Merge branch 'master' of https://github.com/BenLangmead/bowtie2

Dockerfile-aarch64

@@ -18,12 +18,4 @@ RUN add-apt-repository -y universe && \
   apt-get install -yq \
   libtbb-dev
 
-# Patch to run with SIMD Everywhere (simde) for aarch64 case.
-# https://github.com/nemequ/simde
-# https://gitlab.com/arm-hpc/packages/wikis/packages/bowtie2
-RUN sed -i 's/__m/simde__m/g' aligner_*
-RUN sed -i 's/__m/simde__m/g' sse_util*
-RUN sed -i 's/_mm_/simde_mm_/g' aligner_*
-RUN sed -i 's/_mm_/simde_mm_/g' sse_util*
-
 CMD bash

Makefile

@@ -32,7 +32,7 @@ CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
 CXX ?= $(CPP)
 CXXFLAGS += -std=c++98
 ifeq (aarch64,$(shell uname -m))
-	CXXFLAGS += -fopenmp-simd -DWITH_AARCH64
+	CXXFLAGS += -fopenmp-simd
 	CPPFLAGS += -Ithird_party/simde
 endif
 
@@ -326,8 +326,8 @@ both-sanitized: bowtie2-align-s-sanitized bowtie2-build-s-sanitized bowtie2-alig
 
 DEFS := -fno-strict-aliasing \
         -DBOWTIE2_VERSION="\"`cat VERSION`\"" \
-        -DBUILD_HOST="\"`hostname`\"" \
-        -DBUILD_TIME="\"`date`\"" \
+        -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" \
+        -DBUILD_TIME="\"`date -u -r NEWS`\"" \
         -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
         $(FILE_FLAGS) \
         $(PREF_DEF) \

aligner_sw.h

@@ -70,11 +70,7 @@
 #include <iostream>
 #include <limits>
 #include "threading.h"
-#ifdef WITH_AARCH64
-#include "simde/x86/sse2.h"
-#else
-#include <emmintrin.h>
-#endif
+#include "sse_wrap.h"
 #include "aligner_sw_common.h"
 #include "aligner_sw_nuc.h"
 #include "ds.h"

sse_util.h

@@ -24,11 +24,7 @@
 #include "ds.h"
 #include "limit.h"
 #include <iostream>
-#ifdef WITH_AARCH64
-#include "simde/x86/sse2.h"
-#else
-#include <emmintrin.h>
-#endif
+#include "sse_wrap.h"
 
 class EList_m128i {
 public:

sse_wrap.h

@@ -0,0 +1,67 @@
+/*
+ * Copyright 2011, Ben Langmead <[email protected]>
+ *
+ * This file is part of Bowtie 2.
+ *
+ * Bowtie 2 is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Bowtie 2 is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/*
+ * sse_wrap.h
+ *
+ * Routines to wrap Streaming SIMD Extensions (SSE) emmintrin.h
+ * for an Intel x86 CPU and SIMD Everywhere (simde) for other CPUs.
+ */
+
+#ifndef SSE_WRAP_H_
+#define SSE_WRAP_H_
+
+#ifdef __aarch64__
+#include "simde/x86/sse2.h"
+#else
+#include <emmintrin.h>
+#endif
+
+#ifdef __aarch64__
+typedef simde__m128i __m128i;
+#define _mm_adds_epi16(x, y) simde_mm_adds_epi16(x, y)
+#define _mm_adds_epu8(x, y) simde_mm_adds_epu8(x, y)
+#define _mm_cmpeq_epi16(x, y) simde_mm_cmpeq_epi16(x, y)
+#define _mm_cmpeq_epi8(x, y) simde_mm_cmpeq_epi8(x, y)
+#define _mm_cmpgt_epi16(x, y) simde_mm_cmpgt_epi16(x, y)
+#define _mm_cmpgt_epi8(x, y) simde_mm_cmpgt_epi8(x, y)
+#define _mm_cmplt_epi16(x, y) simde_mm_cmplt_epi16(x, y)
+#define _mm_cmplt_epu8(x, y) simde_mm_cmplt_epu8(x, y)
+#define _mm_extract_epi16(x, y) simde_mm_extract_epi16(x, y)
+#define _mm_insert_epi16(x, y, z) simde_mm_insert_epi16(x, y, z)
+#define _mm_load_si128(x) simde_mm_load_si128(x)
+#define _mm_max_epi16(x, y) simde_mm_max_epi16(x, y)
+#define _mm_max_epu8(x, y) simde_mm_max_epu8(x, y)
+#define _mm_movemask_epi8(x) simde_mm_movemask_epi8(x)
+#define _mm_or_si128(x, y) simde_mm_or_si128(x, y)
+#define _mm_setzero_si128() simde_mm_setzero_si128()
+#define _mm_shuffle_epi32(x, y) simde_mm_shuffle_epi32(x, y)
+#define _mm_shufflelo_epi16(x, y) simde_mm_shufflelo_epi16(x, y)
+#define _mm_slli_epi16(x, y) simde_mm_slli_epi16(x, y)
+#define _mm_slli_si128(x, y) simde_mm_slli_si128(x, y)
+#define _mm_srli_epi16(x, y) simde_mm_srli_epi16(x, y)
+#define _mm_srli_epu8(x, y) simde_mm_srli_epu8(x, y)
+#define _mm_srli_si128(x, y) simde_mm_srli_si128(x, y)
+#define _mm_store_si128(x, y) simde_mm_store_si128(x, y)
+#define _mm_subs_epi16(x, y) simde_mm_subs_epi16(x, y)
+#define _mm_subs_epu8(x, y) simde_mm_subs_epu8(x, y)
+#define _mm_xor_si128(x, y) simde_mm_xor_si128(x, y)
+#endif
+
+#endif /* SSE_WRAP_H_ */