Fixes for issue #141 and #120: compile fails on i586, ppc64be

All compilation commands need SSE_CFLAGS, VMX_CFLAGS. Vector code is not as well separated in H3 as in H4. impl_{sse,vmx.h} are included in other .c files, not just in impl_{sse,vmx} code. Keep PTHREADS_CFLAGS, SSE_CFLAGS, VMX_CFLAGS separate in Makefiles, rather than adding them to CFLAGS, so user can override CFLAGS without messing up autoconf of pthreads, simd. CFLAGS couldn't be set externally; user setting was being overridden in ./configure. Updates version to 3.2.1-dev in ./configure.
EddyRivasLab · Jun 9, 2018 · e397297 · e397297
1 parent c07ba6b
commit e397297
Show file tree

Hide file tree

Showing 7 changed files with 76 additions and 74 deletions.
diff --git a/Makefile.in b/Makefile.in
@@ -53,10 +53,13 @@ man1ext     = .1
 
 # Compiler configuration
 #
-CC        = @CC@
-CFLAGS    = @CFLAGS@ @PTHREAD_CFLAGS@ 
-LDFLAGS   = -static @LDFLAGS@
-CPPFLAGS  = @CPPFLAGS@
+CC             = @CC@
+CFLAGS         = @CFLAGS@ 
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+SSE_CFLAGS     = @SSE_CFLAGS@
+VMX_CFLAGS     = @VMX_CFLAGS@
+LDFLAGS        = -static @LDFLAGS@
+CPPFLAGS       = @CPPFLAGS@
 
 # Other tools
 #

diff --git a/configure.ac b/configure.ac
@@ -75,7 +75,7 @@ m4_include([easel/m4/ax_pthread.m4])
 # 2. AC_INIT
 ################################################################
 
-AC_INIT(HMMER, 3.2, sean@eddylab.org, hmmer)
+AC_INIT(HMMER, 3.2.1-dev, sean@eddylab.org, hmmer)
 AC_MSG_NOTICE([Configuring HMMER3 for your system.])
 
 # remember if the user is overriding CFLAGS
@@ -84,8 +84,6 @@ if test x"$CFLAGS" != x; then
   esl_cflags_env_set=yes
 fi
 
-
-
 ################################################################
 # 3. Info on the package
 ################################################################
@@ -121,7 +119,7 @@ HMMER_SADIR="libdivsufsort"
 EASEL_DATE="June 2018"
 EASEL_COPYRIGHT="Copyright (C) 2018 Howard Hughes Medical Institute."
 EASEL_LICENSE="Freely distributed under the BSD open source license."
-EASEL_VERSION="0.44"
+EASEL_VERSION="0.45-dev"
 EASEL_URL="http://bioeasel.org/"
 
 AC_SUBST(HMMER_DATE)
@@ -253,7 +251,7 @@ elif test "$enable_debugging" != "no"; then
    if test "$GCC" = "yes"; then
       CFLAGS="-g -Wall"
    fi
-else
+elif test "$esl_cflags_env_set" != "yes"; then
    CFLAGS="-O3"
 fi
 

diff --git a/libdivsufsort/Makefile.in b/libdivsufsort/Makefile.in
@@ -1,31 +1,25 @@
-# Makefile for fm-index
-
 # VPATH and shell configuration
 top_srcdir = @top_srcdir@
 srcdir     = @srcdir@
 VPATH      = @srcdir@ 
 SHELL      = /bin/sh
 
 # sources
-OBJS				= divsufsort.o 
-TARGET				= libdivsufsort.a
-MAKEFILE			= Makefile
+OBJS	       = divsufsort.o 
+TARGET	       = libdivsufsort.a
+MAKEFILE       = Makefile
 
 # options
-CC        = @CC@
-CFLAGS    = @CFLAGS@ @PTHREAD_CFLAGS@ 
-CPPFLAGS  = @CPPFLAGS@
-MPILIBS   = @MPILIBS@
-AR        = @AR@ rc
-RANLIB    = @RANLIB@
-INSTALL   = @INSTALL@
-
-#CC					= gcc 
-#CFLAGS  	 		= -g -O3 -fomit-frame-pointer -fstrict-aliasing 
-#CPPFLAGS			= -Wall 
-#AR       = /usr/bin/ar rc
-#RANLIB   = ranlib
-
+CC             = @CC@
+CFLAGS         = @CFLAGS@ 
+SSE_CFLAGS     = @SSE_CFLAGS@ 
+VMX_CFLAGS     = @VMX_CFLAGS@ 
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+CPPFLAGS       = @CPPFLAGS@
+MPILIBS        = @MPILIBS@
+AR             = @AR@ rc
+RANLIB         = @RANLIB@
+INSTALL        = @INSTALL@
 
 # beautification magic stolen from git (added within hmmer source)
 ifndef V
@@ -39,7 +33,7 @@ all: $(TARGET)
 $(TARGET): $(OBJS)
 
