 2008 - 13:28:46 CST

Thanks Ross for you suggestions and comments.

I will definitely try to interconnect the machines with a crossover
cable and see what happens.

Could you suggest any switch known to work well with Intel e1000-based
network cards ?



On Thu, Nov 6, 2008 at 4:37 PM, Ross Walker <> wrote:

> Hi Alessandro,
>> We are considering to buy a new 'low-cost' computer cluster dedicated
>> to MD simulations. We already have two clusters interconnected by
>> gigabit ethernet. One of these is composed by intel quad-core
>> processors and, as discussed many times in this list, suffers from
>> scaling problems when running Amber in more than two nodes.
>> That said, I would like to ask to users and developers about good
>> choices to be considered when buying gigabit Ethernet cards and
>> switches. My dream is to convince my PI to upgrade myrinet, but price
>> is also an important issue.
> In the 'good old' days when gigabit ethernet was still somewhat usable as an
> interconnect I would have advised you to go for good quality cards and a top
> notch fully non-blocking switch but this advice doesn't really apply anymore
> since even in this scenario it doesn't really help with running in parallel.
> It can help a little bit with NFS say but to be honest most cheap gigabit
> switches even if not non-blocking will still outstrip disk performance so I
> would suggest going for a fairly cheap switch and cards that are compatible
> with Linux. This is probably the key here - making sure they are supported
> under Linux. I would recommend the Intel e1000 chip based cards which are
> effectively guaranteed to work under Linux.
> As for try to at least get some scalability - so you can run 2 node jobs
> something you could try (given that extra network cards are cheap) is to buy
> 2 cards for each machine. Get yourself 1 cheap switch and hook up one set of
> the cards to give you NFS, ssh access / management facilities etc. Then with
> the second card in each machine use cross over cables to hook up each pait
> of machines. E.g.
> Mach 1 eth0 -----------------------
> |
> |
> Mach 2 eth0 ------------------- |
> | |
> Switch ------- File Server / login node
> | |
> Mach 3 eth0 ------------------ |
> |
> |
> Mach 4 eth0 -----------------------
> Mach 1 eth1 ---X--- Mach2 eth1
> Mach 3 eth1 ---X--- Mach4 eth1
> Where X is a cross over cable. Then you just need to assign a different
> private subnet to the eth1 cards and make sure your machine miles are
> modified as necessary to send MPI traffic over the corssover cables. This
> way you should be able to run 8 way jobs (as 2 x quad core) for only a small
> amount of extra outlay and I think the performance would be better than
> trying to run 2 node jobs over the switch. You would of course need to tweak
> your queuing software to hand out nodes in the correct pairs and also create
> the correct machine files but that shouldn't be too hard.
> Note though I have not actually tried this (not for AMBER anyway, just for
> doing private NFS mounts / backups etc) but I figure it should work quite
> well - the thing I don't know is how well things will scale over the
> crossover cable and whether it is worth it based on this so you might want
> to just get a cross over cable and try it quickly on some of your existing
> machines.
> Anyway, just my 3c.
> Good luck,
> Ross
> /\
> \/
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
> | | PGP Key available on request |
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to

[ ]s

--alessandro ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to