[med-svn] [Git][med-team/mmseqs2][master] 3 commits: Revert "Apply patch from Adrian Bunk to revert optimisation for i386"
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Aug 31 09:03:22 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / mmseqs2
Commits:
80446d9b by Michael R. Crusoe at 2020-05-20T08:52:52+02:00
Revert "Apply patch from Adrian Bunk to revert optimisation for i386"
This reverts commit 8d13131cf09bd65340ffc419179cac4efcc1c6b7.
- - - - -
4e7d29d6 by Michael R. Crusoe at 2020-05-20T09:21:17+02:00
debian/patches/simde: Fix for i386
Closes: #961101
- - - - -
2bd1ea29 by Michael R. Crusoe at 2020-08-31T10:02:45+02:00
mark patches as not needing forwarding
- - - - -
8 changed files:
- debian/bin/simd-dispatch
- debian/changelog
- debian/patches/fix_tests.patch
- debian/patches/fix_util_installation.patch
- debian/patches/simde
- debian/patches/use_system_gzstream.patch
- debian/patches/use_system_zstd.patch
- debian/rules
Changes:
=====================================
debian/bin/simd-dispatch
=====================================
@@ -12,7 +12,7 @@ function test_and_run () {
fi
}
-for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse mmx ; do test_and_run ${SIMD} "$@" ; done
+for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 sse ; do test_and_run ${SIMD} "$@" ; done
# fallback to plain option
$BASE-plain "$@"
=====================================
debian/changelog
=====================================
@@ -1,10 +1,10 @@
mmseqs2 (11-e1a1c+ds-4) UNRELEASED; urgency=medium
* Team upload.
- * Apply patch from Adrian Bunk to revert optimisation for i386
- Closes: #961101
+ * debian/patches/simde: Fix for i386 (Closes: #961101).
+ * debian/rules: simplify the multi-build
- -- Andreas Tille <tille at debian.org> Wed, 20 May 2020 08:34:37 +0200
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 20 May 2020 09:17:22 +0200
mmseqs2 (11-e1a1c+ds-3) unstable; urgency=medium
=====================================
debian/patches/fix_tests.patch
=====================================
@@ -2,6 +2,7 @@ Description: Fix some of the test src files to work in autopkgtest
as some of the tests do not work as the paths have either been hardcoded or SIGSEGV is thrown
Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-07-20
+Forwarded: not-needed
---
--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp
=====================================
debian/patches/fix_util_installation.patch
=====================================
@@ -2,6 +2,7 @@ Description: Prevent CMake from installing util/
We handle this within *.installs ourselves
Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-07-16
+Forwarded: not-needed
---
Index: mmseqs2/util/CMakeLists.txt
=====================================
debian/patches/simde
=====================================
@@ -1,5 +1,6 @@
From: Michael R. Crusoe <michael.crusoe at gmail.com>
Subject: Enable building on non-x86 and less than SSE4.1
+Forwarded: not-needed
--- mmseqs2.orig/src/CMakeLists.txt
+++ mmseqs2/src/CMakeLists.txt
@@ -133,21 +133,6 @@
@@ -51,7 +52,7 @@ Subject: Enable building on non-x86 and less than SSE4.1
-#include <xmmintrin.h>
-#endif
+#define SIMDE_ENABLE_NATIVE_ALIASES
-+#include <simde/x86/sse.h>
++#include <simde/x86/sse2.h>
#ifdef AVX512
#include <zmmintrin.h.h> // AVX512
=====================================
debian/patches/use_system_gzstream.patch
=====================================
@@ -1,6 +1,7 @@
Description: We use libgzstream-dev instead of that in lib
Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-07-15
+Fowarded: not-needed
---
--- mmseqs2.orig/CMakeLists.txt
=====================================
debian/patches/use_system_zstd.patch
=====================================
@@ -1,6 +1,7 @@
Description: Use libzstd-dev instead of that in lib
Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2019-07-19
+Forwarded: not-needed
---
--- mmseqs2.orig/CMakeLists.txt
=====================================
debian/rules
=====================================
@@ -18,11 +18,19 @@ libexecdir=$(prefix)/lib/$(DEB_SOURCE)
dh $@
override_dh_auto_configure-arch:
-ifeq (amd64,$(DEB_HOST_ARCH))
- for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
+ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
+ for SIMD in avx2 avx sse4.1 ssse3 sse3 ; do \
export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \
dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} -DVERSION_OVERRIDE=$(DEB_VERSION) ; \
done
+ export CXXFLAGS="$(CXXFLAGS)" && export CFLAGS="$(CFLAGS)" && \
+ dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain -DVERSION_OVERRIDE=$(DEB_VERSION)
+ifeq (i386,$(DEB_HOST_ARCH))
+ for SIMD in sse2 sse ; do \
+ export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \
+ dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} -DVERSION_OVERRIDE=$(DEB_VERSION) ; \
+ done
+endif
else
dh_auto_configure -- -DVERSION_OVERRIDE=$(DEB_VERSION)
endif
@@ -30,11 +38,16 @@ endif
override_dh_auto_configure-indep:
override_dh_auto_build-arch:
-ifeq (amd64,$(DEB_HOST_ARCH))
+ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
mkdir -p $(binprefix)
- for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
+ for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \
dh_auto_build --builddirectory build_$${SIMD} ; \
done
+ifeq (i386,$(DEB_HOST_ARCH))
+ for SIMD in sse2 sse ; do \
+ dh_auto_build --builddirectory build_$${SIMD} ; \
+ done
+endif
else
dh_auto_build
endif
@@ -42,11 +55,16 @@ endif
override_dh_auto_build-indep:
override_dh_auto_install-arch:
-ifeq (amd64,$(DEB_HOST_ARCH))
+ifneq (,$(filter $(DEB_HOST_ARCH),amd64 i386))
dh_install -pmmseqs2 debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/
- for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \
+ for SIMD in avx2 avx sse4.1 ssse3 sse3 plain ; do \
dh_auto_install --builddirectory build_$${SIMD} ; \
done
+ifeq (i386,$(DEB_HOST_ARCH))
+ for SIMD in sse2 sse ; do \
+ dh_auto_install --builddirectory build_$${SIMD} ; \
+ done
+endif
dh_install -pmmseqs2 usr/bin/mmseqs-* usr/bin/
cd $(binprefix) \
&& for prog in mmseqs ; do \
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/8d13131cf09bd65340ffc419179cac4efcc1c6b7...2bd1ea29e1a46f3b2e97849c557ee6d65a34b3fa
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/-/compare/8d13131cf09bd65340ffc419179cac4efcc1c6b7...2bd1ea29e1a46f3b2e97849c557ee6d65a34b3fa
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