Michael R. Crusoe pushed to branch master at Debian Med / kalign
Commits: 239226d6 by Michael R. Crusoe at 2020-03-30T13:42:50+02:00 add simde flags - - - - - 63c805a3 by Michael R. Crusoe at 2020-03-30T14:19:39+02:00 Don't break the Debian architecture baseline - - - - - 33ae524a by Michael R. Crusoe at 2020-03-30T14:52:52+02:00 fix the _mm_malloc fallback - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/no-native-build - debian/patches/series - debian/patches/simde - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,7 +1,7 @@ kalign (1:3.2.3-2) UNRELEASED; urgency=medium * Team upload. - * Add non-x86 compatability using the SIMD Everywhere library + * Add non-AVX2 compatability using the SIMD Everywhere library -- Michael R. Crusoe <[email protected]> Mon, 30 Mar 2020 12:13:37 +0200 ===================================== debian/control ===================================== @@ -13,6 +13,7 @@ Rules-Requires-Root: no Package: kalign Architecture: any +#Architecture: any-amd64 any-i386 Depends: ${shlibs:Depends}, ${misc:Depends} Enhances: t-coffee, ===================================== debian/patches/no-native-build ===================================== @@ -0,0 +1,20 @@ +Author: Michael R. Crusoe <[email protected]> +Description: Don't build with all the SIMD compiler flags + +This breaks the Debian baseline +--- kalign.orig/configure.ac ++++ kalign/configure.ac +@@ -16,13 +16,10 @@ + + AC_CONFIG_MACRO_DIR([m4]) + +-m4_include([m4/ax_ext.m4]) + m4_include([m4/ax_valgrind_check.m4]) + m4_include([m4/ax_check_compile_flag.m4]) + m4_include([m4/ax_set_compile_flags.m4]) + +-AX_EXT +- + AX_ENABLE_DEBUG + + AC_ARG_ENABLE(openmp, [AC_HELP_STRING([--enable-openmp],[use OpenMP directives for parallelism])], enable_openmp=$enableval, enable_openmp=no) ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ simde +no-native-build ===================================== debian/patches/simde ===================================== @@ -13,23 +13,29 @@ Description: leverage the SIMD Everywhere library #include "pick_anchor.h" --- kalign.orig/src/bisectingKmeans.c +++ kalign/src/bisectingKmeans.c -@@ -20,7 +20,7 @@ +@@ -20,7 +20,12 @@ */ -#include <xmmintrin.h> +#include "../debian/include/simde/x86/sse.h" ++#if !defined(SIMDE_SSE_NATIVE) ++ #include <stdlib.h> ++ #define _mm_malloc(size, align) aligned_alloc(align, size) ++ #define _mm_free free ++#endif #include "msa.h" --- kalign.orig/src/bpm.c +++ kalign/src/bpm.c -@@ -28,15 +28,15 @@ +@@ -27,16 +27,16 @@ + ++#include "../debian/include/simde/x86/avx2.h" #ifdef HAVE_AVX2 -#include <immintrin.h> -+#include "../debian/include/simde/x86/avx2.h" -__m256i BROADCAST_MASK[16]; +simde__m256i BROADCAST_MASK[16]; @@ -310,7 +316,7 @@ Description: leverage the SIMD Everywhere library #endif --- kalign.orig/src/euclidean_dist.c +++ kalign/src/euclidean_dist.c -@@ -22,15 +22,15 @@ +@@ -22,15 +22,20 @@ #include "euclidean_dist.h" #include "rng.h" @@ -318,6 +324,11 @@ Description: leverage the SIMD Everywhere library -#include <immintrin.h> +#include "../debian/include/simde/x86/sse.h" +#include "../debian/include/simde/x86/avx.h" ++#if !defined(SIMDE_SSE_NATIVE) ++ #include <stdlib.h> ++ #define _mm_malloc(size, align) aligned_alloc(align, size) ++ #define _mm_free free ++#endif #include "float.h" #include "esl_stopwatch.h" @@ -330,7 +341,7 @@ Description: leverage the SIMD Everywhere library #ifdef ITEST_EDIST -@@ -163,18 +163,18 @@ +@@ -163,18 +168,18 @@ float d = 0.0f; register int i; @@ -357,7 +368,7 @@ Description: leverage the SIMD Everywhere library a+=8; b+=8; } -@@ -187,22 +187,22 @@ +@@ -187,22 +192,22 @@ @@ -403,12 +414,17 @@ Description: leverage the SIMD Everywhere library #include <stdalign.h> --- kalign.orig/src/sequence_distance.c +++ kalign/src/sequence_distance.c -@@ -21,7 +21,7 @@ +@@ -21,7 +21,12 @@ */ -#include <xmmintrin.h> +#include "../debian/include/simde/x86/sse.h" ++#if !defined(SIMDE_SSE_NATIVE) ++ #include <stdlib.h> ++ #define _mm_malloc(size, align) aligned_alloc(align, size) ++ #define _mm_free free ++#endif #include "sequence_distance.h" #include "alphabet.h" ===================================== debian/rules ===================================== @@ -2,6 +2,8 @@ # -*- makefile -*- # Build rules for the Debian package kalign +export DEB_CFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 +export DEB_CXXFLAGS_MAINT_APPEND += -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 export DEB_BUILD_MAINT_OPTIONS = hardening=+all %: View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26 -- View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26 You're receiving this email because of your account on salsa.debian.org.
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