Linux Experts..

[Manchester_Sikhi]

Waheguru Ji Ka Khalsa, Waheguru Ji Ki Fateh!

Are there any LINUX/UNIX experts out there.

I want to hook up and run two PC/Unix base units in parallel sharing both processors to run some scientific software we are using...i was thinking os MPI or something like that.... Any ideas on how to do this?

Cheer

Raj

[khalsaforce]

what are you saying.... you want to run ome scientific program on a computer that has two processors and you want it to use both processors?

[Manchester_Sikhi]

I need to run some computational drug software. It runs off a linux/unix architecture.

The work I need to do is computationally expensive...and would take days to complete.

Most of these sorts of software are able to run in parrallel, in the sense that you have maybe 4 or 5 baseunits connected via ethernet cables (i think) and you run them in parallel so all 5 processors are used to run this calculation.

It similar to what people have done before with Mac G5s, where they hooked up hundreds of them and was able to make a cheap and powerful supercomputer.

Any ideas?

Thank

[ms514]

Sat Sri Akal:

Tell you what...whatever distribution you want to use, try to go on their forum and ask the question. They may have knowledge as to what to do as many of the distribution developers are there and they are the ones who know the details of their OS.

[Harjit_S_Banga]

WGJKK

WGJKF

Veer, please check the following link out...hope it will get you where you want to be.

http://yara.ecn.purdue.edu/~pplinux/PPHOWT...howto.html#toc1

WGJKK

WGJKF

[Harjit_S_Banga]

WGJKK

WGJKF

Also look at this link....http://yara.ecn.purdue.edu/~pplinux/Sites/Index.html

WGJKK

WGJKF

[amorphous_singh]

I need to run some computational drug software. It runs off a linux/unix architecture.

The work I need to do is computationally expensive...and would take days to complete.

Most of these sorts of software are able to run in parrallel, in the sense that you have maybe 4 or 5 baseunits connected via ethernet cables (i think) and you run them in parallel so all 5 processors are used to run this calculation.

It similar to what people have done before with Mac G5s, where they hooked up hundreds of them and was able to make a cheap and powerful supercomputer.

Any ideas?

Thank

144880[/snapback]

Hmm well I guess I might be able to help (but not been very active on forums lately due to other stuff).

I run several unix based clusters (linux, solaris and tru64) and many of my research colleagues work in the field of parallel systems.

MPI is probably a good way to go, also give PVM a go.

However there are factors to consider - is your software latency dependent or have high bandwidth requirements; if so then the interconnect (in this case ethernet) might not be suitable.

Many clusters use specialised interconnects (SCI, myrinet, quadrics etc) to deal with these issues. However if your code is embarrasingly parallel (is it FLOSS code?) then ethernet might work.

To check it out - get your self a simple cluster distro - ie oscar or rocks and install that - or just install MPICH (free implementation of MPI) on your existing distro and if your software has the appropriate calls then it should just work. Famous last words!

You might have a learning curve ahead of you.

If I can help - PM me and I'll drop you my email address - but I'm apologise in advance and say that I am currently swamped - but will try to help is I can.

The best thing as always in these matters (well you're a unix/linux user afterall) is to just do it and see what happens.

Also have a look at the beowulf (a form of linux cluster) mailing list where many many knowledgeable folks hang out - but read archives before posting :-)

[amorphous_singh]

Sat Sri Akal:

Tell you what...whatever distribution you want to use, try to go on their forum and ask the question.  They may have knowledge as to what to do as many of the distribution developers are there and they are the ones who know the details of their OS.

147102[/snapback]

Just wanted to say that this is not necessarily a problem for the developers of a particular distro, this is a software layer and personally I would suggest that you only ask such questions if the distro concerned has a list for parallel/beowulf/hpc/etc issues?

Also don't forget that getting such codes to work is probably going to involve some admin work if the nodes haven't been set up as such before. ie remote logins (go with rsh if it's on a secure private network), distributed user lists (eg NIS or vi /etc/passwd on each node), shared home areas (NFS), scratch space?

You'll get more luck on specialised lists. But if you're a fairly decent admin already then non of this should be an issue. This is where clusters distro's make life easier for ppl getting started they deal with many of these issues for you.