[Bioclusters] (no subject)

[Dan Bolser]

On Tue, 30 Mar 2004, LAI Loong Fong wrote:

> The limitation actually lies in the 32 bit architecture of Xeon. 
> Physical 32 bit limitation is 4GB, PAE gives us up to 64 GB. For normal 
> Linux, you should have about 3GB per process and maybe can tune the 
> kernel to use 3.5GB per process.

Hmmm..... Looks like we are only getting 2GB per process (2GB per CPU?).

We are using standard linux, but with a swap space below the size of the
ram (2GB). Could this be a problem? (i.e. true64 style).

ulimit -a
core file size        (blocks, -c) 0
data seg size         (kbytes, -d) unlimited
file size             (blocks, -f) unlimited
max locked memory     (kbytes, -l) unlimited
max memory size       (kbytes, -m) unlimited
open files                    (-n) 1024
pipe size          (512 bytes, -p) 8
stack size            (kbytes, -s) 8192
cpu time             (seconds, -t) unlimited
max user processes            (-u) 7168
virtual memory        (kbytes, -v) unlimited

Mem:  4124724k av,
Swap: 2040244k av

Thanks very much for your help,

Dan.


> 
> LAI Loong-Fong
> 
> On Mar 30, 2004, at 2:46 PM, Dan Bolser wrote:
> 
> >
> > I have a question about Xeon and memory... It looks like I have one Gb 
> > per
> > CPU, and not 4 Gb for the 4 CPU without restriction. Is this problem at
> > the hardware level?
> >
> > What is the maximum amount of memory a CPU can use?
> >
> > I heard talk of a Tb memory machine, but it was part of a 1000 node
> > cluster, so I am thinking OK 1 Gb per node.
> >
> > Can anyone clarify this for me?
> >
> > Cheers,
> > Dan.
> >
> > On Mon, 29 Mar 2004, Philip MacMenamin wrote:
> >
> >> On Monday 29 March 2004 05:38 am, you wrote:
> >>> hello all,
> >>>
> >>> i'm interested to the constructiong of a linux cluster of computer 
> >>> for
> >>> bioinformatics purpose. but i dont have a cluu about the performans 
> >>> it
> >>> should have. is there any one who can give any suggestion?
> >>>
> >>> in  the hope of an answer
> >>>
> >> Its kind of a nebulous question.
> >>
> >> Basically... buy Xeon || AMD two way boxes. Be boring, look at Dell or
> >> penguin computing or something. Dont bother with 64 bit. Think about 
> >> that in
> >> about 2 years time. It will irritate you in 2 months after you buy 
> >> it, *i
> >> promise*.
> >>
> >> Dont buy from some indy very cheap manufacturer, cause, if the nodes 
> >> will
> >> fail, you will be left waiting... or make them give you a decent 
> >> guarantee.
> >> Or a big box of bits.
> >>
> >> Look at the price of the chip : speed ratio. This graph will have an
> >> inflection point, at which more money input gives diminishing returns
> >> speed-wise. Buy at this inflection point. This changes all the 
> >> time... of
> >> course. There is no point in buying the *best* out there right this 
> >> second.
> >> Just buy a little behind it, and buy an extra box or two.
> >>
> >> Find out what you want to run.
> >> Buy as enough memory so it doesn't thrash your disks. (Or just fill 
> >> it with
> >> memory).
> >>
> >> Spending about 2 grand (USD) on them a piece (I dont know what that 
> >> is in
> >> Lira) should buy you something decent operating at 3 gigs, with a 
> >> couple of
> >> gigs ram.
> >>
> >> Then have a look at
> >> http://bioinformatics.org/biobrew/
> >> www.rocksclusters.org/
> >>
> >> Sorry if this is very uninspiring/boring advice... its just, you want 
> >> to keep
> >> everything as simple as you can. There will be tricky bits no matter 
> >> how
> >> simple you make everything.
> >> Good luck.
> >> Philip.
> >> _______________________________________________
> >> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> >> https://bioinformatics.org/mailman/listinfo/bioclusters
> >>
> >
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters
>