[Bioclusters] Need some advice on a cluster for EST/cDNA assembly, clustering

[Elia Stupka]

>  Future revs of publically available Opteron boards will be able to go 
> a bit higher than 32 GB (8GB/CPU).  IBM's units are based on an MSI 
> motherboard, and last I checked, IBM still sees a limited role for 
> Opteron's in it's lineup.

Definitely, we just went through a quote with them, we asked for 
Opterons, they sent us a quote of under-spec'ed and over-priced 
Opterons, and super-spec'ed and under-priced Xeons and Power5s ;)

> Sun is offering 2 way and 4 way today.

That's what we'll probably end up getting, 4-way Sun Opteron, we got 
two 2-way Sun Opterons and they are very neat.

> Same with HP.

HP recently announced blade Opterons, we are waiting for the 
quote/specs.

> Some of the smaller vendors are offering real 8-way units today (2 
> Iwill or Arima MB's joined with a hypertransport HTX link or similar). 
>  Very interesting stuff is coming in the near future from a number of 
> vendors in this space.  Saw some amazing stuff at SC04 (not the stuff 
> on the show floor).

Sounds interesting, will wait to see... I wonder how the new IBM 8-way 
Cell Processor (which is meant to go up 64-way) will cope with 
bioinformatics applications...

Elia

>
> Joe
>
> Elia Stupka wrote:
>> I've been hoping to be able to access large amounts of memory on 
>> affordable servers for a while, in reality, though, the 4GB OS limit 
>> has hardly been the issue since unfortunately the cost of memory is 
>> still very high and hardware vendors seldom offer more than 4GBs per 
>> processor.
>> The Sun Opterons are the only ones (among the mainstream vendors) 
>> that offered us a 4-way option with 32 GBs. The Apple G5s are still 
>> limited to 8GB (4 per processor, probably when Tiger will be truly 
>> released they will finally offer more memory slots?), IBM Opterons 
>> offer 16GB (still only 4GB per processor), the blade versions are 
>> always limited in memory, etc... then you are left with the usual 
>> suspects (Power5s, etc.) who have been dealing with more memory for a 
>> long time, but at a nasty price...
>> ...as long as it costs more to equip hardware with good amounts of 
>> memory than it costs to buy the hardware, the refinement of 64-bit OS 
>> for access to large amounts of memory can't take off properly, can 
>> it?
>> Cheers,
>> Elia
>> On 27 Feb 2005, at 15:40, Joe Landman wrote:
>>>
>>>
>>> LAI Loong Fong wrote:
>>>
>>>> The process in OSX 10.3 can only see up to 4GB of ram. From what I
>>>> understand, 10.4 may or may not resolve this issue. I did heard 
>>>> about people
>>>> buying from Apple but run YDL instead.
>>>
>>>
>>> The big issue we keep seeing in 64 linux is running into ABI 
>>> differences.  There are a few distributions that try to create a 
>>> "pure" 64 bit or a mixed 64 bit environment, and neither do a 
>>> perfect job. Usually you see this in terms of broken software 
>>> installation/builds. Other times libraries are broken, or headers, 
>>> or paths to the libraries/headers ...
>>>
>>> It would help if there were simple methods of tying paths to ABI's.
>>>
>>> In terms of the 4GB limit, this is an annoyance today, and I suspect 
>>> for most folks, will become a major issue in short order.  I think 
>>> YDL is a RH variant, so hopefully it has support built in (if it was 
>>> built from the 64 bit ports of RH).  If not, it would be nice if OSX 
>>> came in an OSX64 (if not today, then soon).
>>>
>>> I wonder if that would get compiler support though (the IBM compiler 
>>> specifically).
>>>
>>> Joe
>>>
>>>> LAI Loong-Fong
>>>> _______________________________________________
>>>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>>
>>>
>>> -- 
>>> Joseph Landman, Ph.D
>>> Scalable Informatics LLC,
>>> email: landman at scalableinformatics.com
>>> web  : http://www.scalableinformatics.com
>>> phone: +1 734 786 8423
>>>
>>> _______________________________________________
>>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>> https://bioinformatics.org/mailman/listinfo/bioclusters
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>
> -- 
> Joseph Landman, Ph.D
> Founder and CEO
> Scalable Informatics LLC,
> email: landman at scalableinformatics.com
> web  : http://www.scalableinformatics.com
> phone: +1 734 786 8423
> fax  : +1 734 786 8452
> cell : +1 734 612 4615
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters