[med-svn] [Git][med-team/last-align][simde] any-{amd64, i386}: multi-SIMD compile with dispatcher
Michael R. Crusoe
gitlab at salsa.debian.org
Thu Dec 19 16:18:37 GMT 2019
Michael R. Crusoe pushed to branch simde at Debian Med / last-align
Commits:
641ad37a by Michael R. Crusoe at 2019-12-18T17:58:02Z
any-{amd64,i386}: multi-SIMD compile with dispatcher
- - - - -
4 changed files:
- + debian/bin/simd-dispatch
- debian/changelog
- debian/patches/simde
- debian/rules
Changes:
=====================================
debian/bin/simd-dispatch
=====================================
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+PKG=last-align
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+BASE=${DIR}/../lib/$PKG/$(basename "$0")
+
+function test_and_run () {
+ if grep -q "$1" /proc/cpuinfo && [ -x "${BASE}-$1" ]; then
+ # echo "${BASE}-$1" "$@"
+ "${BASE}-$1" "$@"
+ exit
+ fi
+}
+
+for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse mmx ; do test_and_run ${SIMD} "$@" ; done
+
+# fallback to plain option
+$BASE-plain "$@"
=====================================
debian/changelog
=====================================
@@ -2,13 +2,9 @@ last-align (1021-3) UNRELEASED; urgency=medium
* Team upload.
* Enable building on any architecture via simde. (Closes: #946850)
- * TODO
- any-amd64: build multiple times with decreasing levels of
- -m{avx2,avx,sse4.1,ssse3,sse3,sse2}
- any-i386: build multiple times with decreasing levels of
- -m{sse3,sse2,sse,mmx}
- all of the above: add wrapper script to detect at runtime the highest
- level of SIMD available, and launch the relevant binary
+ * For any-amd64 and any-i386: compile multiple times with reducing levels of
+ SIMD instruction support and ship a dispatching script to pick the best
+ one for the user at run-time.
-- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 16 Dec 2019 19:02:20 +0100
=====================================
debian/patches/simde
=====================================
@@ -186,3 +186,90 @@
s2[-0][s1[0]]);
SimdInt x = simdLoad(x2+i);
SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);
+--- last-align.orig/makefile
++++ last-align/makefile
+@@ -2,15 +2,24 @@
+ all:
+ @cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
+
+-progs = src/lastdb src/lastal src/last-split src/last-merge-batches \
+-src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
++SFX :=
++progs = src/lastdb$(SFX) src/lastal$(SFX) src/last-split$(SFX) \
++ src/last-merge-batches$(SFX) src/last-pair-probs$(SFX) src/lastdb8$(SFX) \
++ src/lastal8$(SFX) src/last-split8$(SFX)
+
+ prefix = /usr/local
+ exec_prefix = $(prefix)
+ bindir = $(exec_prefix)/bin
++libexecdir = $(exec_prefix)/libexec
++
+ install: all
+ mkdir -p $(bindir)
+- cp $(progs) scripts/* $(bindir)
++ cp scripts/* $(bindir)
++ifeq (,$(SFX))
++ cp $(progs) $(bindir)
++else
++ cp $(progs) $(libexecdir)
++endif
+
+ clean:
+ @cd src && $(MAKE) clean
+--- last-align.orig/src/makefile
++++ last-align/src/makefile
+@@ -56,8 +56,10 @@
+
+ MBOBJ = last-merge-batches.o
+
+-ALL = lastdb lastal last-split last-merge-batches last-pair-probs \
+-lastdb8 lastal8 last-split8
++SFX :=
++
++ALL = lastdb$(SFX) lastal$(SFX) last-split$(SFX) last-merge-batches$(SFX) \
++ last-pair-probs$(SFX) lastdb8$(SFX) lastal8$(SFX) last-split8$(SFX)
+
+ indexObj8 = $(indexObj4:.o=.o8)
+ alignObj8 = $(alignObj4:.o=.o8)
+@@ -66,33 +68,33 @@
+ all: $(ALL)
+
+ indexAllObj4 = $(indexObj0) $(indexObj4)
+-lastdb: $(indexAllObj4)
++lastdb$(SFX): $(indexAllObj4)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj4) -lz
+
+ indexAllObj8 = $(indexObj0) $(indexObj8)
+-lastdb8: $(indexAllObj8)
++lastdb8$(SFX): $(indexAllObj8)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj8) -lz
+
+ alignAllObj4 = $(alignObj0) $(alignObj4)
+-lastal: $(alignAllObj4)
++lastal$(SFX): $(alignAllObj4)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj4) -lz
+
+ alignAllObj8 = $(alignObj0) $(alignObj8)
+-lastal8: $(alignAllObj8)
++lastal8$(SFX): $(alignAllObj8)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj8) -lz
+
+ splitAllObj4 = $(splitObj0) $(splitObj4)
+-last-split: $(splitAllObj4)
++last-split$(SFX): $(splitAllObj4)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj4)
+
+ splitAllObj8 = $(splitObj0) $(splitObj8)
+-last-split8: $(splitAllObj8)
++last-split8$(SFX): $(splitAllObj8)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj8)
+
+-last-pair-probs: $(PPOBJ)
++last-pair-probs$(SFX): $(PPOBJ)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(PPOBJ) -lz
+
+-last-merge-batches: $(MBOBJ)
++last-merge-batches$(SFX): $(MBOBJ)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)
+
+ .SUFFIXES:
=====================================
debian/rules
=====================================
@@ -8,7 +8,9 @@
include /usr/share/dpkg/default.mk
-mandir=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/man1/
+prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
+mandir=$(prefix)/share/man/man1
+libexecdir=$(prefix)/lib/$(DEB_SOURCE)
