1# -*- Autoconf -*- 2# Process this file with autoconf to produce a configure script. 3 4# $Id: configure.ac,v 1.46 2010-07-21 22:05:35 twu Exp $ 5 6AC_PREREQ(2.57) 7 8## We want to get the version number from file 'VERSION' (rather than 9## specifying the version info in 'configure.ac'. Hence, we need a bit 10## of M4 magic. Note that M4 esyscmd has a trailing newline because the 11## shell command output has one, hence the patsubst() trick. 12#m4_define([PKG_VERSION], 13# m4_bpatsubst(m4_esyscmd([cat VERSION]), 14# [\([0-9.]*\)\(\w\|\W\)*], 15# [\1])) 16#m4_define([PKG_VERSION],m4_esyscmd([cat VERSION])) 17m4_define([PKG_VERSION],esyscmd([cat VERSION])) 18 19AC_INIT([gmap],PKG_VERSION,[Thomas Wu <twu@gene.com>]) 20AC_MSG_CHECKING(package version) 21AC_MSG_RESULT(PKG_VERSION) 22 23 24### Read defaults 25 26# Handle CONFIG_SITE better than Autoconf does 27for ac_site_file in $CONFIG_SITE; do 28 if { (eval echo $ac_site_file | grep '^\./' >/dev/null 2>&1) 29 ac_status=$? 30 (exit $ac_status); }; then 31 # ac_site_file starts with ./ 32 if test -r "$ac_site_file"; then 33 ac_site_file="$ac_site_file" 34 echo "really loading site script $ac_site_file: file was found" 35 . "$ac_site_file" 36 ax_user_site_file_loaded=yes 37 else 38 AC_MSG_ERROR([cannot find $ac_site_file]) 39 fi 40 else 41 # ac_site_file does not start with ./ 42 if test -r "./$ac_site_file"; then 43 echo "really loading site script ./$ac_site_file: file was found" 44 . "./$ac_site_file" 45 ax_user_site_file_loaded=yes 46 elif test -r "$ac_site_file"; then 47 echo "really loading site script $ac_site_file: file was found" 48 . "$ac_site_file" 2>/dev/null 49 ax_user_site_file_loaded=yes 50 else 51 AC_MSG_ERROR([cannot find $ac_site_file]) 52 fi 53 fi 54done 55 56if test x"$ax_user_site_file_loaded" != x"yes"; then 57 if test -r "./config.site"; then 58 echo "loading default site script ./config.site" 59 . "./config.site" 60 fi 61fi 62 63 64 65 66# Set default CFLAGS if not already set by user 67AC_MSG_CHECKING(CFLAGS) 68AC_ARG_VAR([CFLAGS], [Compiler flags (default: -O3 -fomit-frame-pointer)]) 69if test x"$CFLAGS" = x; then 70 AC_MSG_RESULT(not set by user so using default -O3 -fomit-frame-pointer) 71 ACX_EXPAND(CFLAGS,'-O3 -fomit-frame-pointer') 72else 73 AC_MSG_RESULT($CFLAGS) 74fi 75 76#AC_MSG_CHECKING(MPI_CFLAGS) 77#AC_ARG_VAR([MPI_CFLAGS], [Compiler flags (default: -O3)]) 78#AC_MSG_RESULT($MPI_CFLAGS) 79#AC_SUBST(MPI_CFLAGS) 80 81 82AC_CONFIG_SRCDIR([src/gmap.c]) 83AC_CONFIG_HEADER([src/config.h]) 84AC_CONFIG_AUX_DIR([config]) 85# For autotest: AC_CONFIG_TESTDIR([tests],[tests:src:util]) 86 87AC_CONFIG_MACRO_DIR([config]) 88 89AC_SUBST([LIBGMAP_SO_VERSION], [1:0:0]) 90#AC_SUBST([LIBGMAP_API_VERSION], [1.0]) 91 92AC_CANONICAL_SYSTEM 93 94AC_MSG_CHECKING(for non-Intel CPU) 95case $host_cpu in 96 powerpc64le) 97 AC_MSG_RESULT(yes, power8) 98 AC_DEFINE(AX_HOST_POWER8,1,[Define to 1 if host is Power8]) 99 ;; 100 101 x86_64) 102 AC_MSG_RESULT(no) 103 ;; 104 105 *) 106 AC_MSG_RESULT(no) 107 ;; 108esac 109 110 111AC_SYS_LARGEFILE 112AC_ARG_PROGRAM 113 114#AM_INIT_AUTOMAKE([no-dependencies]) 