patch to enable non-x86 builds again (no -msse, etc..)

diamond-aligner (0.9.29+dfsg-3) UNRELEASED; urgency=medium

  * Team upload.

  * patch to enable non-x86 builds again (no -msse, etc..)

 -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 13 Jan 2020 17:11:06 +0100

diamond-aligner (0.9.29+dfsg-2) unstable; urgency=medium

  [ Frédéric Bonnard ]

From: Michael R. Crusoe <michael.crusoe@gmail.com>

Subject: handle non-x86 builds again

--- diamond-aligner.orig/CMakeLists.txt

+++ diamond-aligner/CMakeLists.txt

@@ -5,6 +5,7 @@

 option(EXTRA "EXTRA" OFF)

 option(STATIC_LIBGCC "STATIC_LIBGCC" OFF)

 option(STATIC_LIBSTDC++ "STATIC_LIBSTDC++" OFF)

+option(X86 "X86" ON)

 IF(STATIC_LIBSTDC++)

   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -static-libstdc++")

@@ -61,9 +62,12 @@

 add_library(arch_generic OBJECT ${DISPATCH_OBJECTS})

 target_compile_options(arch_generic PUBLIC -DDISPATCH_ARCH=ARCH_GENERIC)

+if(X86)

 add_library(arch_sse4_1 OBJECT ${DISPATCH_OBJECTS})

 target_compile_options(arch_sse4_1 PUBLIC -DDISPATCH_ARCH=ARCH_SSE4_1 -mssse3 -mpopcnt -msse4.1)

+endif()

+if(X86)

 add_executable(diamond $<TARGET_OBJECTS:arch_generic>

   $<TARGET_OBJECTS:arch_sse4_1>

   src/run/main.cpp

@@ -149,6 +153,91 @@

   src/lib/tantan/LambdaCalculator.cc

   src/data/taxonomy_filter.cpp

 )

+else()

