HOWTO PARALLELIZE MIGRATE (by hand)
===================================
Peter Beerli
beerli@genetics.washington.edu


(1) Secure as many computers for the analysis as you have loci
    in your dataset.

(2) On one machine prepare a directory with

    - migrate-n

    run the program once, and adjust the run parameters using
    the menu. Use the sumfile option in the (I)nput menu
    and then save the parmfile with the 
    (W)rite parmfile option. Then (Q)uit.
    Edit the created parmfile and check if you can find 
    write-sumfile=YES
    then change menu=YES to menu=NO

(2) Copy this directory on each machine and name the directories
    e.g. locus1 locus2 .....
    If you use Appleshare be careful that you have also 
    directories for each locus.
     
(3) Prepare the infiles. One for each locus
    Copy the infiles into the directories.

(4) Start migrate-n on all machines

(5) Once all the migrate-n runs have finished, 
    copy all sumfiles onto a single machine
    it would be helpful if this is your fastest 
    with lots of RAM. Be careful not ot overwrite
    individual files (the have the same name" sumfile").
 
(6) Concatenate the sumfiles 

(7) The combined sumfile needs hand editing
    or you can use the PERL script 
    concat-sumfile
    if you cannot run the PERL script or 
    want to do it by hand, see the xample at the bottom.

(8) make a save copy of the fixed combined sumfile

(9) run migrate-n
    and use option (D)atatype and there (g)enealogy
    and change other menu items if you want.
    
(10) voila, a multilocus outfile in a fraction of
     the time the program needs to run on a single machine.


[Reminder: eventually this will be done automatically using
MPI (message passing interface) that can use  one of the standard 
parallele machineries: on UNIX clusters there are MPICH, 
PVM and LAM; on Macintoshes there is APPLESEED; on Windows
there is PVM ? 
 

=========================================================================
What to edit in a sumfile 

(1) the heading of a sumfile needs the two first comment lines
# begin genealogy-summary file of migrate 0.9.8 ------
#

(2) the third line needs editing, the first number is the number of loci
for single locus data it is 1, change it to the number of loci
1 3 9 0 1  [before]
4 3 9 0 1  [after, 4 loci]

(3) Search for ####### you will find  lines like the following
0 0 ####### locus 0, replicate 0 ################
the file start couting with 0, so the lines reads locus 1 and replicate 1
leave the first occurrence as it is. Goto the end of the file and 
remove
# end genealogy-summary file of migrate 0.9.8 ------

(4) Prepare the next sumfile.x to the master sumfile
    - Remove everything above 0 0 ######## locus 0, replicate 0 ..... 
    - change the number to    1 0 ######## locus 1, .....
      if you use replicates you need to change the replicates accordingly.
    - Remove the last line [except for the very last sumfile
(5) concatenate the above sufmile-fragment to the master sumfile

(6) Goto (4) until done 
   
======================================================================

Example of a sumfile

# begin genealogy-summary file of migrate 0.9.8 ------
#
1 3 9 0 1
0 0 ####### locus 0, replicate 0 ################    <<<<<<<<<<<<<<change this
1 0 0
                   0                    0                    0
101 0.01224715726902237366 0.24028906596661075978 68
0.01797109426997086853 0.46646854779862101381 88
0.00810026471633800565 0.36704951583234807222 98
0.010000 0.010000 0.010000 32.000000 23.000000 23.000000 29.000000 21.000000 27.000000 
3.53366272929252732415e-03 3.53366273324574875492e-03
5.30077896995009931885e-03 5.30077895638609870171e-03
3.74540337472894320145e-03 3.74540325539807769997e-03
2.61285099904684057037e+03 2.61285112767777718545e+03
1.87798679166376041394e+03 1.87798680725500389599e+03
1.27983305210177809386e+03 1.27983304107036315145e+03
1.61370252198881439654e+03 1.61370251775554697815e+03
2.59250790064689090286e+03 2.59250788575867818508e+03
3.33322424226003886361e+03 3.33322432150516533511e+03
39 1.71782306759650010393e-06
# end genealogy-summary file of migrate 0.9.8 ------

$Id: HOWTO-PARALLEL,v 1.1 2000/10/10 17:57:49 beerli Exp $





