115#AM_INIT_AUTOMAKE(AC_PACKAGE_NAME, AC_PACKAGE_VERSION) 116AM_INIT_AUTOMAKE 117AM_MAINTAINER_MODE([disable]) 118 119 120AM_CONDITIONAL(FULLDIST,test "x$enable_fulldist" = xyes) 121AC_ARG_ENABLE([fulldist], 122 AC_HELP_STRING([--enable-fulldist], 123 [For use by program maintainer]), 124 [enable_fulldist="yes"], 125 [enable_fulldist="no"]) 126 127AM_CONDITIONAL(MAINTAINER,test "x$enable_maintainer" = xyes) 128AC_ARG_ENABLE([maintainer], 129 AC_HELP_STRING([--enable-maintainer], 130 [For use by program maintainer]), 131 [enable_maintainer="yes"], 132 [enable_maintainer="no"]) 133 134AM_CONDITIONAL(MAKE_LIB,test "x$enable_library" = xyes) 135AC_ARG_ENABLE([lib], 136 AC_HELP_STRING([--enable-lib], 137 [Build and install a GMAP library (Warning: will put headers into include subdirectory) (default=disable-lib)]), 138 [enable_library="yes"], 139 [enable_library="no"]) 140 141# For Perl scripts, because otherwise configure inserts 142# @bindir@ => "${exec_prefix}/bin"; 143AC_MSG_CHECKING(bindir) 144ACX_EXPAND(BINDIR,$bindir) 145AC_SUBST(BINDIR) 146AC_MSG_RESULT($BINDIR) 147 148 149 150# Checks for programs. 151#AC_PATH_PROG([PERL],[perl]) 152ACX_PATH_PERL 153 154AC_PROG_CC 155AM_PROG_CC_C_O 156# AC_PROG_LIBTOOL -- No longer working 157AX_COMPILER_VENDOR 158# AM_CONDITIONAL(INTEL_COMPILER,test "x$ax_cv_c_compiler_vendor" = xintel) 159 160 161# AX_MPI # Sets MPICC to use for isolated source files that need it 162# AC_PROG_CC_MPI # This sets CC to mpicc 163# AM_CONDITIONAL(MPI_FOUND,test "x$MPILIBS" != x) 164 165 166# Checks for libraries. 167AC_CHECK_LIB([m], rint) 168 169#AC_CHECK_LIB(popt, poptGetContext, [answer="yes"], [answer="no"]) 170#if test x"$answer" == xyes; then 171# AC_DEFINE([HAVE_LIBPOPT],[1],[Define to 1 if you have the 'popt' library (-lpopt)]) 172# POPT_LIBS="-lpopt" 173#else 174# POPT_LIBS="" 175#fi 176#AC_SUBST(POPT_LIBS) 177 178 179AC_MSG_CHECKING(whether to use MPI_File for input) 180AC_ARG_ENABLE([mpi-file-input], 181 AC_HELP_STRING([--enable-mpi-file-input], 182 [Enable MPI_File for input for MPI versions (default=yes). Note: Use only if you have a parallel I/O file system, like Lustre]), 183 [answer="$enableval"], 184 [answer=""]) 185case x"$answer" in 186 xyes) 187 AC_MSG_RESULT(enabled) 188 AC_DEFINE(USE_MPI_FILE_INPUT,1,[Define to 1 if you want to use MPI_File for input.]) 189 ;; 190 191 xno) 192 AC_MSG_RESULT(disabled) 193 ;; 194 195 x) 196 AC_MSG_RESULT([not specified so enabled by default]) 197 AC_DEFINE(USE_MPI_FILE_INPUT,1,[Define to 1 if you want to use MPI_File for input.]) 198 ;; 199esac 200 201 202# In call to ACX_PTHREAD, don't provide ACTION-IF-FOUND; otherwise, 203# HAVE_PTHREAD won't be defined 204AC_MSG_CHECKING(for pthreads feature) 205AC_ARG_ENABLE([pthreads], 206 AC_HELP_STRING([--enable-pthreads], 207 [Enable pthreads (default=yes)]), 208 [answer="$enableval"], 209 [answer=""]) 210case x"$answer" in 211 xyes) 212 AC_MSG_RESULT(enabled) 213 ACX_PTHREAD([],[pthread_warning=yes]) 214 ;; 215 216 xno) 217 AC_MSG_RESULT(disabled) 218 ;; 219 220 x) 221 AC_MSG_RESULT([not specified so enabled by default]) 222 ACX_PTHREAD([],[pthread_warning=yes]) 223 ;; 224esac 225 226 227# Checks for header files. 