Description: Implementation of the MrsRF algorithm for Linux systems
             using the MapReduce framework in Phoenix.

Directions: To create executables, type 'make' in the src directory. 
Also run 'make' in the hashtable directory.
            All MrsRF executables are stored in src/.
            hashbase's executable is located in hashbase/.

Executable descriptions:  

mrsrf-pq: 
  - Used in conjunction with mrsrf.
  - Creates a matrix of size pxq.

mrsrf:
  - Works on k nodes to create a t x t matrix.
  - Calls mrsrf-pq to create RF submatrices.


Usage:
To run MrsRF on N nodes and c cores, run the following command in the 
main directory:

mpirun -np <N> src/mrsrf <cores> <input file> <number of taxa> <number 
of trees> <output> <rounds>

Where:
<N> represents the number of nodes
<cores> represents the number of cores
<input file> is the input file to the program
<number of taxa> number of taxa represented by the input file
<number of trees> represents the number of the trees in the input file
<output> either 0 or 1. Use "0" if you do not want the matrix to be 
printed out. Use "1" to print out the matrix.
<rounds> Specifies the number of iterations. For all practical purposes, 
please use 1 as the value.

For example, to run mrsrf on 2 nodes and 4 cores, using an input file 
specified by "test.tre" which contains 12 trees with 10 taxa each, run 
the following:

mpirun -np 2 src/mrsrf 4 test.tre 10 12 1 1 

Other notes:
If the code does not compile out of box:
It may be necessary to reset the CPU_SET definitions. 
Please comment out the code associated with "new definitions" and 
uncomment the code section associated with "old definitions". This 
should be located near the top of src/MapReduceScheduler.c