# Copy upstream CXXFLAGS here because makefile enables only overriding them
CXXFLAGS += -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3
@@ -18,18 +20,72 @@ CPPFLAGS += -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP
LDFLAGS += -pthread
+NUMJOBS = 1
+ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
+ NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
+ MAKEFLAGS += -j$(NUMJOBS)
+endif
+
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
override_dh_auto_build:
- make all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
+ifeq (amd64,$(DEB_HOST_ARCH))
+ mkdir -p $(prefix)
+ mkdir -p $(libexecdir)
+ for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
+ $(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \
+ rm src/*.o? ; \
+ done
+else ifeq (i386,$(DEB_HOST_ARCH))
+ mkdir -p $(prefix)
+ mkdir -p $(libexecdir)
+ for SIMD in ssse3 sse3 sse2 sse mmx; do \
+ $(MAKE) -j$(NUMJOBS) all SFX=-$${SIMD} CXXFLAGS="$(CXXFLAGS) -m$$SIMD" CFLAGS="$(CFLAGS) -m$$SIMD" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" ; \
+ rm src/*.o? ; \
+ done
+ $(MAKE) -j$(NUMJOBS) all SFX=-plain CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
+else
+ $(MAKE) -j$(NUMJOBS) all CXXFLAGS="$(CXXFLAGS)" CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)"
+endif
HELP2MAN = help2man --no-info --version-string="$(DEB_VERSION_UPSTREAM)"
override_dh_auto_install:
- make install prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr
+ifeq (amd64,$(DEB_HOST_ARCH))
+ dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
+ for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
+ $(MAKE) -j$(NUMJOBS) install SFX=-$${SIMD} prefix=$(prefix) libexecdir=$(libexecdir) ; \
+ done
+ mkdir -p $(prefix)/bin
+ cd $(prefix)/bin \
+ && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 ; do \
+ ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done
+else ifeq (i386,$(DEB_HOST_ARCH))
+ dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
+ for SIMD in ssse3 sse3 sse2 sse mmx plain; do \
+ $(MAKE) -j$(NUMJOBS) install SFX=-$${SIMD} prefix=$(prefix) libexecdir=$(libexecdir) ; \
+ done
+ mkdir -p $(prefix)/bin
+ cd $(prefix)/bin \
+ && for prog in lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 ; do \
+ ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done
+else
+ $(MAKE) -j$(NUMJOBS) install prefix=$(prefix)
+endif
+
+override_dh_auto_clean:
+ifeq (amd64,$(DEB_HOST_ARCH))
+ for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
+ dh_auto_clean -- SFX=-$${SIMD} ; done
+else ifeq (i386,$(DEB_HOST_ARCH))
+ for SIMD in ssse3 sse3 sse2 sse mmx plain; do \
+ dh_auto_clean -- SFX=-$${SIMD} ; done
+else
+ dh_auto_clean
+endif
override_dh_installman:
dh_installman
@@ -39,16 +95,16 @@ override_dh_installman:
$(HELP2MAN) \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
- $(CURDIR)/src/lastal > $(mandir)/lastal.1
+ $(prefix)/bin/lastal > $(mandir)/lastal.1
$(HELP2MAN) \
--name="genome-scale comparison of biological sequences" \
--help-option="-h" \
- $(CURDIR)/src/lastal8 > $(mandir)/lastal8.1
+ $(prefix)/bin/lastal8 > $(mandir)/lastal8.1
# help2man output needs manual postprocessing - see debian/mans
#$(HELP2MAN) \
# --name="genome-scale comparison of biological sequences" \
# --help-option="-h" \
- # $(CURDIR)/src/lastdb > $(mandir)/lastdb.1
+ # $(prefix)/bin/lastdb > $(mandir)/lastdb.1
$(HELP2MAN) \
--name="Sort MAF-format alignments by sequence name" \
$(CURDIR)/scripts/maf-sort > $(mandir)/maf-sort.1
@@ -72,10 +128,10 @@ override_dh_installman:
# $(CURDIR)/scripts/last-remove-dominated > $(mandir)/last-remove-dominated.1
$(HELP2MAN) \
--name='Estimates "split" or "spliced" alignments.' \
- $(CURDIR)/src/last-split > $(mandir)/last-split.1
+ $(prefix)/bin/last-split > $(mandir)/last-split.1
$(HELP2MAN) \
--name='Estimates "split" or "spliced" alignments.' \
- $(CURDIR)/src/last-split8 > $(mandir)/last-split8.1
+ $(prefix)/bin/last-split8 > $(mandir)/last-split8.1
$(HELP2MAN) \
--name="Join two or more sets of MAF-format multiple alignments" \
$(CURDIR)/scripts/maf-join > $(mandir)/maf-join.1
@@ -87,11 +143,11 @@ override_dh_installman:
$(CURDIR)/scripts/fastq-interleave > $(mandir)/fastq-interleave.1
$(HELP2MAN) \
--name="Read files of lastal output, merge corresponding batches, and write them" \
- $(CURDIR)/src/last-merge-batches > $(mandir)/last-merge-batches.1
+ $(prefix)/bin/last-merge-batches > $(mandir)/last-merge-batches.1
# help2man output needs manual postprocessing - see debian/mans
#$(HELP2MAN) \
# --name="Read alignments of paired DNA reads to a genome, and do estimations" \
- # $(CURDIR)/src/last-pair-probs > $(mandir)/last-pair-probs.1
+ # $(prefix)/bin/last-pair-probs > $(mandir)/last-pair-probs.1
$(HELP2MAN) \
--name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \
$(CURDIR)/scripts/last-postmask > $(mandir)/last-postmask.1
View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/641ad37a52bbf34df643d00101f0dc4b806f8cd7
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/641ad37a52bbf34df643d00101f0dc4b806f8cd7
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