[med-svn] [Git][med-team/plast][master] 7 commits: Attempt enabling simde

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / plast


Commits:
7d7bfae4 by Nilesh Patra at 2020-12-06T00:55:49+05:30
Attempt enabling simde

- - - - -
538640d5 by Nilesh Patra at 2020-12-06T00:55:54+05:30
Add Build-Dep and Built-Using since the license is AGPL

- - - - -
a2e06f5d by Nilesh Patra at 2020-12-06T00:55:54+05:30
Enable simde flags

- - - - -
faed4f0c by Nilesh Patra at 2020-12-06T01:07:14+05:30
Do not hardcode the arch for running test

- - - - -
51e387cf by Nilesh Patra at 2020-12-06T01:33:23+05:30
Update changelog

- - - - -
af4d25f8 by Nilesh Patra at 2020-12-06T03:21:43+05:30
Merge branch 'simde'

- - - - -
90f479b0 by Nilesh Patra at 2020-12-06T03:22:59+05:30
Update changelog

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/patches/adapt_auto_test_script.sh
- debian/patches/series
- + debian/patches/simde.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+plast (2.3.2+dfsg-5) unstable; urgency=medium
+
+  * Team Upload.
+  * Attempt enabling simde
+  * Add Build-Dep and Built-Using since the license is AGPL
+  * Enable simde flags
+  * Do not hardcode the arch for running test
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Sun, 06 Dec 2020 01:33:09 +0530
+
 plast (2.3.2+dfsg-4) unstable; urgency=medium
 
   * Do nothing in dh_auto_configure and dh_auto_build for indep binaries


=====================================
debian/control
=====================================
@@ -7,6 +7,7 @@ Build-Depends: debhelper-compat (= 13),
                cmake,
                libpcre3-dev,
                default-jdk
+               libsimde-dev
 Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/plast
 Vcs-Git: https://salsa.debian.org/med-team/plast.git
@@ -14,7 +15,9 @@ Homepage: https://plast.inria.fr/
 Rules-Requires-Root: no
 
 Package: plast
-Architecture: any-amd64 x32
+Architecture: any
+# Since the license of this package is AGPL, adding a Built-Using
+Built-Using: ${simde:Built-Using}
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${java:Depends}


=====================================
debian/patches/adapt_auto_test_script.sh
=====================================
@@ -12,7 +12,7 @@ Description: Adapt test script to Debian installation
 -_result=$_scripts_dir/out.txt
 +BUILD_DIR=obj-$(dpkg-architecture -qDEB_HOST_GNU_TYPE)
 +DATA_DIR=$(pwd)/db
-+_script=`find $(pwd)/obj-x86_64-linux-gnu/bin -name plast -executable`
++_script=`find $(pwd)/obj-*-linux-gnu/bin -name plast -executable`
 +_result=`dirname $_script`/out.txt
  
  echo


=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ use_debian_packaged_pcre.patch
 adapt_auto_test_script.sh
 no_msse3.patch
 reproducible.patch
+simde.patch


=====================================
debian/patches/simde.patch
=====================================
@@ -0,0 +1,60 @@
+--- a/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp
++++ b/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp
+@@ -19,15 +19,8 @@
+ 
+ #include <algo/hits/gap/SmallGapHitIteratorSSE8.hpp>
+ 
+-#if __SSE3__
+-    #include <pmmintrin.h>
+-#else
+-    #if __SSE2__
+-        #include <emmintrin.h>
+-    #else
+-        #warning error undefined __SSE3__ or __SSE2__
+-    #endif
+-#endif
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse3.h>
+ 
+ using namespace std;
+ using namespace misc;
+--- a/src/algo/hits/ungap/UngapHitIteratorSSE16.cpp
++++ b/src/algo/hits/ungap/UngapHitIteratorSSE16.cpp
+@@ -21,15 +21,8 @@
+ 
+ #include <algo/hits/ungap/UngapHitIteratorSSE16.hpp>
+ 
+-#if __SSE3__
+-    #include <pmmintrin.h>
+-#else
+-#if __SSE2__
+-    #include <emmintrin.h>
+-#else
+-    #warning error undefined __SSE3__ or __SSE2__
+-#endif
+-#endif
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse3.h>
+ 
+ using namespace std;
+ using namespace misc;
+--- a/src/algo/hits/ungap/UngapHitIteratorSSE8.cpp
++++ b/src/algo/hits/ungap/UngapHitIteratorSSE8.cpp
+@@ -20,15 +20,8 @@
+ 
+ #include <algo/hits/ungap/UngapHitIteratorSSE8.hpp>
+ 
+-#if __SSE3__
+-    #include <pmmintrin.h>
+-#else
+-#if __SSE2__
+-    #include <emmintrin.h>
+-#else
+-    #warning error undefined __SSE3__ or __SSE2__
+-#endif
+-#endif
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde/x86/sse3.h>
+ 
+ using namespace std;
+ using namespace misc;


=====================================
debian/rules
=====================================
@@ -8,6 +8,8 @@ BUILD_DIR := obj-$(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
 BUILD_DATE := $(shell TZ=UTC LC_ALL=C dpkg-parsechangelog | grep Date: | cut -d' ' -f2-7)
 export BDATE=$(shell TZ=UTC LC_ALL=C date -d"$(BUILD_DATE)" +'%Y-%m-%d')
 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 $@ --buildsystem=cmake
@@ -24,6 +26,9 @@ override_dh_auto_build-indep:
 override_dh_auto_install-indep:
 	echo "I: Nothing to do for arch:indep binary"
 
+override_dh_gencontrol:
+	dh_gencontrol -- -Vsimde:Built-Using="$(shell dpkg-query -f '$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")"
+
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	scripts/test-plast.sh



View it on GitLab: https://salsa.debian.org/med-team/plast/-/compare/afb3ddccf6b364e7ca4d0fb9e3b1a6ff1d5f6773...90f479b02938865b434bed12d460ef7fd9e77e5e

-- 
View it on GitLab: https://salsa.debian.org/med-team/plast/-/compare/afb3ddccf6b364e7ca4d0fb9e3b1a6ff1d5f6773...90f479b02938865b434bed12d460ef7fd9e77e5e
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