| diff --git a/configure.ac b/configure.ac |
| index 68453ef..3ecfd21 100644 |
| --- a/configure.ac |
| +++ b/configure.ac |
| @@ -28,13 +28,11 @@ AC_CHECK_FUNCS([floor memset clock pow sqrt strchr strdup strtol strtoul]) |
| dnl 1) threads options |
| |
| dnl abc) : with-threads option |
| -AC_ARG_WITH( |
| - threads, |
| - [ --with-threads compile with all threads], |
| - [threads="yes"], |
| - [threads="no"]) |
| +AC_ARG_ENABLE( |
| + [threads], |
| + AS_HELP_STRING([--enable-threads], [compile with all threads])) |
| |
| -if test "$threads" = "yes"; then |
| +AS_IF([test "x$enable_threads" = "xyes"], [ |
| AC_MSG_RESULT(detected cpu parameter: threads); |
| |
| dnl pthread library here ? (UNIX system) |
| @@ -46,167 +44,25 @@ if test "$threads" = "yes"; then |
| AC_MSG_RESULT(yes) |
| AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) |
| CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN -DTHREAD_FORWARD_REVERSE -DTHREAD_QUERY_CHUNK " |
| - LDFLAGS="$LDFLAGS -lpthread" |
| + LIBS="$LIBS -lpthread" |
| else |
| AC_MSG_RESULT(no : disabling \"--with-threads\" parameter) |
| fi |
| - |
| -else |
| - if test -s /proc/cpuinfo; then |
| - AC_MSG_CHECKING(for multi-processor) |
| - dnl Multithread advice |
| - if test `grep -c '^processor' /proc/cpuinfo` -gt 2; then |
| - AC_MSG_RESULT(yes) |
| - AC_MSG_RESULT(- try \"configure --with-threads\") |
| - else |
| - AC_MSG_RESULT(no) |
| - fi; |
| - fi; |
| -fi |
| - |
| - |
| - |
| - |
| - |
| -dnl a) : with-thread-fr option |
| -AC_ARG_WITH( |
| - thread-fr, |
| - [ --with-thread-fr compile with two separate threads for Forward and Reverse sequence], |
| - [thread_forward_reverse="yes"], |
| - [thread_forward_reverse="no"]) |
| - |
| -if test "$thread_forward_reverse" = "yes"; then |
| - AC_MSG_RESULT(detected cpu parameter: thread-fr); |
| - |
| - dnl pthread library here ? (UNIX system) |
| - AC_MSG_CHECKING(for pthread lib) |
| - AC_CHECK_LIB(pthread, pthread_create, |
| - [have_pthread="yes"], |
| - [have_pthread="no"]) |
| - if test "$have_pthread" = "yes"; then |
| - AC_MSG_RESULT(yes) |
| - AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) |
| - CFLAGS=" $CFLAGS -DTHREAD_FORWARD_REVERSE " |
| - LDFLAGS="$LDFLAGS -lpthread" |
| - else |
| - AC_MSG_RESULT(no : disabling \"--with-thread-fr\" parameter) |
| - fi |
| - |
| -else |
| - if test -s /proc/cpuinfo; then |
| - AC_MSG_CHECKING(for multi-processor) |
| - dnl Multithread advice |
| - if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then |
| - AC_MSG_RESULT(yes) |
| - AC_MSG_RESULT(- try \"configure --with-thread-fr\") |
| - else |
| - AC_MSG_RESULT(no) |
| - fi; |
| - fi; |
| -fi |
| - |
| - |
| - |
| - |
| - |
| -dnl b) : with-thread-aa option |
| -AC_ARG_WITH( |
| - thread-aa, |
| - [ --with-thread-aa compile with two separate threads for Assemble and Align steps], |
| - [thread_assemble_align="yes"], |
| - [thread_assemble_align="no"]) |
| - |
| -if test "$thread_assemble_align" = "yes"; then |
| - AC_MSG_RESULT(detected cpu parameter: thread-aa); |
| - |
| - dnl pthread library here ? (UNIX system) |
| - AC_MSG_CHECKING(for pthread lib) |
| - AC_CHECK_LIB(pthread, pthread_create, |
| - [have_pthread="yes"], |
