Faster LINKAGE v1.1

Robert Cottingham bwc at bcm.tmc.edu
Thu Sep 9 11:01:12 EST 1993


In article <1993Sep9.101352.1 at kean.ucs.mun.ca>, roger at kean.ucs.mun.ca writes:
|> In article <26118c$ke9 at gazette.bcm.tmc.edu>, bwc at bcm.tmc.edu (Robert Cottingham) writes:
|> > As described in the paper "Faster Sequential Genetic Linkage
|> > Computations" (American Journal of Human Genetics, v53, p252-63, 
|> > July 1993), modified versions of the general pedigree programs
|> > of LINKAGE 5.1 are available via ftp as follows:
|> > 
|> 
|> 	What are the hardware and operating system requirements for running
|> FASTLINK?  

We are using Sun Sparc 2s with 16-64Mb running SunOS 4.1.3.  However the programs
are distributed as C source code and therefore could be run on a variety of other
machines.  These programs are based on p2c translations of the original pascal
LINKAGE programs, and require the p2c libraries.  In general I would recommend
that a minimum configuration be a 32-bit cpu with 16Mb of memory and an operating
system with an efficient swapping mechanism on a 100Mb swap file.

Of course the requirements vary considerably depending on the size of the problem
being solved.  More loci and more alleles per locus dramatically increase the
memory requirements.

We have run fastlink on DECstation 5000s, and I will be attempting a port to a
DEC Alpha.  Ellen Wijsman has reported running fastlink on a DEC VAX under VMS.

-Bob

        ------------------------------------------------------------
        Bob Cottingham                        Phone:  713/798-4275
        Cell Biology & Human Genome Center    Fax:        798-5386
        Baylor College of Medicine            Email: bwc at bcm.tmc.edu
        Houston, TX   77030
        ------------------------------------------------------------



More information about the Gen-link mailing list