added modified makefiles that will do a clean build (i.e. remove all …

….o and the corresponding executable prior to compiling) to avoid frequent erroneous use and questions on the RAxML google group when users forgot to remove .o files prior to building a different binary. For development purposes this can be disabled by specifying the dev target
johnkslang · Aug 10, 2015 · 4c26b88 · 4c26b88
1 parent a9b2aa2
commit 4c26b88
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Showing 25 changed files with 89 additions and 39 deletions.
diff --git a/Makefile.AVX.HYBRID.gcc b/Makefile.AVX.HYBRID.gcc
@@ -10,7 +10,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-HYBRID-AVX
+all : clean raxmlHPC-HYBRID-AVX
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
@@ -50,3 +50,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-HYBRID-AVX
+
+dev: raxmlHPC-HYBRID-AVX
diff --git a/Makefile.AVX.MPI.gcc b/Makefile.AVX.MPI.gcc
@@ -10,7 +10,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-MPI-AVX
+all : clean raxmlHPC-MPI-AVX
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
@@ -50,3 +50,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-MPI-AVX
+
+dev: raxmlHPC-MPI-AVX
diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o  
 
-all : raxmlHPC
+all : clean raxmlHPC-PTHREADS-AVX
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
-raxmlHPC : $(objs)
+raxmlHPC-PTHREADS-AVX : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -52,3 +52,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS-AVX
+
+dev: raxmlHPC-PTHREADS-AVX
diff --git a/Makefile.AVX.PTHREADS.mac b/Makefile.AVX.PTHREADS.mac
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-PTHREADS-AVX
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
-raxmlHPC : $(objs)
+raxmlHPC-PTHREADS-AVX : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -52,3 +52,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS-AVX
+
+dev: raxmlHPC-PTHREADS-AVX
diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc
@@ -11,11 +11,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o   mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-AVX
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h
 
-raxmlHPC : $(objs)
+raxmlHPC-AVX : $(objs)
 	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) $(LDFLAGS)
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -51,3 +51,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-AVX
+
+dev : raxmlHPC-AVX
diff --git a/Makefile.AVX.mac b/Makefile.AVX.mac
@@ -11,11 +11,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-AVX
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
-raxmlHPC : $(objs)
+raxmlHPC-AVX : $(objs)
 	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -53,3 +53,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-AVX
+
+dev: raxmlHPC-AVX
diff --git a/Makefile.AVX2.HYBRID.gcc b/Makefile.AVX2.HYBRID.gcc
@@ -10,7 +10,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-HYBRID-AVX2
+all : clean raxmlHPC-HYBRID-AVX2
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
@@ -50,3 +50,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-HYBRID-AVX2
+
+dev: raxmlHPC-HYBRID-AVX2
diff --git a/Makefile.AVX2.MPI.gcc b/Makefile.AVX2.MPI.gcc
@@ -10,7 +10,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-MPI-AVX2
+all : clean raxmlHPC-MPI-AVX2
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
@@ -50,3 +50,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-MPI-AVX2
+
+dev: raxmlHPC-MPI-AVX2
diff --git a/Makefile.AVX2.PTHREADS.gcc b/Makefile.AVX2.PTHREADS.gcc
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o  
 
-all : raxmlHPC
+all : clean raxmlHPC-PTHREADS-AVX2
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
-raxmlHPC : $(objs)
+raxmlHPC-PTHREADS-AVX2 : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-AVX2 $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -52,3 +52,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS-AVX2
+
+dev: raxmlHPC-PTHREADS-AVX2
diff --git a/Makefile.AVX2.PTHREADS.mac b/Makefile.AVX2.PTHREADS.mac
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-PTHREADS-AVX2
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
-raxmlHPC : $(objs)
+raxmlHPC-PTHREADS-AVX2 : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-AVX2 $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -52,3 +52,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS-AVX2
+
+dev: raxmlHPC-PTHREADS-AVX2
diff --git a/Makefile.AVX2.gcc b/Makefile.AVX2.gcc
@@ -11,11 +11,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o   mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-AVX2
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h
 
