Autonomous local masters

Makefile

@@ -1,6 +1,5 @@
 #
-#
-# 'make'            make executable file 'mspar'
+# 'make'            make executable file 'msparsm'
 # 'make clean'      removes all .o and executable files
 #
 
@@ -33,22 +32,15 @@ RND=rand2.c
 $(BIN)/%.o: %.c $(DEPS)
 	$(CC) $(CFLAGS) -c -o $@ $<
 
-default: $(BIN)/mspar
-
-# download: packages
-#	wget http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.2.tar.gz
-#	tar -xf openmpi-1.8.2.tar.gz -C $(CURDIR)/packages
-
-#packages:
-#	mkdir packages
+default: $(BIN)/msparsm
 
 clean:
 	rm -f $(BIN)/*
 	@echo ""
 	@echo "*** All resources were cleaned-up ***"
 	@echo ""
 
-$(BIN)/mspar: $(OBJ)
+$(BIN)/msparsm: $(OBJ)
 	$(CC) $(CFLAGS) -o $@ $^ $(RND_48) $(LIBS)
 	@echo ""
-	@echo "*** make complete: generated executable 'mspar' ***"
+	@echo "*** make complete: generated executable 'bin/msparsm' ***"

README.md

@@ -1,15 +1,39 @@
-msparsm
+msParSm
 =======
 
-Parallel version of "ms" coalescent simulator using a master worker approach and a MPI implementation with on-demand scheduling.
+The _msParSm_ application is an evolution of _msPar_ <sup>[(1)][1]</sup>, the parallel version of the coalescent simulation program 
+_ms_ <sup>[(2)][2]</sup>, 
+which removes the limitation for simulating long stretches of DNA sequences with large recombination rates, 
+without compromising the accuracy of the standard coalescence.
+
+## Pre-requisites
+- Linux GNU Compiler 4.9.1 (or greater)
+- OpenMPI 1.10.1 (other releases in the branch 1.10 should be fine)
+    - Version 1.8.x could potentially be fine, but please notice that _msParSm_ was not fully tested with such version.
+- CMake 3.5.1 (or greather) **OR** GNU Make 3.81 (or greater)
 
 ## How to Build
-Create the makefile using CMake:
+There are two ways for building _msParSm_: CMake and Make. If you have installed CMAKE with version greater than 3.5.0,
+then go with CMake, otherwise you should use Make.
+
+### CMake
 ```bash
 cmake <src-path> -DCMAKE_INSTALL_PREFIX=<install-path>
 ```
 
-Install using make:
+### Make
 ```bash
 make install
 ```
+Binary files will be put into the `bin` folder (which is already _git ignored_).
+
+## How to Use
+Usage is the mostly the same as with traditional _ms_, but you need to run it through _OpenMPI_. Next example
+will run the application using 4 threads:
+
+```bash
+mpirun -n 4 bin/msparsm 10 20 -seeds 40328 19150 54118 -t 100 -r 100 100000 -I 2 2 8 -eN 0.4 10.01 -eN 1 0.01 -en 0.25 2 0.2 -ej 3 2 1 -T > results.out
+```
+
+[1]: http://link.springer.com/chapter/10.1007/978-3-642-54420-0_32
+[2]: http://home.uchicago.edu/~rhudson1/popgen356/OxfordSurveysEvolBiol7_1-44.pdf

mspar.c

@@ -250,8 +250,8 @@ char *generateSamples(int samples, struct params parameters, unsigned maxsites,
  */
 char* generateSample(struct params parameters, unsigned maxsites, int *bytes)
 {
-    int segsites, offset;
-    size_t positionStrLength, gametesStrLenght;
+    int segsites;
+    size_t offset, positionStrLength, gametesStrLenght;
     double probss, tmrca, ttot;
     char *results;
     char **gametes;
@@ -263,32 +263,38 @@ char* generateSample(struct params parameters, unsigned maxsites, int *bytes)
         gametes = cmatrix(parameters.cp.nsam, parameters.mp.segsitesin+1 );
 
     gensamResults = gensam(gametes, &probss, &tmrca, &ttot, parameters, &segsites);
-    results = doPrintWorkerResultHeader(segsites, probss, parameters, gensamResults.tree, &offset);
+
+    results = doPrintWorkerResultHeader(segsites, probss, parameters, gensamResults.tree);
+
+    offset = strlen(results);
+    *bytes = offset;
 
     if(segsites > 0)
     {
         char *positionsStr = doPrintWorkerResultPositions(segsites, parameters.output_precision, gensamResults.positions);
         positionStrLength = strlen(positionsStr);
 
-
         char *gametesStr = doPrintWorkerResultGametes(segsites, parameters.cp.nsam, gametes);
         gametesStrLenght = strlen(gametesStr);
 
-        results = realloc(results, offset + positionStrLength + gametesStrLenght + 1);
-        //sprintf(results, "%s%s", results, positionsStr);
+        results = realloc(results, offset + positionStrLength + gametesStrLenght + 2);
+
         memcpy(results+offset, positionsStr, positionStrLength+1);
 
         offset += positionStrLength;
+        *bytes += positionStrLength;
+
         memcpy(results+offset, gametesStr, gametesStrLenght+1);
+
+        *bytes += gametesStrLenght;
+
         free(positionsStr);
         free(gametesStr);
         if( parameters.mp.timeflag ) {
             free(gensamResults.tree);
         }
     }
 
-    *bytes = offset;
-
     return results;
 }
 
@@ -299,7 +305,7 @@ char* generateSample(struct params parameters, unsigned maxsites, int *bytes)
  *    // xxx.x xx.xx x.xxxx x.xxxx
  *    segsites: xxx
  */
-char *doPrintWorkerResultHeader(int segsites, double probss, struct params pars, char *treeOutput, int *bytes){
+char *doPrintWorkerResultHeader(int segsites, double probss, struct params pars, char *treeOutput){
     char *results;
 
     int length = 3 + 1; // initially "\n//" and optionally a "\n" when there is no treeOutput;
@@ -332,8 +338,6 @@ char *doPrintWorkerResultHeader(int segsites, double probss, struct params pars,
         sprintf(results, "%ssegsites: %d\n", results, segsites);
     }
 
-    *bytes = length;
-
     return results;
 }