| - [have_pthread="no"]) |
| - if test "$have_pthread" = "yes"; then |
| - AC_MSG_RESULT(yes) |
| - AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) |
| - CFLAGS=" $CFLAGS -DTHREAD_ASSEMBLE_ALIGN " |
| - LDFLAGS="$LDFLAGS -lpthread" |
| - else |
| - AC_MSG_RESULT(no : disabling \"--with-thread-aa\" parameter) |
| - fi |
| - |
| -else |
| - if test -s /proc/cpuinfo; then |
| - AC_MSG_CHECKING(for multi-processor) |
| - dnl Multithread advice |
| - if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then |
| - AC_MSG_RESULT(yes) |
| - AC_MSG_RESULT(- try \"configure --with-thread-aa\") |
| - else |
| - AC_MSG_RESULT(no) |
| - fi; |
| - fi; |
| -fi |
| - |
| - |
| -dnl c) : with-thread-qc option |
| -AC_ARG_WITH( |
| - thread-qc, |
| - [ --with-thread-qc compile with threads for the query chunks], |
| - [thread_query_chunk="yes"], |
| - [thread_query_chunk="no"]) |
| - |
| -if test "$thread_query_chunk" = "yes"; then |
| - AC_MSG_RESULT(detected cpu parameter: thread-qc); |
| - |
| - dnl pthread library here ? (UNIX system) |
| - AC_MSG_CHECKING(for pthread lib) |
| - AC_CHECK_LIB(pthread, pthread_create, |
| - [have_pthread="yes"], |
| - [have_pthread="no"]) |
| - if test "$have_pthread" = "yes"; then |
| - AC_MSG_RESULT(yes) |
| - AC_DEFINE([HAVE_PTHREAD],[1],[pthread available on the computer]) |
| - CFLAGS=" $CFLAGS -DTHREAD_QUERY_CHUNK " |
| - LDFLAGS="$LDFLAGS -lpthread" |
| - else |
| - AC_MSG_RESULT(no : disabling \"--with-thread-qc\" parameter) |
| - fi |
| - |
| -else |
| - if test -s /proc/cpuinfo; then |
| - AC_MSG_CHECKING(for multi-processor) |
| - dnl Multithread advice |
| - if test `grep -c '^processor' /proc/cpuinfo` -gt 1; then |
| - AC_MSG_RESULT(yes) |
| - AC_MSG_RESULT(- try \"configure --with-thread-qc\") |
| - else |
| - AC_MSG_RESULT(no) |
| - fi; |
| - fi; |
| -fi |
| - |
| - |
| - |
| +]) |
| |
| dnl 2) : low-memory option |
| -AC_ARG_WITH( |
| - low-memory, |
| - [ --with-low-memory use less memory, but can miss some repeats], |
| - [low_memory="yes"], |
| - [low_memory="no"]) |
| +AC_ARG_ENABLE( |
| + [lowmemory], |
| + AS_HELP_STRING([--enable-lowmemory], [use less memory, but can miss some repeats])) |
| |
| -if test "$low_memory" = "yes"; then |
| +AS_IF([test "x$enable_lowmemory" = "xyes"], [ |
| AC_MSG_RESULT(detected memory parameter: low memory); |
| CFLAGS=" $CFLAGS -DLOW_MEMORY " |
| -else |
| - AC_MSG_RESULT(detected memory parameter : plain memory) |
| -fi |
| - |
| - |
| -CFLAGS="$CFLAGS -O3 -Wall -ansi -pedantic -funroll-loops -pipe -fomit-frame-pointer " |
| -LDFLAGS="$LDFLAGS -lm" |
| +]) |
| |
| AC_SUBST(CFLAGS) |
| AC_SUBST(LDFLAGS) |
| + |
| AM_WITH_DMALLOC |
| AM_INIT_AUTOMAKE |
| AC_CONFIG_FILES([Makefile |
| diff --git a/src/Makefile.am b/src/Makefile.am |
| index e456f94..8d90ca9 100644 |
| --- a/src/Makefile.am |
| +++ b/src/Makefile.am |
| @@ -6,3 +6,4 @@ |
| bin_PROGRAMS = yass |
| yass_SOURCES = align.c assemble.c avl.c display.c global_var.c hash.c kword.c list.c main.c prdyn.c proba.c red_black.c regroup.c threads.c tuple.c util.c \ |
| align.h assemble.h avl.h display.h global_var.h hash.h kword.h list.h prdyn.h proba.h red_black.h regroup.h threads.h tuple.h util.h |
| +yass_LDADD = -lm |