-fixed some minor compiler issues with the Makefiles and source files

-updated version number
johnkslang · Jun 24, 2013 · 4caba56 · 4caba56
1 parent 818fab9
commit 4caba56
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Showing 41 changed files with 26 additions and 64 deletions.
diff --git a/Makefile.AVX.HYBRID.gcc b/Makefile.AVX.HYBRID.gcc
@@ -12,7 +12,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-HYBRID-AVX
 
-GLOBAL_DEPS = axml.h globalVariables.h  mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC-HYBRID-AVX : $(objs)
 	$(CC) -o raxmlHPC-HYBRID-AVX $(objs) $(LIBRARIES) 

diff --git a/Makefile.AVX.MPI.gcc b/Makefile.AVX.MPI.gcc
@@ -12,7 +12,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-MPI-AVX
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC-MPI-AVX : $(objs)
 	$(CC) -o raxmlHPC-MPI-AVX $(objs) $(LIBRARIES) 

diff --git a/Makefile.AVX.PTHREADS.gcc b/Makefile.AVX.PTHREADS.gcc
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h  mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) 

diff --git a/Makefile.AVX.PTHREADS.mac b/Makefile.AVX.PTHREADS.mac
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) 

diff --git a/Makefile.AVX.gcc b/Makefile.AVX.gcc
@@ -13,7 +13,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h # compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) 

diff --git a/Makefile.AVX.mac b/Makefile.AVX.mac
@@ -13,7 +13,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) 

diff --git a/Makefile.HYBRID.gcc b/Makefile.HYBRID.gcc
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-HYBRID
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC-HYBRID : $(objs)
 	$(CC) -o raxmlHPC-HYBRID $(objs) $(LIBRARIES) 

diff --git a/Makefile.MPI.gcc b/Makefile.MPI.gcc
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-MPI
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC-MPI : $(objs)
 	$(CC) -o raxmlHPC-MPI $(objs) $(LIBRARIES) 

diff --git a/Makefile.PTHREADS.gcc b/Makefile.PTHREADS.gcc
@@ -15,7 +15,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-PTHREADS
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC-PTHREADS : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) 

diff --git a/Makefile.PTHREADS.mac b/Makefile.PTHREADS.mac
@@ -15,7 +15,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-PTHREADS
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC-PTHREADS : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) 

diff --git a/Makefile.QuartetMPI.gcc b/Makefile.QuartetMPI.gcc
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-QUARTET-MPI $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.HYBRID.gcc b/Makefile.SSE3.HYBRID.gcc
@@ -12,7 +12,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-HYBRID-SSE3
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC-HYBRID-SSE3 : $(objs)
 	$(CC) -o raxmlHPC-HYBRID-SSE3 $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.MPI.gcc b/Makefile.SSE3.MPI.gcc
@@ -12,7 +12,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC-MPI-SSE3
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC-MPI-SSE3 : $(objs)
 	$(CC) -o raxmlHPC-MPI-SSE3 $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.PTHREADS.gcc b/Makefile.SSE3.PTHREADS.gcc
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.PTHREADS.mac b/Makefile.SSE3.PTHREADS.mac
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.QuartetMPI.gcc b/Makefile.SSE3.QuartetMPI.gcc
@@ -13,7 +13,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-SSE3-QUARTET-MPI $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.gcc b/Makefile.SSE3.gcc
@@ -13,7 +13,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) 

diff --git a/Makefile.SSE3.mac b/Makefile.SSE3.mac
@@ -13,7 +13,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) 

diff --git a/Makefile.gcc b/Makefile.gcc
@@ -14,7 +14,7 @@ objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePart
 
 all : raxmlHPC
 
-GLOBAL_DEPS = axml.h globalVariables.h mem_alloc.h
+GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
 
 raxmlHPC : $(objs)
 	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 

diff --git a/ancestralStates.c b/ancestralStates.c
@@ -44,7 +44,6 @@
 #include <string.h>
 
 #include "axml.h"
-#include "mem_alloc.h"
 
 extern char  workdir[1024];
 extern char run_id[128];

diff --git a/axml.c b/axml.c
@@ -72,7 +72,6 @@
 #endif
 
 #include "axml.h"
-#include "mem_alloc.h"
 #include "globalVariables.h"
 
 

diff --git a/axml.h b/axml.h
@@ -163,8 +163,8 @@
 #define PointGamma(prob,alpha,beta)  PointChi2(prob,2.0*(alpha))/(2.0*(beta))
 
 #define programName        "RAxML"
-#define programVersion     "7.6.1"
-#define programDate        "June 21 2013"
+#define programVersion     "7.6.2"
+#define programDate        "June 24 2013"
 
 
 #define  TREE_EVALUATION                 0
@@ -1326,6 +1326,11 @@ extern void newviewGenericAncestral(tree *tr, nodeptr p, boolean atRoot);
 extern void computeAncestralStates(tree *tr, double referenceLikelihood);
 extern void makeP_Flex(double z1, double z2, double *rptr, double *EI,  double *EIGN, int numberOfCategories, double *left, double *right, const int numStates);
 
+extern void *rax_malloc( size_t size );
+extern void *rax_realloc(void *p, size_t size, boolean needsMemoryAlignment);
+extern void rax_free(void *p);
+extern void *rax_calloc(size_t n, size_t size);
+
 #ifdef _WAYNE_MPI
 
 extern boolean computeBootStopMPI(tree *tr, char *bootStrapFileName, analdef *adef, double *pearsonAverage);

diff --git a/bipartitionList.c b/bipartitionList.c
@@ -68,8 +68,6 @@ extern int processID;
 extern int processes;
 #endif
 
