[Bioclusters] RE: About the parallel Blast on PVM

Akpodigha Filatei bioclusters@bioinformatics.org
Tue, 20 Aug 2002 10:29:33 -0400

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.


> -----Original Message-----
> From: Joseph Landman [mailto:landman@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. =20
>   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=20
> specifics).  Do the
> following on the target machine.
> 1) Uncompress it, untar it. =20
> 2) Edit the ncbi/platform/solaris64.ncbi.mk to reflect any option
> changes you wish, specifically looking at the following flags:
>     NCBI_CC =3D cc -xtarget=3Dultra -xarch=3Dv9 -xildoff
>     NCBI_CFLAGS1 =3D -c -Xa
>     NCBI_LDFLAGS1 =3D -Xa
>     NCBI_OPTFLAG =3D -fast -xtarget=3Dultra -xarch=3Dv9
> You may wish to change the options, specifically NCBI_OPTFLAG and
> 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.=20
> 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=20
> 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).=20
> 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=20
> 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=20
> running twice faster on a 2-processor Intel Linux box than=20
> 4-processor UltraSparc server(SUN E3500, Solaris 8).  It is=20
> not using more than 1 processor on the solaris server even=20
> when we specify 4 or more for the -a parameter, as it does on=20
> the Linux server.  Is there any known implementation that=20
> takes advantange of the 64-bit architecture of Sun servers? =20
> Please let me know if you have any useful info on this.
> >=20
> > Filatei=20
> --=20
> Joseph Landman, Ph.D
> Scalable Informatics LLC
> email: landman@scalableinformatics.com
>   web: http://scalableinformatics.com
> phone: +1 734 612 4615
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