Switching back to .md to allow github to render.

README → README.md

@@ -1,4 +1,4 @@
-#Installing INDDGO
+##Installing INDDGO
 
 To install INDDGO, follow the steps listed in the INSTALL file.
 
@@ -16,7 +16,7 @@ Note that although it is not a prerequisite for using INDDGO, if you
 wish to use the optional functionality of solving mixed integer programming 
 formulations of MWIS, you should have glpsol installed and available.
 
-#Running INDDGO binaries
+##Running INDDGO binaries
 
 The main INDDGO binaries are placed in the "bin" subdirectory of your
 source tree.
@@ -44,48 +44,48 @@ these executables will find and run on the largest connected component.
 All components will be written to separate .comp files, and the one used
 will be identified through a message to standard out. 
 
-##Examples of common use cases
+###Examples of common use cases
 Two sample input graph files, as well as an example tree decomposition
 file and elimination order file can be found in the sample_graphs directory.
  All examples use these files. The optimal MWIS value for each is in the 
  comments at the top of the DIMACS file. Additional information on both input and 
  output formatting for the weighted independent set binaries is in max_wis/README.
 
-#Generating Test Data
+##Generating Test Data
  Create 3 partial k-trees on 1000 vertices with width 20, 60 percent of 
  full k-tree edges, randomized vertex labels, and names of the form 
  mygraph.1000.20.60_.dimacs
 * ./bin/gen_pkt -t 3 -n 1000 -k 20 -p 60 -r -fn ./sample_graphs/mygraph
 
-#Find Tree Decomposition
+##Find Tree Decomposition
  Generate a tree decomposition (serial) and save elimination ordering
  and decomposition to file for future use.
 * ./bin/serial_wis -f sample_graphs/1dc.64.dimacs -gavril -mind -decompose_only -w sample_graphs/1dc.64.tree -eorder sample_graphs/1dc.64.mind.eorder
 
-#Run MWIS (serial, find set)
+##Run MWIS (serial, find set)
  Computes max weighted independent set and saves vertices to solution file 
  named <inputfile>.WIS.sol
 * ./bin/serial_wis -f sample_graphs/1dc.64.dimacs -gavril -mind 
 
-#Run MWIS (serial, find objective) 
+##Run MWIS (serial, find objective) 
  Computes objective (set weight) only, but reduces memory use drastically. 
 * ./bin/serial_wis -f sample_graphs/1dc.64.dimacs -gavril -mind -no_reconstruct -del_ch
 
-#Run MWIS (all parallel) 
+##Run MWIS (all parallel) 
  Complete run from graph to final solution. Requires PARMETIS.
 * export MAD_NUM_THREADS=4
 * export OMP_NUM_THREADS=4
 * export PTD_NUM_THREADS=4 
 * mpirun -n 4 ./bin/parallel_wis -f sample_graphs/1dc.64.dimacs -gavril -mind -pbag -parmetis
 
-#Run MWIS (only DP parallel) 
+##Run MWIS (only DP parallel) 
  Reads EO from file, serial tree decomposition, parallel (MADNESS) DP.  
 * export MAD_NUM_THREADS=4
 * export OMP_NUM_THREADS=4
 * export PTD_NUM_THREADS=4 
 * mpirun -n 4 ./bin/parallel_wis -ord sample_graphs/1dc.64.mind.eorder -f sample_graphs/1dc.64.dimacs -gavril 
 
-#Generate visualization
+##Generate visualization
  Create a basic DOT file of the tree decomposition for use with graphviz where
  bags are labelled with the vertices they contain 
  (sample graphviz command: neato -Tpdf -o tree.pdf tree.dot).