-#include "mem_alloc.h"
-
 #define _NEW_MRE
 
 extern FILE *INFILE;

diff --git a/classify.c b/classify.c
@@ -57,8 +57,6 @@ extern volatile int NumberOfThreads;
 extern volatile int NumberOfJobs;
 #endif
 
-#include "mem_alloc.h"
-
 static double getBranch(tree *tr, double *b, double *bb)
 {
   double z = 0.0;

diff --git a/evaluatePartialGenericSpecial.c b/evaluatePartialGenericSpecial.c
@@ -45,7 +45,6 @@
 #include <pmmintrin.h>
 #endif
 
-#include "mem_alloc.h"
 
 /********************** GTRCAT ***************************************/
 

diff --git a/fastDNAparsimony.c b/fastDNAparsimony.c
@@ -76,8 +76,6 @@
 
 #include "axml.h"
 
-#include "mem_alloc.h"
-
 extern const unsigned int mask32[32]; 
 /* vector-specific stuff */
 

diff --git a/fastSearch.c b/fastSearch.c
@@ -42,8 +42,6 @@
 #include <ctype.h>
 #include <string.h>
 
-#include "mem_alloc.h"
-
 #include "axml.h"
 
 #define POSTERIOR_THRESHOLD 0.90

diff --git a/leaveDropping.c b/leaveDropping.c
@@ -4,7 +4,6 @@
 #include <math.h>
 #include <assert.h>
 #include "axml.h"
-#include "mem_alloc.h"
 
 
 /* the define below makes the algorithm run much faster and should therefore always be used :-) */

diff --git a/makenewzGenericSpecial.c b/makenewzGenericSpecial.c
@@ -49,8 +49,6 @@
 /*#include <tmmintrin.h>*/
 #endif
 
-#include "mem_alloc.h"
-
 #ifdef _USE_PTHREADS
 extern volatile double *reductionBuffer;
 extern volatile double *reductionBufferTwo;

diff --git a/mem_alloc.c b/mem_alloc.c
@@ -1,7 +1,6 @@
 
 #define MEM_ALLOC_NO_GUARDS 1
 
-#include "mem_alloc.h"
 #include "axml.h"
 
 #include <stdio.h>

diff --git a/mem_alloc.h b/mem_alloc.h
diff --git a/models.c b/models.c
@@ -44,7 +44,6 @@
 #include <string.h>
 
 #include "axml.h"
-#include "mem_alloc.h"
 
 extern int optimizeRatesInvocations;
 extern int optimizeRateCategoryInvocations;

diff --git a/multiple.c b/multiple.c
@@ -40,7 +40,6 @@
 #include <ctype.h>
 #include <string.h>
 #include "axml.h"
-#include "mem_alloc.h"
 
 #ifdef _WAYNE_MPI
 #include <mpi.h>

diff --git a/newviewGenericSpecial.c b/newviewGenericSpecial.c
@@ -65,7 +65,6 @@ extern volatile int NumberOfThreads;
 extern pthread_mutex_t          mutex;
 #endif
 
-#include "mem_alloc.h"
 
 extern const unsigned int mask32[32];
 

diff --git a/optimizeModel.c b/optimizeModel.c
@@ -40,7 +40,6 @@
 #include <ctype.h>
 #include <string.h>
 #include "axml.h"
-#include "mem_alloc.h"
 
 
 static const double MNBRAK_GOLD =    1.618034;

diff --git a/parsePartitions.c b/parsePartitions.c
@@ -44,9 +44,6 @@
 #include <string.h>
 #include <strings.h>
 
-
-#include "mem_alloc.h"
-
 #include "axml.h"
 
 /*****************************FUNCTIONS FOR READING MULTIPLE MODEL SPECIFICATIONS************************************************/

diff --git a/rapidBootstrap.c b/rapidBootstrap.c
@@ -42,8 +42,6 @@
 #include <ctype.h>
 #include <string.h>
 
-#include "mem_alloc.h"
-
 #include "axml.h"
 
 extern int Thorough;

diff --git a/rogueEPA.c b/rogueEPA.c
@@ -40,7 +40,6 @@
 #include <ctype.h>
 #include <string.h>
 #include "axml.h"
-#include "mem_alloc.h"
 
 extern char run_id[128];
 extern char workdir[1024];

diff --git a/searchAlgo.c b/searchAlgo.c
@@ -42,7 +42,6 @@
 #include <ctype.h>
 #include <string.h>
 
-#include "mem_alloc.h"
 
 #include "axml.h"
 

diff --git a/topologies.c b/topologies.c
@@ -44,7 +44,6 @@
 #include <string.h>
 
 #include "axml.h"
-#include "mem_alloc.h"
 
 
 

diff --git a/treeIO.c b/treeIO.c
@@ -43,7 +43,6 @@
 #include <string.h>
 
 #include "axml.h"
-#include "mem_alloc.h"
 
 extern FILE *INFILE;
 extern char infoFileName[1024];
-Original file line number
+Diff line change
@@ Expand Up / @@ -72,7 +72,6 @@ @@
     #endif
     #include "axml.h"
-    #include "mem_alloc.h"
     #include "globalVariables.h"
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -44,7 +44,6 @@
		#include <string.h>

		#include "axml.h"
		#include "mem_alloc.h"



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