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#!/bin/bash
# Slackware build script for RAxML
# Copyright 2019-2021 Petar Petrov slackalaxy@gmail.com
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
# permitted provided that the following conditions are met:
#
# 1. Redistributions of this script must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
PRGNAM=RAxML
VERSION=${VERSION:-8.2.12}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
if [ -z "$ARCH" ]; then
case "$( uname -m )" in
i?86) ARCH=i586 ;;
arm*) ARCH=arm ;;
*) ARCH=$( uname -m ) ;;
esac
fi
CWD=$(pwd)
TMP=${TMP:-/tmp/SBo}
PKG=$TMP/package-$PRGNAM
OUTPUT=${OUTPUT:-/tmp}
if [ "$ARCH" = "i586" ]; then
SLKCFLAGS="-O2 -march=i586 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "i686" ]; then
SLKCFLAGS="-O2 -march=i686 -mtune=i686"
LIBDIRSUFFIX=""
elif [ "$ARCH" = "x86_64" ]; then
SLKCFLAGS="-O2 -fPIC"
LIBDIRSUFFIX="64"
else
SLKCFLAGS="-O2"
LIBDIRSUFFIX=""
fi
set -e
rm -rf $PKG
mkdir -p $TMP $PKG $OUTPUT
cd $TMP
rm -rf standard-$PRGNAM-$VERSION
tar xvf $CWD/standard-$PRGNAM-$VERSION.tar.gz
cd standard-$PRGNAM-$VERSION
chown -R root:root .
find -L . \
\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
-o -perm 511 \) -exec chmod 755 {} \; -o \
\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
# Build executables with the default Slackware compiler flags.
# Sequential version
cp Makefile.gcc Makefile
sed -i "/^CFLAGS/s/=/+=/" Makefile
sed -i "s|raxmlHPC|raxml|g" Makefile
CFLAGS="$SLKCFLAGS" \
make -f Makefile -j1
install -D -m755 raxml $PKG/usr/bin/raxml
# Openmpi version
cp Makefile.MPI.gcc Makefile.MPI
sed -i "/^CFLAGS/s/=/+=/" Makefile.MPI
sed -i "s|raxmlHPC-MPI|raxml-MPI|g" Makefile.MPI
CFLAGS="$SLKCFLAGS" \
make -f Makefile.MPI -j1
install -D -m755 raxml-MPI $PKG/usr/bin/raxml-MPI
##########################################################################
### You are highly encouraged to try the other optimisations below for ###
### performance enhancements. Just uncomment the corresponding lines. ###
##########################################################################
## Default sequential version
#make -f Makefile.gcc
#install -D -m755 raxmlHPC $PKG/usr/bin/raxmlHPC
#make -f Makefile.SSE3.gcc
#install -D -m755 raxmlHPC-SSE3 $PKG/usr/bin/raxmlHPC-SSE3
#make -f Makefile.AVX.gcc
#install -D -m755 raxmlHPC-AVX $PKG/usr/bin/raxmlHPC-AVX
## Pthreads version
#make -f Makefile.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS $PKG/usr/bin/raxmlHPC-PTHREADS
#make -f Makefile.SSE3.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS-SSE3 $PKG/usr/bin/raxmlHPC-PTHREADS-SSE3
#make -f Makefile.AVX.PTHREADS.gcc
#install -D -m755 raxmlHPC-PTHREADS-AVX $PKG/usr/bin/raxmlHPC-PTHREADS-AVX
## Default coarse-grain MPI version
#make -f Makefile.MPI.gcc
#install -D -m755 raxmlHPC-MPI $PKG/usr/bin/raxmlHPC-MPI
#make -f Makefile.SSE3.MPI.gcc
#install -D -m755 raxmlHPC-MPI-SSE3 $PKG/usr/bin/raxmlHPC-MPI-SSE3
#make -f Makefile.AVX.MPI.gcc
#install -D -m755 raxmlHPC-MPI-AVX $PKG/usr/bin/raxmlHPC-MPI-AVX
## Hybrid MPI/Pthreads version
# Before using this version, please read this paper here:
# http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf
# and look at these slides:
# http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf
#make -f Makefile.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID $PKG/usr/bin/raxmlHPC-HYBRID
#make -f Makefile.SSE3.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID-SSE3 $PKG/usr/bin/raxmlHPC-HYBRID-SSE3
#make -f Makefile.AVX.HYBRID.gcc
#install -D -m755 raxmlHPC-HYBRID-AVX $PKG/usr/bin/raxmlHPC-HYBRID-AVX
find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
# Copy the useful scripts
mkdir -p $PKG/usr/share/$PRGNAM
cp -a usefulScripts $PKG/usr/share/$PRGNAM
mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
cp -a README manual $PKG/usr/doc/$PRGNAM-$VERSION
cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References
mkdir -p $PKG/install
cat $CWD/slack-desc > $PKG/install/slack-desc
cd $PKG
/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz}
|
