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corburn/Makefile

Created November 25, 2015 21:23
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SC15 Student Cluster Competition
Raw
gcc.mk
${SRC}/gmp:
wget https://ftp.gnu.org/gnu/gmp/gmp-6.0.0a.tar.xz && \
tar xvf gmp-6.0.0a.tar.xz && rm gmp-6.0.0a.tar.xz && \
mv gmp-6.0.0 $@
${LOCAL}/gmp: ${SRC}/gmp
cd $< && ./configure --prefix=$@ \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && \
make && make install
${SRC}/mpfr:
wget http://www.mpfr.org/mpfr-current/mpfr-3.1.3.tar.xz && \
tar xvf mpfr-3.1.3.tar.xz && rm mpfr-3.1.3.tar.xz && \
mv mpfr-3.1.3 $@
# TODO: review INSTALL. building with gmp internals
#--enable-decimal-float
${LOCAL}/mpfr: ${SRC}/mpfr ${LOCAL}/gmp
cd $< && ./configure --prefix=$@ \
--with-gmp=${LOCAL}/gmp \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && \
make && make install
${SRC}/mpc:
wget ftp://ftp.gnu.org/gnu/mpc/mpc-1.0.3.tar.gz && \
tar xvf mpc-1.0.3.tar.gz && rm mpc-1.0.3.tar.gz && \
mv mpc-1.0.3 $@
${LOCAL}/mpc: ${SRC}/mpc ${LOCAL}/gmp ${LOCAL}/mpfr
cd $< && \
./configure --prefix=$@ \
--with-gmp=${LOCAL}/gmp \
--with-mpfr=${LOCAL}/mpfr && \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && \
make && make install
# https://gcc.gnu.org/install/prerequisites.html
# If an ISL source distribution is found in a subdirectory of your GCC sources
# named isl, it will be built together with GCC
${SRC}/isl:
wget ftp://gcc.gnu.org/pub/gcc/infrastructure/isl-0.14.tar.bz2 && \
tar xvf isl-0.14.tar.bz2 && rm isl-0.14.tar.bz2 && mv isl-0.14 $@
#--with-gmp=build \
# configure: error: Setting /home/jlt256/local/gmp implies use of system gmp
${LOCAL}/isl: ${SRC}/isl ${LOCAL}/gmp
cd $< && ./configure --prefix=$@ \
--with-gmp-prefix=${LOCAL}/gmp \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && \
make && make install
# error: cloog/version.h: No such file or directory
${SRC}/cloog:
wget http://www.bastoul.net/cloog/pages/download/count.php3?url=./cloog-0.18.4.tar.gz -O cloog-0.18.4.tar.gz && \
tar xvf cloog-0.18.4.tar.gz && rm cloog-0.18.4.tar.gz && \
mv cloog-0.18.4 $@
# gcc4.9 checks for isl0.14
# --with-isl=bundled
${LOCAL}/cloog: ${SRC}/cloog ${LOCAL}/gmp
cd $< && \
./configure --prefix=$@ \
--with-isl-prefix=${LOCAL}/isl \
--with-gmp-prefix=${LOCAL}/gmp \
--with-osl=bundled \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && \
make && make install
#git clone --depth=1 https://github.com/gcc-mirror/gcc.git
${SRC}/gcc:
wget http://mirrors-usa.go-parts.com/gcc/releases/gcc-4.9.3/gcc-4.9.3.tar.bz2 && \
tar xvf gcc-4.9.3.tar.bz2 && rm gcc-4.9.3.tar.bz2 && \
mv gcc-4.9.3 gcc
# g++: unrecognized option '-static-libstdc++'
${LOCAL}/gcc: ${SRC}/gcc ${LOCAL}/mpc ${LOCAL}/gmp ${LOCAL}/mpfr ${LOCAL}/cloog
export AR=ar; export LD=ld; export CC=gcc; export CXX=g++; export CFLAGS=""; export CXXFLAGS=""; export LDFLAGS=""; \
mkdir gcc-build && cd gcc-build && \
trap "rm -rf gcc-build" EXIT && \
${SRC}/gcc/configure --prefix=$@ \
--with-mpc=${LOCAL}/mpc \
--with-gmp=${LOCAL}/gmp \
--with-mpfr=${LOCAL}/mpfr \
--disable-multilib \
--disable-libstdcxx \
--enable-lto && \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && \
make AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" LDFLAGS="" && make install
Raw
hpcg.mk
${SRC}/hpcg:
git clone --depth=1 https://github.com/hpcg-benchmark/hpcg.git
#trap "rm -rf $${BUILD_DIR}" EXIT &&
${LOCAL}/hpcg: ${SRC}/hpcg
MPdir="/packages/parallel_studio_xe/2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64"; \
BUILD_DIR=$(shell mktemp --directory --tmpdir=${SRC}) && \
cd $${BUILD_DIR} && \
sed "s|-openmp|-qopenmp|g; s|ARCHIVER\s*= ar|ARCHIVER = xiar|g" $</setup/Make.MPIICPC_OMP > $</setup/Make.SC15 && \