228AC_HEADER_STDC 229AC_HEADER_DIRENT 230AC_CHECK_HEADERS([fcntl.h limits.h stddef.h stdlib.h string.h strings.h unistd.h sys/types.h]) 231 232# Checks for typedefs, structures, and compiler characteristics. 233AC_C_INLINE 234if test "$ac_cv_c_line" != no; then 235 AC_DEFINE(HAVE_INLINE,1,[Define to 1 if compiler supports extern inline]) 236 AC_SUBST(HAVE_INLINE) 237fi 238 239AC_C_BIGENDIAN 240AC_C_CONST 241AC_C_VOLATILE 242AC_TYPE_SIZE_T 243AC_TYPE_OFF_T 244AC_CHECK_TYPES([caddr_t]) 245AC_CHECK_SIZEOF(unsigned long) 246AC_CHECK_SIZEOF(unsigned long long) 247AC_CHECK_SIZEOF(off_t) 248 249 250# Checks for library functions. 251#AC_FUNC_MALLOC -- Causes use of rpl_malloc 252#AC_FUNC_REALLOC -- Causes use of rpl_realloc 253#AC_FUNC_CLOSEDIR_VOID -- We are checking return value 254 255AC_FUNC_FSEEKO 256 257#AC_FUNC_MMAP # Checks only private fixed mapping of already-mapped memory 258 259 260AC_MSG_CHECKING(whether alloca is enabled) 261AC_ARG_ENABLE([alloca], 262 AC_HELP_STRING([--enable-alloca], 263 [Enable alloca (default=no) for stack-based memory allocation. Warning: Can cause GMAP to crash on long sequences.]), 264 [answer="$enableval"], 265 [answer=""]) 266case x"$answer" in 267 xyes) 268 AC_MSG_RESULT(enabled) 269 AC_FUNC_ALLOCA 270 ;; 271 272 xno) 273 AC_MSG_RESULT(disabled) 274 ;; 275 276 x) 277 AC_MSG_RESULT([not specified so disabled by default]) 278 ;; 279esac 280 281 282AC_MSG_CHECKING(whether mmap is enabled) 283AC_ARG_ENABLE([mmap], 284 AC_HELP_STRING([--enable-mmap], 285 [Enable mmap (default=yes). Recommend that you do not disable this unless absolutely necessary.]), 286 [answer="$enableval"], 287 [answer=""]) 288case x"$answer" in 289 xyes) 290 AC_MSG_RESULT(enabled) 291 ACX_MMAP_FIXED # Checks fixed mapping 292 ACX_MMAP_VARIABLE # Checks variable mapping 293 ;; 294 295 xno) 296 AC_MSG_RESULT(disabled) 297 ;; 298 299 x) 300 AC_MSG_RESULT([not specified so enabled by default]) 301 ACX_MMAP_FIXED # Checks fixed mapping 302 ACX_MMAP_VARIABLE # Checks variable mapping 303 ;; 304esac 305 306 307if test x"$acx_mmap_fixed_ok" = xyes; then 308 AC_DEFINE(HAVE_MMAP,1,[Define to 1 if you have a working 'mmap' system call.]) 309else 310 if test x"$acx_mmap_variable_ok" = xyes; then 311 AC_DEFINE(HAVE_MMAP,1,[Define to 1 if you have a working 'mmap' system call.]) 312 fi 313fi 314 315ACX_MMAP_FLAGS 316ACX_MADVISE_FLAGS 317ACX_SHM_FLAGS 318 319AC_CHECK_FUNCS([ceil floor index log madvise memcpy memmove memset munmap pow rint stat64 strtoul sysconf sysctl sigaction \ 320 shmget shmctl shmat shmdt semget semctl semop]) 321 322ACX_STRUCT_STAT64 323ACX_PAGESIZE 324 325ACX_FUNC_FOPEN_BINARY 326ACX_FUNC_FOPEN_TEXT 327 328 329#AC_MSG_CHECKING(for builtin popcount/clz/ctz features) 330#AC_ARG_ENABLE([builtin-popcount], 331# AC_HELP_STRING([--enable-builtin-popcount], 332# [Enable -mpopcnt if it __builtin_popcount compiles and runs (default=yes). May want to disable if compiling on one machine and running on another.]), 333# [answer="$enableval"], 334# [answer=""]) 335#case x"$answer" in 336# xyes) 337# AC_MSG_RESULT(enabled) 