Nilesh Patra pushed to branch master at Debian Med / rna-star
Commits: 0748e186 by Nilesh Patra at 2021-02-26T18:00:27+05:30 Attempt adding simde support to build across more arches - - - - - 529c6bd5 by Nilesh Patra at 2021-02-26T18:00:54+05:30 Add Build-Dep on libsimde-dev, propagaret relevant flags - - - - - ad8e47ae by Nilesh Patra at 2021-02-26T18:02:26+05:30 Add a Built-Using field for simde - - - - - 4cc0e70f by Nilesh Patra at 2021-02-26T18:03:02+05:30 Update email - - - - - 4 changed files: - debian/control - debian/patches/series - + debian/patches/simde.patch - debian/rules Changes: ===================================== debian/control ===================================== @@ -3,14 +3,15 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]>, Sascha Steinbiss <[email protected]>, - Nilesh Patra <[email protected]> + Nilesh Patra <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 13), libhts-dev, vim-common, xxd, - zlib1g-dev + zlib1g-dev, + libsimde-dev Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/rna-star Vcs-Git: https://salsa.debian.org/med-team/rna-star.git @@ -21,6 +22,7 @@ Package: rna-star Architecture: amd64 arm64 ppc64el mips64el Depends: ${misc:Depends}, ${shlibs:Depends} +Built-Using: ${simde:Built-Using} Description: ultrafast universal RNA-seq aligner Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential ===================================== debian/patches/series ===================================== @@ -2,3 +2,4 @@ donotuse_own_htslib.patch mips_shm_noreserve.patch reproducible.patch mathRoutinesNotInScope.patch +simde.patch ===================================== debian/patches/simde.patch ===================================== @@ -0,0 +1,26 @@ +Description: Use simde instead of intel intrinsics +Author: Nilesh Patra <[email protected]> +Last-Update: 2021-02-26 +--- a/source/opal/opal.cpp ++++ b/source/opal/opal.cpp +@@ -6,7 +6,8 @@ + #include <vector> + + extern "C" { +-#include <immintrin.h> // AVX2 and lower ++#define SIMDE_ENABLE_NATIVE_ALIASES ++#include <simde/x86/avx2.h> // AVX2 and lower + } + + #include "opal.h" +--- a/source/Makefile ++++ b/source/Makefile +@@ -84,7 +84,7 @@ + + opal/opal.o : opal/opal.cpp opal/opal.h + cd opal && \ +- $(CXX) -c -O3 -std=c++11 -march=native opal.cpp ++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) -std=c++11 opal.cpp + + .PHONY: clean + clean: ===================================== debian/rules ===================================== @@ -10,6 +10,8 @@ export CCFLAGS=-flto $(CXXFLAGS) $(CPPFLAGS) -std=c++0x # export LDFLAGS+=-flto -pthread -lhts -lz export DEB_BUILD_MAINT_OPTIONS = hardening=+all +export DEB_CFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 +export DEB_CXXFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 %: dh $@ @@ -29,3 +31,6 @@ override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) debian/tests/run_test.sh $(CURDIR)/source/STAR endif + +override_dh_gencontrol: + dh_gencontrol -- -Vsimde:Built-Using="$(shell dpkg-query -f '$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")" View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/b81811f3ec802e7056a90c0376fcb6c54f12a1d7...4cc0e70f4a97bbc77e2d38992d949258cd530f8a -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/compare/b81811f3ec802e7056a90c0376fcb6c54f12a1d7...4cc0e70f4a97bbc77e2d38992d949258cd530f8a You're receiving this email because of your account on salsa.debian.org.
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