 .c.o:
-	${QUIET_CC}${CC} -I. ${CFLAGS} ${CPPFLAGS} -o $@ -c $<
+	${QUIET_CC}${CC} -I. ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${CPPFLAGS} -o $@ -c $<
 
 
 libdivsufsort.a: $(OBJS)
@@ -58,5 +52,4 @@ endif
 distclean:
 	$(RM) $(TARGET) $(OBJS) $(MAKEFILE) divsufsort.h
 
-# dependencies
-$(OBJS): divsufsort.h $(MAKEFILE)
+
diff --git a/profmark/Makefile.in b/profmark/Makefile.in
@@ -2,17 +2,19 @@ top_srcdir = @top_srcdir@
 srcdir     = @srcdir@
 VPATH      = @srcdir@ 
 
-CC       = @CC@
-CFLAGS   = @CFLAGS@ @PTHREAD_CFLAGS@
-CPPFLAGS = @CPPFLAGS@
-LDFLAGS  = @LDFLAGS@
-DEFS     = @DEFS@
-LIBS     = -lhmmer -leasel @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ -lm
-MPILIBS  = @MPILIBS@
-IMPLDIR  = impl_@IMPL_CHOICE@
+CC             = @CC@
+CFLAGS         = @CFLAGS@ 
+SSE_CFLAGS     = @SSE_CFLAGS@ 
+VMX_CFLAGS     = @VMX_CFLAGS@ 
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+CPPFLAGS       = @CPPFLAGS@
+LDFLAGS        = @LDFLAGS@
+DEFS           = @DEFS@
+LIBS           = -lhmmer -leasel @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ -lm
+MPILIBS        = @MPILIBS@
+IMPLDIR        = impl_@IMPL_CHOICE@
 
 ESLDIR    = @HMMER_ESLDIR@
-
 ESLINC   = -I../${ESLDIR} -I${top_srcdir}/easel
 SRCINC   = -I../src   -I${top_srcdir}/src
 
@@ -41,12 +43,12 @@ all:    ${PROGS}
 dev:    ${PROGS}
 
 ${PROGS}: % : %.o ../${ESLDIR}/libeasel.a ../src/libhmmer.a 
-	${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L../${ESLDIR} -L../src -o $@ $@.o ${LIBS}
 
 ${PROGOBJS}: ../src/hmmer.h ../src/p7_config.h
 
 .c.o: 
-	${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${DEFS} -o $@ -c $<		
+	${QUIET_CC}${CC} ${ESLINC} ${SRCINC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} -o $@ -c $<		
 
 clean:
 	-rm -f *.o *~ ${PROGS} 

diff --git a/src/Makefile.in b/src/Makefile.in
@@ -19,13 +19,16 @@ mandir      = @mandir@
 man1dir     = ${mandir}/man1
 man1ext     = .1
 
-CC        = @CC@
-CFLAGS    = @CFLAGS@ @PTHREAD_CFLAGS@ 
-CPPFLAGS  = @CPPFLAGS@
-LDFLAGS   = @LDFLAGS@
-DEFS      = @DEFS@
-LIBS      = -lhmmer -leasel -ldivsufsort  @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ -lm
-MPILIBS   = @MPILIBS@
+CC             = @CC@
+CFLAGS         = @CFLAGS@
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+SSE_CFLAGS     = @SSE_CFLAGS@ 
+VMX_CFLAGS     = @VMX_CFLAGS@ 
+CPPFLAGS       = @CPPFLAGS@
+LDFLAGS        = @LDFLAGS@
+DEFS           = @DEFS@
+LIBS           = -lhmmer -leasel -ldivsufsort  @LIBS@ @LIBGSL@ @PTHREAD_LIBS@ -lm
+MPILIBS        = @MPILIBS@
 
 AR        = @AR@ 
 RANLIB    = @RANLIB@
@@ -256,13 +259,13 @@ ${PROGOBJS}:    ${HDRS} p7_config.h
 ${AUXPROGOBJS}: ${HDRS} p7_config.h
 
 ${PROGS} ${AUXPROGS}: % : %.o  libhmmer.a ../${ESLDIR}/libeasel.a 
-	${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
 
 .c.o:
-	${QUIET_CC}${CC} ${CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
+	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${CPPFLAGS} ${MYINCDIRS} -o $@ -c $<
 
 ${ITESTS}: % : %.o libhmmer.a ${HDRS} p7_config.h
-	${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
+	${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${DEFS} ${LDFLAGS} ${MYLIBDIRS} -o $@ $@.o ${MPILIBS} ${LIBS}
 