338# ACX_BUILTIN_POPCOUNT 339# ;; 340# 341# xno) 342# AC_MSG_RESULT(disabled) 343# ;; 344# 345# x) 346# AC_MSG_RESULT([not specified so enabled by default]) 347# ACX_BUILTIN_POPCOUNT 348# ;; 349#esac 350#if test x"$acx_mpopcnt_ok" = x"yes"; then 351# POPCNT_CFLAGS="$POPCNT_CFLAGS -mpopcnt" 352#fi 353#AC_SUBST(POPCNT_CFLAGS) 354 355 356ACX_BUILTIN_POPCOUNT 357ACX_ASM_BSR 358 359 360ACX_SSE2_SHIFT_DEFECT 361ACX_SIMD_INTRINSICS 362 363AC_MSG_CHECKING(for whether simd is enabled) 364AC_ARG_ENABLE([simd], 365 AC_HELP_STRING([--enable-simd], 366 [Enable simd commands in general if they compile and run (default=yes).]), 367 [answer="$enableval"], 368 [answer=""]) 369case x"$answer" in 370 xyes) 371 AC_MSG_RESULT(enabled) 372 ax_cv_want_simd=yes 373 ;; 374 375 xno) 376 AC_MSG_RESULT(disabled) 377 ax_cv_want_simd=no 378 ;; 379 380 x) 381 AC_MSG_RESULT([not specified so enabled by default]) 382 ax_cv_want_simd=yes 383 ;; 384esac 385 386 387if test x"$ax_cv_c_compiler_vendor" = xintel; then 388AX_CPUID_INTEL 389else 390AX_CPUID_NON_INTEL 391fi 392 393AX_EXT # Sets SIMD_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,... 394if test "x$ax_cv_want_simd" = xno; then 395 compile_level=none 396elif test "x$ax_make_avx512bw" = xyes; then 397 compile_level=avx512bw 398elif test "x$ax_make_avx512" = xyes; then 399 compile_level=avx512 400elif test "x$ax_make_avx2" = xyes; then 401 compile_level=avx2 402elif test "x$ax_make_sse42" = xyes; then 403 compile_level=sse42 404elif test "x$ax_make_sse41" = xyes; then 405 compile_level=sse41 406elif test "x$ax_make_ssse3" = xyes; then 407 compile_level=ssse3 408elif test "x$ax_make_sse2" = xyes; then 409 compile_level=sse2 410else 411 compile_level=none 412fi 413 414 415# User-selected compile level 416AC_ARG_WITH([simd-level], 417 AC_HELP_STRING([--with-simd-level=STRING], 418 [User-selected SIMD level (none, sse2, ssse3, sse41/sse4.1, sse42/sse4.2, avx2, avx512, avx512bw)]), 419 [answer="$withval"], 420 [answer=""]) 421if test x"$answer" != x; then 422 AC_MSG_CHECKING(for user-selected SIMD level) 423 compile_level=$answer 424 AC_MSG_RESULT($compile_level) 425 case $compile_level in 426 avx512bw) 427 ;; 428 avx512) 429 ;; 430 avx2) 431 ;; 432 sse42) 433 ;; 434 sse4.2) 435 compile_level = sse42; 436 ;; 437 sse41) 438 ;; 439 sse4.1) 440 compile_level = sse41; 441 ;; 442 ssse3) 443 ;; 444 sse2) 445 ;; 446 none) 447 ;; 448 *) 449 AC_MSG_ERROR([Compiler level $compile_level not recognized. Allowed values: none, sse2, ssse3, sse4.1 (or sse41), sse4.2 (or sse42), avx2, avx512, avx512bw]) 450 ;; 451 esac 452fi 453 454 455 456AM_CONDITIONAL(MAKE_AVX512BW,[test "$compile_level" = avx512bw]) 457AM_CONDITIONAL(MAKE_AVX512,[test "$compile_level" = avx512]) 458AM_CONDITIONAL(MAKE_AVX2,[test "$compile_level" = avx2]) 459AM_CONDITIONAL(MAKE_SSE4_2,[test "$compile_level" = sse42]) 460AM_CONDITIONAL(MAKE_SSE4_1,[test "$compile_level" = sse41]) 461AM_CONDITIONAL(MAKE_SSSE3,[test "$compile_level" = ssse3]) 462AM_CONDITIONAL(MAKE_SSE2,[test "$compile_level" = sse2]) 463 464 465 466# Genome directory 467AC_MSG_CHECKING(gmapdb) 468AC_ARG_WITH([gmapdb], 