-raxmlHPC : $(objs)
+raxmlHPC-AVX2 : $(objs)
 	$(CC) -o raxmlHPC-AVX2 $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -51,3 +51,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-AVX2
+
+dev: raxmlHPC-AVX2
diff --git a/Makefile.AVX2.mac b/Makefile.AVX2.mac
@@ -11,11 +11,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-AVX2
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
-raxmlHPC : $(objs)
+raxmlHPC-AVX2 : $(objs)
 	$(CC) -o raxmlHPC-AVX2 $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
@@ -53,3 +53,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-AVX2
+
+dev : raxmlHPC-AVX2
diff --git a/Makefile.HYBRID.gcc b/Makefile.HYBRID.gcc
@@ -12,7 +12,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-HYBRID
+all : clean raxmlHPC-HYBRID
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
@@ -47,3 +47,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-HYBRID
+
+dev : raxmlHPC-HYBRID
diff --git a/Makefile.MPI.gcc b/Makefile.MPI.gcc
@@ -12,7 +12,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-MPI
+all : clean raxmlHPC-MPI
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
@@ -47,3 +47,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-MPI
+
+dev : raxmlHPC-MPI
diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc
@@ -13,7 +13,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o  fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o  
 
-all : raxmlHPC-PTHREADS
+all : clean raxmlHPC-PTHREADS
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
@@ -48,3 +48,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS
+
+dev : raxmlHPC-PTHREADS
diff --git a/Makefile.PTHREADS.mac b/Makefile.PTHREADS.mac
@@ -13,7 +13,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o  fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o  
 
-all : raxmlHPC-PTHREADS
+all : clean raxmlHPC-PTHREADS
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
@@ -48,3 +48,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS
+
+dev : raxmlHPC-PTHREADS
diff --git a/Makefile.QuartetMPI.gcc b/Makefile.QuartetMPI.gcc
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-QUARTET-MPI
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
-raxmlHPC : $(objs)
+raxmlHPC-QUARTET-MPI : $(objs)
 	$(CC) -o raxmlHPC-QUARTET-MPI $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 rmqs.o : rmqs.c $(GLOBAL_DEPS)
@@ -47,3 +47,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-QUARTET-MPI
+
+dev : raxmlHPC-QUARTET-MPI
diff --git a/Makefile.SSE3.HYBRID.gcc b/Makefile.SSE3.HYBRID.gcc
@@ -10,7 +10,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o  
 
-all : raxmlHPC-HYBRID-SSE3
+all : clean raxmlHPC-HYBRID-SSE3
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
@@ -45,3 +45,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-HYBRID-SSE3
+
+dev : raxmlHPC-HYBRID-SSE3
diff --git a/Makefile.SSE3.MPI.gcc b/Makefile.SSE3.MPI.gcc
@@ -10,7 +10,7 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o  fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC-MPI-SSE3
+all : clean raxmlHPC-MPI-SSE3
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h
 
@@ -45,3 +45,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-MPI-SSE3
+
+dev : raxmlHPC-MPI-SSE3
diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o  fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o  
 
-all : raxmlHPC
+all : clean raxmlHPC-PTHREADS-SSE3
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
-raxmlHPC : $(objs)
+raxmlHPC-PTHREADS-SSE3 : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 #rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
@@ -47,3 +47,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS-SSE3
+
+dev : raxmlHPC-PTHREADS-SSE3
diff --git a/Makefile.SSE3.PTHREADS.mac b/Makefile.SSE3.PTHREADS.mac
@@ -12,11 +12,11 @@ RM = rm -f
 
 objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o  fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o  mem_alloc.o eigen.o 
 
-all : raxmlHPC
+all : clean raxmlHPC-PTHREADS-SSE3
 
 GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
-raxmlHPC : $(objs)
+raxmlHPC-PTHREADS-SSE3 : $(objs)
 	$(CC)  -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
 
 #rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
@@ -47,3 +47,5 @@ eigen.o : eigen.c $(GLOBAL_DEPS)
 	$(CC) -c -o eigen.o eigen.c 
 clean : 
 	$(RM) *.o raxmlHPC-PTHREADS-SSE3
+
+dev : raxmlHPC-PTHREADS-SSE3