 ${UTESTS}: libhmmer.a  ${HDRS} p7_config.h
 	@BASENAME=`echo $@ | sed -e 's/_utest//' | sed -e 's/^p7_//'` ;\
@@ -274,10 +277,10 @@ ${UTESTS}: libhmmer.a  ${HDRS} p7_config.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "{CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "{CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
         fi ;\
-	${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 ${BENCHMARKS}: libhmmer.a  ${HDRS} p7_config.h
 	@BASENAME=`echo $@ | sed -e 's/_benchmark//' | sed -e 's/^p7_//'` ;\
@@ -289,10 +292,10 @@ ${BENCHMARKS}: libhmmer.a  ${HDRS} p7_config.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "{CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "{CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
         fi ;\
-	${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 ${STATS}: libhmmer.a ${HDRS} p7_config.h
 	@BASENAME=`echo $@ | sed -e 's/_stats//' | sed -e 's/^p7_//'` ;\
@@ -304,10 +307,10 @@ ${STATS}: libhmmer.a ${HDRS} p7_config.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "{CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "{CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
         fi ;\
-	${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 ${EXAMPLES}: libhmmer.a ${HDRS} p7_config.h
 	@BASENAME=`echo $@ | sed -e 's/_example[0-9]*//' | sed -e 's/^p7_//'` ;\
@@ -318,10 +321,10 @@ ${EXAMPLES}: libhmmer.a ${HDRS} p7_config.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "{CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "{CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
         fi ;\
-	${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 install:
 	for file in ${PROGS}; do \

diff --git a/src/impl_vmx/Makefile.in b/src/impl_vmx/Makefile.in
@@ -10,13 +10,14 @@ bindir      = @bindir@
 libdir      = @libdir@
 includedir  = @includedir@
 
-CC          = @CC@
-CFLAGS      = @CFLAGS@ @PTHREAD_CFLAGS@ 
-VMX_CFLAGS  = @VMX_CFLAGS@
-CPPFLAGS    = @CPPFLAGS@
-LDFLAGS     = @LDFLAGS@
-DEFS        = @DEFS@
-LIBS        = -lhmmer -leasel @LIBS@ -lm
+CC             = @CC@
+CFLAGS         = @CFLAGS@ 
+PTHREAD_CFLAGS = @PTHREAD_CFLAGS@ 
+VMX_CFLAGS     = @VMX_CFLAGS@
+CPPFLAGS       = @CPPFLAGS@
+LDFLAGS        = @LDFLAGS@
+DEFS           = @DEFS@
+LIBS           = -lhmmer -leasel @LIBS@ -lm
 
 AR          = @AR@ 
 RANLIB      = @RANLIB@
@@ -103,7 +104,7 @@ libhmmer-impl.stamp: ${OBJS}
 ${OBJS}:   ${HDRS} ../hmmer.h 
 
 .c.o:  
-	${QUIET_CC}${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${DEFS} ${PTHREAD_CFLAGS} ${MYINCDIRS} -c $<
+	${QUIET_CC}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${DEFS} ${MYINCDIRS} -c $<
 
 ${UTESTS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
 	@BASENAME=`echo $@ | sed -e 's/_utest//'| sed -e 's/^p7_//'` ;\
@@ -115,10 +116,10 @@ ${UTESTS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 ${BENCHMARKS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
 	@BASENAME=`echo $@ | sed -e 's/_benchmark//' | sed -e 's/^p7_//'`;\
@@ -130,10 +131,10 @@ ${BENCHMARKS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 ${EXAMPLES}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
 	@BASENAME=`echo $@ | sed -e 's/_example//'| sed -e 's/^p7_//'` ;\
@@ -145,10 +146,10 @@ ${EXAMPLES}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
            DFILE=${srcdir}/$${BASENAME}.c ;\
 	fi;\
 	if test ${V} ;\
-	   then echo "${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
+	   then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}" ;\
 	   else echo '    ' GEN $@ ;\
 	fi ;\
-	${CC} ${CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+	${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${VMX_CFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 clean:
 	-rm -f impl_lib.stamp

diff --git a/src/impl_vmx/impl_vmx.h b/src/impl_vmx/impl_vmx.h
@@ -269,6 +269,8 @@ extern size_t       p7_oprofile_Sizeof(P7_OPROFILE *om);
 extern P7_OPROFILE *p7_oprofile_Copy(P7_OPROFILE *om);
 extern P7_OPROFILE *p7_oprofile_Clone(const P7_OPROFILE *om);
 extern int          p7_oprofile_UpdateFwdEmissionScores(P7_OPROFILE *om, P7_BG *bg, float *fwd_emissions, float *sc_arr);
+extern int          p7_oprofile_UpdateVitEmissionScores(P7_OPROFILE *om, P7_BG *bg, float *fwd_emissions, float *sc_arr);
+extern int          p7_oprofile_UpdateMSVEmissionScores(P7_OPROFILE *om, P7_BG *bg, float *fwd_emissions, float *sc_arr);
 
 extern int          p7_oprofile_Convert(const P7_PROFILE *gm, P7_OPROFILE *om);
 extern int          p7_oprofile_ReconfigLength    (P7_OPROFILE *om, int L);