469 AC_HELP_STRING([--with-gmapdb=DIR], 470 [Default GMAP database directory]), 471 [answer="$withval"], 472 [answer=""]) 473if test x"$answer" = x; then 474 ACX_EXPAND(GMAPDB,'${prefix}/share') 475else 476 GMAPDB=$answer 477fi 478AC_SUBST(GMAPDB) 479AC_MSG_RESULT($GMAPDB) 480 481 482# MAX_STACK_READLENGTH 483AC_MSG_CHECKING(MAX_STACK_READLENGTH) 484AC_ARG_VAR([MAX_STACK_READLENGTH], [Maximum read length for GSNAP allocating on stack rather than heap (default 300)]) 485if test x"$MAX_STACK_READLENGTH" = x; then 486 ACX_EXPAND(MAX_STACK_READLENGTH,'300') 487fi 488AC_MSG_RESULT($MAX_STACK_READLENGTH) 489 490 491# zlib package 492 493AC_MSG_CHECKING(for zlib support) 494AC_ARG_ENABLE([zlib], 495 AC_HELP_STRING([--enable-zlib], 496 [Enable zlib support (option needed for uncompressing gzip files) (default=yes)]), 497 [answer="$enableval"], 498 [answer=""]) 499case x"$answer" in 500 xno) 501 AC_MSG_RESULT(disabled) 502 ZLIB_LIBS="" 503 have_zlib=no 504 ;; 505 506 *) 507 AC_MSG_RESULT(enabled) 508 failed=0; 509 passed=0; 510 AC_CHECK_HEADER(zlib.h,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 511 AC_CHECK_LIB(z,gzopen,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 512 AC_CHECK_LIB(z,gzeof,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 513 AC_CHECK_LIB(z,gzgetc,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 514 AC_CHECK_LIB(z,gzgets,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 515 AC_CHECK_LIB(z,gzclose,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 516 AC_MSG_CHECKING(if zlib package is complete) 517 if test $failed -gt 0 518 then 519 AC_MSG_RESULT(no -- some components failed test) 520 ZLIB_LIBS="" 521 have_zlib=no 522 else 523 AC_MSG_RESULT(working) 524 AC_DEFINE(HAVE_ZLIB,1,[Define to 1 if you have a working zlib library.]) 525 ZLIB_LIBS="-lz" 526 have_zlib=yes 527 528 AC_CHECK_LIB(z,gzbuffer,have_gzbuffer=1,have_gzbuffer=0) 529 if test $have_gzbuffer -gt 0 530 then 531 AC_DEFINE(HAVE_ZLIB_GZBUFFER,1,[Define to 1 if your zlib library has a gzbuffer function.]) 532 fi 533 fi 534 ;; 535 536esac 537AC_SUBST(ZLIB_LIBS) 538 539 540# bzip2 package 541 542AC_MSG_CHECKING(for bzlib support) 543AC_ARG_ENABLE([bzlib], 544 AC_HELP_STRING([--enable-bzlib], 545 [Enable bzlib support (option needed for uncompressing bzip2 files) (default=yes)]), 546 [answer="$enableval"], 547 [answer=""]) 548case x"$answer" in 549 xno) 550 AC_MSG_RESULT(disabled) 551 BZLIB_LIBS="" 552 have_bzlib=no 553 ;; 554 555 *) 556 AC_MSG_RESULT(enabled) 557 failed=0; 558 passed=0; 559 AC_CHECK_HEADER(bzlib.h,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 560 AC_CHECK_LIB(bz2,BZ2_bzReadOpen,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 561 AC_CHECK_LIB(bz2,BZ2_bzRead,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 562 AC_CHECK_LIB(bz2,BZ2_bzReadClose,passed=`expr $passed + 1`,failed=`expr $failed + 1`) 563 AC_MSG_CHECKING(if bzlib package is complete) 564 if test $failed -gt 0 565 then 566 AC_MSG_RESULT(no -- some components failed test) 567 BZLIB_LIBS="" 568 have_bzlib=no 569 else 570 AC_MSG_RESULT(working) 571 AC_DEFINE(HAVE_BZLIB,1,[Define to 1 if you have a working bzlib library.]) 