[med-svn] [Git][med-team/rna-star][master] 4 commits: Attempt adding simde support to build across more arches

[Nilesh Patra]

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 <debian-med-packaging at lists.alioth.debian.
 Uploaders: Steffen Moeller <moeller at debian.org>,
            Andreas Tille <tille at debian.org>,
            Sascha Steinbiss <satta at debian.org>,
-           Nilesh Patra <npatra974 at gmail.com>
+           Nilesh Patra <nilesh at debian.org>
 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 <nilesh at debian.org>
+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
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