Michael R. Crusoe pushed to branch master at Debian Med / minimap2
Commits: 0bc2dbcf by Michael R. Crusoe at 2021-11-07T19:24:38+01:00 Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch - - - - - 4 changed files: - debian/changelog - debian/patches/python-sse4-arch.patch - debian/patches/simde - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +minimap2 (2.22+dfsg-3) unstable; urgency=medium + + * Team upload + * Add SIMDe bits to python-sse4-arch.patch ; adjust SIMDe patch. + Closes: #998015 + + -- Michael R. Crusoe <[email protected]> Sun, 07 Nov 2021 19:23:30 +0100 + minimap2 (2.22+dfsg-2) unstable; urgency=medium * Team upload ===================================== debian/patches/python-sse4-arch.patch ===================================== @@ -5,12 +5,28 @@ Description: Only pass -msse4.1 to the compiler on amd64 --- minimap2.orig/setup.py +++ minimap2/setup.py -@@ -16,8 +16,6 @@ - if platform.machine() in ["aarch64", "arm64"]: - include_dirs.append("sse2neon/") - extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__']) +@@ -5,6 +5,7 @@ + from distutils.extension import Extension + + import sys, platform ++import subprocess + + sys.path.append('python') + +@@ -13,11 +14,11 @@ + extra_objects = ['libminimap2.a'] + include_dirs = ["."] + +-if platform.machine() in ["aarch64", "arm64"]: +- include_dirs.append("sse2neon/") +- extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__']) -else: - extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4 ++arch = subprocess.run(["dpkg-architecture", "-qDEB_HOST_ARCH"], capture_output=True, text=True).stdout.strip() ++if arch in ["aarch64", "arm64"]: ++ extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-D__SSE2__', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP']) ++elif arch != "amd64": ++ extra_compile_args.extend(['-DKSW_SSE2_ONLY', '-DUSE_SIMDE', '-DSIMDE_ENABLE_NATIVE_ALIASES', '-fopenmp-simd', '-O3', '-DSIMDE_ENABLE_OPENMP']) def readme(): with open('python/README.rst') as f: ===================================== debian/patches/simde ===================================== @@ -1,13 +1,12 @@ --- minimap2.orig/Makefile.simde +++ minimap2/Makefile.simde -@@ -1,8 +1,9 @@ +@@ -1,8 +1,8 @@ -CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra -CPPFLAGS= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -INCLUDES= -Ilib/simde -OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o map.o format.o pe.o seed.o esterr.o splitidx.o \ - ksw2_extz2_simde.o ksw2_extd2_simde.o ksw2_exts2_simde.o ksw2_ll_simde.o -+CFLAGS+= -g -Wall -O2 -Wc++-compat #-Wextra -+CPPFLAGS+= -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES ++CFLAGS+= -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES +INCLUDES= +OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \ + lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o \ @@ -15,7 +14,7 @@ PROG= minimap2 PROG_EXTRA= sdust minimap2-lite LIBS= -lm -lz -lpthread -@@ -37,28 +38,27 @@ +@@ -37,28 +37,27 @@ extra:all $(PROG_EXTRA) minimap2:main.o libminimap2.a @@ -56,14 +55,13 @@ # other non-file targets -@@ -80,10 +80,6 @@ +@@ -80,9 +79,6 @@ index.o: kthread.h bseq.h minimap.h mmpriv.h kseq.h kvec.h kalloc.h khash.h index.o: ksort.h kalloc.o: kalloc.h -ksw2_extd2_sse.o: ksw2.h kalloc.h -ksw2_exts2_sse.o: ksw2.h kalloc.h -ksw2_extz2_sse.o: ksw2.h kalloc.h --ksw2_ll_sse.o: ksw2.h kalloc.h + ksw2_ll_sse.o: ksw2.h kalloc.h kthread.o: kthread.h main.o: bseq.h minimap.h mmpriv.h kseq.h ketopt.h - map.o: kthread.h kvec.h kalloc.h sdust.h mmpriv.h minimap.h bseq.h kseq.h ===================================== debian/rules ===================================== @@ -15,7 +15,7 @@ override_dh_auto_clean: rm -f tex/minimap2.aux tex/minimap2.bbl tex/minimap2.blg tex/minimap2.log tex/minimap2.out tex/minimap2.pdf rm -f libminimap2.a -ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64)) +ifeq (,$(filter $(DEB_HOST_ARCH_CPU),amd64 i386)) build_vars = -f Makefile.simde export DEB_CFLAGS_MAINT_APPEND += -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP endif View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44 -- View it on GitLab: https://salsa.debian.org/med-team/minimap2/-/commit/0bc2dbcf576c2554da3acbf1fa4ccfc1a60ddb44 You're receiving this email because of your account on salsa.debian.org.
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