572 BZLIB_LIBS="-lbz2" 573 have_bzlib=yes 574 fi 575 ;; 576 577esac 578AC_SUBST(BZLIB_LIBS) 579 580 581AC_CONFIG_FILES([Makefile]) 582AC_CONFIG_FILES([src/Makefile]) 583#AC_CONFIG_FILES([lib/gmap-${LIBGMAP_API_VERSION}.pc:lib/gmap.pc.in]) 584#AC_CONFIG_FILES([mpi/Makefile]) 585AC_CONFIG_FILES([util/Makefile]) 586AC_CONFIG_FILES([util/gmap_process.pl]) 587AC_CONFIG_FILES([util/gmap_build.pl]) 588AC_CONFIG_FILES([util/gmap_cat.pl]) 589AC_CONFIG_FILES([util/md_coords.pl]) 590AC_CONFIG_FILES([util/fa_coords.pl]) 591AC_CONFIG_FILES([util/psl_splicesites.pl]) 592AC_CONFIG_FILES([util/psl_introns.pl]) 593AC_CONFIG_FILES([util/psl_genes.pl]) 594AC_CONFIG_FILES([util/ensembl_genes.pl]) 595AC_CONFIG_FILES([util/gtf_splicesites.pl]) 596AC_CONFIG_FILES([util/gtf_transcript_splicesites.pl]) 597AC_CONFIG_FILES([util/gtf_introns.pl]) 598AC_CONFIG_FILES([util/gtf_genes.pl]) 599AC_CONFIG_FILES([util/gff3_splicesites.pl]) 600AC_CONFIG_FILES([util/gff3_introns.pl]) 601AC_CONFIG_FILES([util/gff3_genes.pl]) 602AC_CONFIG_FILES([util/dbsnp_iit.pl]) 603AC_CONFIG_FILES([util/gvf_iit.pl]) 604AC_CONFIG_FILES([util/vcf_iit.pl]) 605AC_CONFIG_FILES([tests/Makefile]) 606AC_CONFIG_FILES([tests/align.test],[chmod +x tests/align.test]) 607AC_CONFIG_FILES([tests/coords1.test],[chmod +x tests/coords1.test]) 608AC_CONFIG_FILES([tests/setup1.test],[chmod +x tests/setup1.test]) 609AC_CONFIG_FILES([tests/iit.test],[chmod +x tests/iit.test]) 610 611AC_OUTPUT 612 613if test x"$perl_warning" = xyes; then 614 AC_MSG_WARN([ 615 616WARNING: You don't seem to have perl installed with working 617versions of the IO::File and Getopt::Std modules. If you know 618where such a version of Perl exists, please specify its full 619path under PERL in the config.site file and run configure again. 620]) 621fi 622 623if test x"$pthread_warning" = xyes; then 624 AC_MSG_WARN([ 625 626WARNING: You don't seem to have headers and libraries for pthreads. 627GMAP will work without these, but the program can run faster on 628multiprocessor machines if POSIX threads are available. If you wish 629to enable pthreads, please specify the appropriate values for CC, 630PTHREAD_CFLAGS, and PTHREAD_LIBS in the config.site file and run 631configure again. Otherwise, you may proceed with the rest of the 632installation. 633]) 634fi 635 636if test x"$acx_mmap_fixed_ok" != xyes; then 637 if test x$"acx_mmap_variable_ok" != xyes; then 638 AC_MSG_WARN([ 639 640WARNING: You don't seem to have memory mapping. GMAP will work 641without this, but the program can run faster if memory mapping is 642available. If you wish to enable memory mapping, please specify the 643appropriate values for CC, PTHREAD_CFLAGS, and PTHREAD_LIBS in the 644config.site file and run configure again. Otherwise, you may proceed 645with the rest of the installation. 