+add_executable(diamond $<TARGET_OBJECTS:arch_generic>

+  src/run/main.cpp

+  src/basic/config.cpp

+  src/basic/score_matrix.cpp

+  src/blast/blast_filter.cpp

+  src/blast/blast_seg.cpp

+  src/blast/sm_blosum45.c

+  src/blast/sm_blosum50.c

+  src/blast/sm_blosum62.c

+  src/blast/sm_blosum80.c

+  src/blast/sm_blosum90.c

+  src/blast/sm_pam30.c

+  src/blast/sm_pam70.c

+  src/blast/sm_pam250.c

+  src/data/queries.cpp

+  src/data/reference.cpp

+  src/data/seed_histogram.cpp

+  src/output/daa_record.cpp

+  src/util/command_line_parser.cpp

+  src/util/seq_file_format.cpp

+  src/util/util.cpp 

+  src/util/Timer.cpp

+  src/basic/basic.cpp

+  src/basic/hssp.cpp

+  src/dp/ungapped_align.cpp

+  src/run/tools.cpp

+  src/dp/greedy_align.cpp

+  src/output/output_format.cpp

+  src/output/join_blocks.cpp

+  src/data/frequent_seeds.cpp

+  src/align/query_mapper.cpp

+  src/output/blast_tab_format.cpp

+  src/dp/padded_banded_sw.cpp

+  src/dp/needleman_wunsch.cpp

+  src/output/blast_pairwise_format.cpp

+  src/dp/comp_based_stats.cpp

+  src/run/double_indexed.cpp

+  src/output/sam_format.cpp

+  src/align/align.cpp

+  src/search/setup.cpp

+  src/dp/diag_scores.cpp

+  src/data/taxonomy.cpp

+  src/lib/tantan/tantan.cc

+  src/basic/masking.cpp

+  src/dp/banded_sw.cpp

+  src/data/seed_set.cpp

+  src/util/simd.cpp

+  src/output/taxon_format.cpp

+  src/output/view.cpp

+  src/output/output_sink.cpp

+  src/output/target_culling.cpp

+  src/align/greedy_pipeline.cpp

+  src/align/swipe_pipeline.cpp

+  src/align/banded_swipe_pipeline.cpp

+  src/data/ref_dictionary.cpp

+  src/util/io/compressed_stream.cpp

+  src/util/io/deserializer.cpp

+  src/util/io/file_sink.cpp

+  src/util/io/file_source.cpp

+  src/util/io/input_file.cpp

+  src/util/io/input_stream_buffer.cpp

+  src/util/io/output_file.cpp

+  src/util/io/output_stream_buffer.cpp

+  src/util/io/serializer.cpp

+  src/util/io/temp_file.cpp

+  src/util/io/text_input_file.cpp

+  src/data/taxon_list.cpp

+  src/data/taxonomy_nodes.cpp

+  src/util/algo/MurmurHash3.cpp

+  src/search/stage0.cpp

+  src/data/seed_array.cpp

+  src/output/paf_format.cpp

+  src/util/system/system.cpp

+  src/run/cluster.cpp

+  src/util/algo/greedy_vortex_cover.cpp

+  src/util/algo/greedy_vortex_cover_weighted.cpp

+  src/util/sequence/sequence.cpp

+  src/tools/tsv_record.cpp

+  src/tools/tools.cpp

+  src/util/system/getRSS.cpp

+  src/util/math/sparse_matrix.cpp

+  src/lib/tantan/LambdaCalculator.cc

+  src/data/taxonomy_filter.cpp

+endif()

 if(EXTRA)

   target_sources(diamond

--- diamond-aligner.orig/src/tools/benchmark.cpp

+++ diamond-aligner/src/tools/benchmark.cpp

@@ -92,6 +92,7 @@

 }

 #endif

+#ifdef __SSE__

 void benchmark_transpose() {

 	static const size_t n = 100000000llu;

 	static char in[256], out[256];

@@ -103,6 +104,7 @@

 	}

 	cout << "Matrix transpose 16x16 bytes:\t" << (double)duration_cast<std::chrono::nanoseconds>(high_resolution_clock::now() - t1).count() / (n * 256) * 1000 << " ps/Letter" << endl;

 }

+#endif

 #ifdef __SSE2__

 void swipe_cell_update() {

@@ -169,7 +171,9 @@

 #ifdef __SSSE3__

 	benchmark_ungapped_sse(s1, s2);

 #endif

+#ifdef __SSE__

 	benchmark_transpose();

+#endif

 #ifdef __SSE2__

 	banded_swipe(s1, s2);

 	swipe_cell_update();

@@ -179,4 +183,4 @@

 #endif

 }

-}}

\ No newline at end of file

+}}

--- diamond-aligner.orig/src/util/simd.h

+++ diamond-aligner/src/util/simd.h

@@ -53,6 +53,7 @@

 enum Flags { SSSE3 = 1, POPCNT = 2, SSE4_1 = 4 };

 Arch arch();

+#ifdef __SSE__

 #define DECL_DISPATCH(ret, name, param) namespace ARCH_GENERIC { ret name param; }\

 namespace ARCH_SSE4_1 { ret name param; }\

 inline std::function<decltype(ARCH_GENERIC::name)> dispatch_target_##name() {\

@@ -61,9 +62,17 @@

 default: return ARCH_GENERIC::name;\

 }}\

 const std::function<decltype(ARCH_GENERIC::name)> name = dispatch_target_##name();

+#else

+#define DECL_DISPATCH(ret, name, param) namespace ARCH_GENERIC { ret name param; }\

+namespace ARCH_SSE4_1 { ret name param; }\

+inline std::function<decltype(ARCH_GENERIC::name)> dispatch_target_##name() {\

+return ARCH_GENERIC::name;\

+}\

+const std::function<decltype(ARCH_GENERIC::name)> name = dispatch_target_##name();

+#endif

 std::string features();

 };

-#endif

\ No newline at end of file

+#endif

--- diamond-aligner.orig/src/util/simd/transpose.h

+++ diamond-aligner/src/util/simd/transpose.h

@@ -21,6 +21,8 @@

 #include "../simd.h"

+#ifdef __SSE__

+

 inline void merge(__m128i &first, __m128i &second, __m128i &temp)

 {

 	temp = first;

@@ -118,4 +120,5 @@

 	merge_fast_write(xmm0, xmm1, 0, 1, xmm9, (__m128i*)out);

 }

+#endif /* __SSE__ */

 #endif /* TRANSPOSE_H_ */

avoid_unwanted_optimisation.patch

82feea2aee5c82e283704b9317cb5e8abc625f90.patch

multi_arch

include /usr/share/dpkg/default.mk

MSSSSE3=$(shell if [ `dpkg-architecture -qDEB_BUILD_ARCH` = 'amd64' ] ; then echo "-mssse3" ; fi)

ifeq (,$(filter(DEB_HOST_ARCH),i386 amd64))

	EXTRA=-DX86=OFF

endif

%:

	dh $@

override_dh_auto_configure:

	dh_auto_configure -- $(EXTRA)

override_dh_compress:

	dh_compress --exclude=.pdf

build_simple:

	MSSSSE3=$(MSSSSE3) build_simple.sh