[med-svn] [Git][med-team/hisat2][master] 3 commits: Fix simde patch for ppc64el
Michael R. Crusoe
gitlab at salsa.debian.org
Wed May 6 19:48:45 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / hisat2
Commits:
649f4578 by Michael R. Crusoe at 2020-05-06T20:40:00+02:00
Fix simde patch for ppc64el
- - - - -
2ed28bb7 by Michael R. Crusoe at 2020-05-06T20:45:02+02:00
Fix missing $(LDFLAGS) in hardening patch
- - - - -
74f3a2c2 by Michael R. Crusoe at 2020-05-06T20:48:29+02:00
release 2.2.0-2 to unstable.
- - - - -
3 changed files:
- debian/changelog
- debian/patches/hardening
- debian/patches/simde
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+hisat2 (2.2.0-2) unstable; urgency=medium
+
+ * Fix simde patch for ppc64el
+ * Fix missing $(LDFLAGS) in hardening patch
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 06 May 2020 20:48:11 +0200
+
hisat2 (2.2.0-1) unstable; urgency=medium
* Use the libsimde-dev package instead of our code copy.
=====================================
debian/patches/hardening
=====================================
@@ -29,6 +29,24 @@ Description: Enable the passing of extra compilation flags, for hardening
#
# hisat2-repeat targets
+@@ -329,7 +329,7 @@
+ $(INC) \
+ -o $@ $< \
+ $(SHARED_CPPS) $(HISAT2_REPEAT_CPPS_MAIN) \
+- $(LIBS) $(BUILD_LIBS)
++ $(LIBS) $(BUILD_LIBS) $(LDFLAGS)
+
+ hisat2-repeat-debug: hisat2_repeat.cpp $(REPEAT_CPPS) $(SHARED_CPPS) $(HEADERS)
+ $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \
+@@ -337,7 +337,7 @@
+ $(INC) \
+ -o $@ $< \
+ $(SHARED_CPPS) $(HISAT2_REPEAT_CPPS_MAIN) \
+- $(LIBS) $(BUILD_LIBS)
++ $(LIBS) $(BUILD_LIBS) $(LDFLAGS)
+
+
+ #
@@ -350,7 +350,7 @@
$(INC) \
-o $@ $< \
=====================================
debian/patches/simde
=====================================
@@ -2,221 +2,44 @@ From: Michael R. Crusoe <michael.crusoe at gmail.com>
Description: use the simde header library for greater compatibility
--- hisat2.orig/aligner_sw.h
+++ hisat2/aligner_sw.h
-@@ -70,7 +70,8 @@
+@@ -66,11 +66,17 @@
+
+ #define INLINE_CUPS
+
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
++#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)
++# undef vector
++# undef pixel
++# undef bool
++#endif
+ #include <stdint.h>
#include <iostream>
#include <limits>
#include "threading.h"
-#include <emmintrin.h>
-+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include <simde/x86/sse2.h>
#include "aligner_sw_common.h"
#include "aligner_sw_nuc.h"
#include "ds.h"
---- hisat2.orig/aligner_swsse_ee_i16.cpp
-+++ hisat2/aligner_swsse_ee_i16.cpp
-@@ -228,10 +228,7 @@
- #ifdef NDEBUG
-
- #define assert_all_eq0(x)
--#define assert_all_gt(x, y)
--#define assert_all_gt_lo(x)
- #define assert_all_lt(x, y)
--#define assert_all_lt_hi(x)
-
- #else
-
-@@ -243,19 +240,6 @@
- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
- }
-
--#define assert_all_gt(x, y) { \
-- __m128i tmp = _mm_cmpgt_epi16(x, y); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
--#define assert_all_gt_lo(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_xor_si128(z, z); \
-- tmp = _mm_cmpgt_epi16(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
- #define assert_all_lt(x, y) { \
- __m128i tmp = _mm_cmplt_epi16(x, y); \
- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
-@@ -265,15 +249,6 @@
- __m128i tmp = _mm_cmpgt_epi16(x, y); \
- assert_eq(0x0000, _mm_movemask_epi8(tmp)); \
- }
--
--#define assert_all_lt_hi(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_cmpeq_epi16(z, z); \
-- z = _mm_srli_epi16(z, 1); \
-- tmp = _mm_cmplt_epi16(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
- #endif
-
- /**
---- hisat2.orig/aligner_swsse_ee_u8.cpp
-+++ hisat2/aligner_swsse_ee_u8.cpp
-@@ -231,10 +231,7 @@
- #ifdef NDEBUG
-
- #define assert_all_eq0(x)
--#define assert_all_gt(x, y)
--#define assert_all_gt_lo(x)
- #define assert_all_lt(x, y)
--#define assert_all_lt_hi(x)
-
- #else
-
-@@ -246,19 +243,6 @@
- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