646]) 647 fi 648fi 649 650if test x"$ax_cv_sse2_shift_defect" = xyes; then 651 AC_MSG_WARN([ 652 653WARNING: Your C compiler does not know how to handle a particular 654form of the SSE2 shift commands, and must be somewhat old (probably 655gcc 4.1 or gcc 4.2). The configure script has therefore substituted 656alternate C code that your compiler can handle. However, for 657optimal performance, you may want to obtain a more recent C compiler 658and build the code with that. 659]) 660fi 661 662if test x"$ax_cv_ext_compiler_problem" = x"yes"; then 663 AC_MSG_WARN([ 664 665WARNING: Your C compiler appears not to take advantage of all of the 666SIMD features available on your computer, and must be somewhat old. 667The configure script has therefore substituted alternate C code that 668your compiler can handle. However, for optimal performance, you may 669want to obtain a more recent C compiler and build the code with that. 670Here are the compiler flags to be used for SIMD: 671]) 672fi 673 674if test x"$ax_cv_ext_linker_problem" = x"yes"; then 675 AC_MSG_WARN([ 676 677WARNING: Your C linker appears not to work on SIMD header files that 678your C compiler accepts, so there appears to be some incompatibility 679between your compiler and linker. The configure script has therefore 680substituted alternate C code that your linker can handle. However, 681for optimal performance, you may need to set your LDFLAGS or 682LD_LIBRARY_PATH environment variable to the correct directory, or 683rebuild your compiler and linker. 684]) 685fi 686 687AC_MSG_CHECKING(standard compiler and flags to be used) 688AC_MSG_RESULT($CC $CFLAGS) 689AC_MSG_CHECKING(standard linker flags to be used) 690AC_MSG_RESULT($LD_FLAGS) 691 692#AC_MSG_CHECKING(MPI compiler and flags to be used) 693#AC_MSG_RESULT($MPICC $MPI_CFLAGS) 694#AC_MSG_CHECKING(MPI linker flags to be used) 695#AC_MSG_RESULT($MPI_CLDFLAGS) 696 697AC_MSG_CHECKING(pthread compiler flags to be used) 698AC_MSG_RESULT($PTHREAD_CFLAGS) 699 700AC_MSG_CHECKING(popcnt flags to be used) 701AC_MSG_RESULT($POPCNT_CFLAGS) 702 703AC_MSG_CHECKING(compile level) 704AC_MSG_RESULT($compile_level) 705 706 707# Re-using SIMD_AVX512_CFLAGS here 708if test "$compile_level" = avx512bw; then 709 AC_MSG_CHECKING(AVX512BW compiler flags to be used) 710 AC_MSG_RESULT($SIMD_AVX512_CFLAGS) 711fi 712 713if test "$compile_level" = avx512; then 714 AC_MSG_CHECKING(AVX512 compiler flags to be used) 715 AC_MSG_RESULT($SIMD_AVX512_CFLAGS) 716fi 717 718if test "$compile_level" = avx2; then 719 AC_MSG_CHECKING(AVX2 compiler flags to be used) 720 AC_MSG_RESULT($SIMD_AVX2_CFLAGS) 721fi 722 723if test "$compile_level" = sse42; then 724 AC_MSG_CHECKING(SSE4.2 compiler flags to be used) 725 AC_MSG_RESULT($SIMD_SSE4_2_CFLAGS) 726fi 727 728if test "$compile_level" = sse41; then 729 AC_MSG_CHECKING(SSE4.1 compiler flags to be used) 730 AC_MSG_RESULT($SIMD_SSE4_1_CFLAGS) 731fi 732 733if test "$compile_level" = ssse3; then 734 AC_MSG_CHECKING(SSSE3 compiler flags to be used) 735 AC_MSG_RESULT($SIMD_SSSE3_CFLAGS) 736fi 737 738if test "$compile_level" = sse2; then 739 AC_MSG_CHECKING(SSE2 compiler flags to be used) 740 AC_MSG_RESULT($SIMD_SSE2_CFLAGS) 741fi 742 743 744#AC_MSG_CHECKING(SIMD features available on computer) 745#AC_MSG_RESULT($ax_cv_cpu_features) 746#AC_MSG_CHECKING(SIMD compiler flags to be used) 747#AC_MSG_RESULT($SIMD_CFLAGS) 748 749