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

Keep PTHREADS_CFLAGS separate from CFLAGS, so user can override CFLAGS
without messing with autoconf of pthreads.

Updates version to 0.45-dev.
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cryptogenomicon committed Jun 9, 2018
1 parent 08f155f commit b368d6bdd8ddf4364cf446e6ac2ba7adee402811
Showing with 29 additions and 26 deletions.
  1. +11 −10 Makefile.in
  2. +2 −2 configure.ac
  3. +8 −7 miniapps/Makefile.in
  4. +8 −7 testsuite/Makefile.in
@@ -56,7 +56,8 @@ man1ext = .1
# Compiler configuration
#
CC = @CC@
CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@
CFLAGS = @CFLAGS@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
SSE_CFLAGS = @SSE_CFLAGS@
AVX_CFLAGS = @AVX_CFLAGS@
AVX512_CFLAGS = @AVX512_CFLAGS@
@@ -518,7 +519,7 @@ libeasel.a: ${ALL_OBJS}
@${RANLIB} libeasel.a

${ALL_OBJS}: %.o : %.c ${HDRS} esl_config.h
${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<
${QUIET_CC}${CC} -I. -I${srcdir} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} -c $<


# Driver compilation:
@@ -542,10 +543,10 @@ ${ALL_UTESTS}: libeasel.a
else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
fi;\
if test ${V} ;\
then echo "${CC} ${CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${UTEST_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
else echo ' ' GEN $@ ;\
fi ;\
${CC} ${CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}

${ALL_BENCHMARKS}: libeasel.a
@BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
@@ -556,10 +557,10 @@ ${ALL_BENCHMARKS}: libeasel.a
else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
fi;\
if test ${V} ;\
then echo "${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
else echo ' ' GEN $@ ;\
fi ;\
${CC} ${CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}

${ALL_EXPERIMENTS}: libeasel.a
@BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
@@ -570,10 +571,10 @@ ${ALL_EXPERIMENTS}: libeasel.a
else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
fi;\
if test ${V} ;\
then echo "${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
else echo ' ' GEN $@ ;\
fi ;\
${CC} ${CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}

${ALL_EXAMPLES}: libeasel.a
@BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
@@ -583,10 +584,10 @@ ${ALL_EXAMPLES}: libeasel.a
else DFILE=${srcdir}/esl_$${BASENAME}.c ;\
fi ;\
if test ${V}; \
then echo "${CC} ${CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
then echo "${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMDFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}" ;\
else echo ' ' GEN $@ ;\
fi ;\
${CC} ${CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}
${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${SIMD_CFLAGS} ${DEFS} ${LDFLAGS} -o $@ -I. -I${srcdir} -L. -D$${DFLAG} $${DFILE} -leasel -lm ${LIBS}



@@ -72,7 +72,7 @@ m4_include([m4/ax_pthread.m4])
################################################################
# 2. AC_INIT
################################################################
AC_INIT(Easel, 0.44, sean@eddylab.org, easel)
AC_INIT(Easel, 0.45-dev, sean@eddylab.org, easel)
AC_MSG_NOTICE([Configuring the Easel library for your system.])

# remember if the user is overriding CFLAGS
@@ -219,7 +219,7 @@ 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

@@ -33,12 +33,13 @@ INSTALL = @INSTALL@

## your compiler and compiler flags.
#
CC = @CC@
CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
DEFS = @DEFS@
LIBS = -leasel @LIBGSL@ @LIBS@ @PTHREAD_LIBS@ -lm
CC = @CC@
CFLAGS = @CFLAGS@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
DEFS = @DEFS@
LIBS = -leasel @LIBGSL@ @LIBS@ @PTHREAD_LIBS@ -lm

## list of the miniapps to compile.
#
@@ -87,7 +88,7 @@ tests: ${PROGS}
check: ${PROGS}

${PROGS}: % : %.c ../libeasel.a
${QUIET_GEN}${CC} ${CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}
${QUIET_GEN}${CC} ${CFLAGS} ${PTHREAD_CFLAGS} ${DEFS} ${LDFLAGS} -L.. -I. -I.. -I${srcdir} -I${srcdir}/.. -o $@ $< ${LIBS}

install: ${PROGS}
for file in ${PROGS}; do \
@@ -3,13 +3,14 @@ srcdir = @srcdir@
VPATH = @srcdir@ @top_srcdir@
SHELL = /bin/sh

CC = @CC@
CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
DEFS = @DEFS@
LIBS = @LIBGSL@ @LIBS@ -lm
MPILIBS = @MPILIBS@
CC = @CC@
CFLAGS = @CFLAGS@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
CPPFLAGS = @CPPFLAGS@
LDFLAGS = @LDFLAGS@
DEFS = @DEFS@
LIBS = @LIBGSL@ @LIBS@ -lm
MPILIBS = @MPILIBS@

SQCLEVEL = 2

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