- }
-
--#define assert_all_gt(x, y) { \
-- __m128i tmp = _mm_cmpgt_epu8(x, y); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
--#define assert_all_gt_lo(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_xor_si128(z, z); \
-- tmp = _mm_cmpgt_epu8(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
- #define assert_all_lt(x, y) { \
- __m128i z = _mm_setzero_si128(); \
- z = _mm_xor_si128(z, z); \
-@@ -266,15 +250,6 @@
- tmp = _mm_cmpeq_epi16(tmp, z); \
- assert_eq(0x0000, _mm_movemask_epi8(tmp)); \
- }
--
--#define assert_all_lt_hi(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_cmpeq_epu8(z, z); \
-- z = _mm_srli_epu8(z, 1); \
-- tmp = _mm_cmplt_epu8(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
- #endif
-
- /**
---- hisat2.orig/aligner_swsse_loc_i16.cpp
-+++ hisat2/aligner_swsse_loc_i16.cpp
-@@ -226,10 +226,7 @@
- #ifdef NDEBUG
-
- #define assert_all_eq0(x)
--#define assert_all_gt(x, y)
--#define assert_all_gt_lo(x)
- #define assert_all_lt(x, y)
--#define assert_all_lt_hi(x)
-
- #else
-
-@@ -241,19 +238,6 @@
- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
- }
-
--#define assert_all_gt(x, y) { \
-- __m128i tmp = _mm_cmpgt_epi16(x, y); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
--#define assert_all_gt_lo(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_xor_si128(z, z); \
-- tmp = _mm_cmpgt_epi16(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
- #define assert_all_lt(x, y) { \
- __m128i tmp = _mm_cmplt_epi16(x, y); \
- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
-@@ -263,15 +247,6 @@
- __m128i tmp = _mm_cmpgt_epi16(x, y); \
- assert_eq(0x0000, _mm_movemask_epi8(tmp)); \
- }
--
--#define assert_all_lt_hi(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_cmpeq_epi16(z, z); \
-- z = _mm_srli_epi16(z, 1); \
-- tmp = _mm_cmplt_epi16(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
- #endif
-
- /**
---- hisat2.orig/aligner_swsse_loc_u8.cpp
-+++ hisat2/aligner_swsse_loc_u8.cpp
-@@ -240,10 +240,7 @@
- #ifdef NDEBUG
-
- #define assert_all_eq0(x)
--#define assert_all_gt(x, y)
--#define assert_all_gt_lo(x)
- #define assert_all_lt(x, y)
--#define assert_all_lt_hi(x)
-
- #else
-
-@@ -255,19 +252,6 @@
- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
- }
-
--#define assert_all_gt(x, y) { \
-- __m128i tmp = _mm_cmpgt_epu8(x, y); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
--#define assert_all_gt_lo(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_xor_si128(z, z); \
-- tmp = _mm_cmpgt_epu8(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
--
- #define assert_all_lt(x, y) { \
- __m128i z = _mm_setzero_si128(); \
- z = _mm_xor_si128(z, z); \
-@@ -275,15 +259,6 @@
- tmp = _mm_cmpeq_epi16(tmp, z); \
- assert_eq(0x0000, _mm_movemask_epi8(tmp)); \
- }
--
--#define assert_all_lt_hi(x) { \
-- __m128i z = _mm_setzero_si128(); \
-- __m128i tmp = _mm_setzero_si128(); \
-- z = _mm_cmpeq_epu8(z, z); \
-- z = _mm_srli_epu8(z, 1); \
-- tmp = _mm_cmplt_epu8(x, z); \
-- assert_eq(0xffff, _mm_movemask_epi8(tmp)); \
--}
- #endif
-
- /**
--- hisat2.orig/sse_util.h
+++ hisat2/sse_util.h
-@@ -24,7 +24,8 @@
+@@ -20,11 +20,18 @@
+ #ifndef SSE_UTIL_H_
+ #define SSE_UTIL_H_
+
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse2.h>
++#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)
++# undef vector
++# undef pixel
++# undef bool
++#endif
++
+ #include "assert_helpers.h"
#include "ds.h"
#include "limit.h"
#include <iostream>
-#include <emmintrin.h>
-+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include <simde/x86/sse2.h>
class EList_m128i {
public:
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/a63d242098083b0f09fb681b7e7d875e7ad18741...74f3a2c2b456a52d91b252a10c6a6868469fc34d
--
View it on GitLab: https://salsa.debian.org/med-team/hisat2/-/compare/a63d242098083b0f09fb681b7e7d875e7ad18741...74f3a2c2b456a52d91b252a10c6a6868469fc34d
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