[Biodevelopers] RE: [Bioclusters] RE: About the parallel Blast on PVM

[Akpodigha Filatei]

Thanks Joe for your reply.  I have the source, made some modifications to get it to work with my gcc but, for some reasons, the makedis.csh script could not figure out that it is solaris64.ncbi.mk that it needs to use.  It uses solaris.ncbi.mk to do the build.  One option I am thinking of trying is to copy the solaris64.ncbi.mk to solaris.ncbi.mk.

Will get back to you on how this goes.
Thanks

Filatei 


> -----Original Message-----
> From: Joseph Landman [mailto:landman at scalableinformatics.com]
> Sent: Monday, August 19, 2002 8:00 PM
> To: biocluster
> Cc: biodevelopers
> Subject: [Bioclusters] RE: About the parallel Blast on PVM
> 
> 
> Hi Filatei:
> 
>   There is a solaris64.ncbi.mk target for the NCBI blast.  It is
> possible that your version was built using one of the other tools.  If
> you want to build it for the 64 bit Solaris architecture, you should
> grab the NCBI source code, run the make script, and test the resulting
> binaries.  
> 
>   The NCBI source is at ftp://ftp.ncbi.nlm.nih.gov in the tool_box
> directory (site is down right now, so I cannot give 
> specifics).  Do the
> following on the target machine.
> 
> 1) Uncompress it, untar it.  
> 
> 2) Edit the ncbi/platform/solaris64.ncbi.mk to reflect any option
> changes you wish, specifically looking at the following flags:
> 
>     NCBI_CC = cc -xtarget=ultra -xarch=v9 -xildoff
>     NCBI_CFLAGS1 = -c -Xa
>     NCBI_LDFLAGS1 = -Xa
>     NCBI_OPTFLAG = -fast -xtarget=ultra -xarch=v9
> 
> You may wish to change the options, specifically NCBI_OPTFLAG and
> NCBI_CFLAGS1.  
> 
> 3) Build the system:
> 
> 	ncbi/make/makedis.csh
> 
> After some time (and hopefully without errors), you should have a few
> new binaries in the ncbi/build/ directory.  You should be able to
> execute
> 
> 	ncbi/build/blastall
> 
> and see all the blastall arguments.
> 
> If this doesn't work, call you local IT/support person to give you a
> hand.  This procedure should generate the 64 bit binaries on a 64 bit
> Solaris platform (provided the scripts recognize it as such).
> 
> Please note that there are reasons why the 64 bit code is bound to be
> slightly (to possibly significantly) slower on smaller (e.g. 
> less than 2
> GB) data sets.  Pointer and integer sizes are 64 bit on a true 64 bit
> platform, which means that fewer can fit in cache (which lowers the
> effective size of the cache by decreasing the data stored within it),
> and requires more time to transfer than a 32 bit word (which 
> reduces the
> data rate to the CPU, as the CPU can grab only half as many 64 bit
> variables as 32 bit variables at a time). 
> 
> The net effect for data sets less than 2 GB in size is a speed
> reduction.  Couple this with the speed and price advantage of the IA32
> platforms (Athlon and P III) on BLAST as compared to RISC 
> platforms, and
> it might not be worth the effort to rebuild BLAST for the Sun if you
> already have a few well configured late model PC servers about.
> 
> Joe
> 
> 
> On Mon, 2002-08-19 at 19:08, Akpodigha Filatei wrote:
> > Hi, I am interested in this as well.  I have NCBI blast 
> running twice faster on a 2-processor Intel Linux box than 
> 4-processor UltraSparc server(SUN E3500, Solaris 8).  It is 
> not using more than 1 processor on the solaris server even 
> when we specify 4 or more for the -a parameter, as it does on 
> the Linux server.  Is there any known implementation that 
> takes advantange of the 64-bit architecture of Sun servers?  
> Please let me know if you have any useful info on this.
> > 
> > Filatei 
> 
> -- 
> Joseph Landman, Ph.D
> Scalable Informatics LLC
> email: landman at scalableinformatics.com
>   web: http://scalableinformatics.com
> phone: +1 734 612 4615
> 
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