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

Matt Temple mht at research.dfci.harvard.edu
Sun Feb 27 14:26:49 EST 2005

Hash: SHA1

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...

Why do you reject the quad Opteron computers (supporting 32 GB of RAM)
from vendors like ASAComputers (and, no
doubt, though I haven't checked from PCs for Everyone and others)?  
The computers, themselves, may not be from mainstream
vendors, but they are from motherboard manufacturers that I'd be
inclined to call mainstream -- SuperMicro, Tyan, ASUS.

~            Matt Temple

| ...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

- --
Matthew Temple                Tel:    617/632-2597
Director, Research Computing  Fax:    617/582-7820
Dana-Farber Cancer Institute  mht at research.dfci.harvard.edu
44 Binney Street,  LG300/300  http://research.dfci.harvard.edu
Boston, MA 02115              Choice is the Choice!
Version: GnuPG v1.2.4 (Darwin)
Comment: Using GnuPG with Thunderbird - http://enigmail.mozdev.org


More information about the Bioclusters mailing list