${SRC}/hpcg/configure SC15 && make
Raw
Makefile
# find ./ -type f -exec ldd {} \; 2>/dev/null | less
# LOCAL is the path prefix where the programs will be installed
# The environment variable will supersede the default value
#LOCAL ?= ${HOME}/local
SRC = ${CURDIR}
BIN = ${LOCAL}/bin
ifndef LOCAL
$(error LOCAL is not set)
endif
.PHONY: prebuild
prebuild: ccache
$(MAKE) ${LOCAL}/autotools/bin/pkg-config
#$(MAKE) ${LOCAL}/gperftools/lib/libtcmalloc_minimal.so
#$(MAKE) ${LOCAL}/jemalloc/lib/libjemalloc.so
#$(MAKE) ${LOCAL}/zlib
$(MAKE) all
all: parallel_compression ${LOCAL}/tmux ${LOCAL}/trinityrnaseq ${LOCAL}/milc.qio ${BIN}/wrf
include trinityrnaseq.mk
include milc.mk
include wrf.mk
include repast.mk
include hpcg.mk
include gcc.mk
.PHONY: ccache
ccache:
-@mkdir -p ${BIN}; \
ln -s `which ccache-swig` ${BIN}/gcc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/g++ 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/cc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/c++ 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/icc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/icpc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/mpiicc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/mpiicpc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/mpicc 2>/dev/null; \
ln -s `which ccache-swig` ${BIN}/mpicxx 2>/dev/null; \
ln -s ${BIN}/mpicxx ${BIN}/mpic++ 2>/dev/null
.PHONY: parallel_compression
parallel_compression: ${BIN}/lbzip2 ${BIN}/pigz
-@ln -s ${BIN}/lbzip2 ${BIN}/bzip2 2>/dev/null; \
ln -s ${BIN}/lbzip2 ${BIN}/bunzip2 2>/dev/null; \
ln -s ${BIN}/lbzip2 ${BIN}/bzcat 2>/dev/null; \
ln -s ${BIN}/pigz ${BIN}/gzip 2>/dev/null; \
ln -s ${BIN}/pigz ${BIN}/gunzip 2>/dev/null; \
ln -s ${BIN}/pigz ${BIN}/zcat 2>/dev/null
${SRC}/help2man-1.29:
wget ftp://ftp.gnu.org/gnu/help2man/help2man-1.29.tar.gz
tar xvf help2man-1.29.tar.gz && rm help2man-1.29.tar.gz
#wget https://ftp.gnu.org/gnu/help2man/help2man-1.47.2.tar.xz
#tar xvf help2man-1.47.2.tar.xz && rm help2man-1.47.2.tar.xz
${LOCAL}/autotools/bin/help2man: ${SRC}/help2man-1.29
cd ${SRC}/help2man-1.29 && \
./configure --prefix=${LOCAL}/autotools && make && make install
${SRC}/libtool:
git clone --branch v2.4.6 --depth 1 http://git.savannah.gnu.org/r/libtool.git
# bootstrap: error: Prerequisite 'help2man' not found. Please install it, or
# bootstrap: 'export HELP2MAN=/path/to/help2man'.
# bootstrap: error: HACKING explains how to obtain these prerequisite programs:
# bootstrap: Program Min_version Homepage
# bootstrap: -----------------------------------------------------------
# bootstrap: help2man 1.29 http://www.gnu.org/s/help2man
# bootstrap: make 3.81 http://www.gnu.org/s/make
# bootstrap: makeinfo 4.8 http://www.gnu.org/s/texinfo
# bootstrap: xz 4.999.8beta http://tukaani.org/xz
# bootstrap: autoconf 2.62 http://www.gnu.org/s/autoconf
# bootstrap: automake 1.11.1 http://www.gnu.org/s/automake
# bootstrap: -----------------------------------------------------------
# --disable-ltdl-install assuming it is not required
# See https://www.gnu.org/software/libtool/manual/html_node/Using-libltdl.html
# error: Prerequisite 'help2man' not found. Please install it, or 'export HELP2MAN=/path/to/help2man'
${LOCAL}/autotools/bin/libtool: ${SRC}/libtool ${LOCAL}/autotools/bin/help2man
export HELP2MAN="${LOCAL}/autotools/bin/help2man"; \
cd ${SRC}/libtool && \
./bootstrap --force && \
./configure --prefix=${LOCAL}/autotools --disable-ltdl-install && make VERSION=v2.4.6 && make install
${SRC}/autoconf:
#git clone --depth 1 http://git.savannah.gnu.org/r/autoconf.git
wget https://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.xz && \
tar xvf autoconf-2.69.tar.xz && rm autoconf-2.69.tar.xz
mv autoconf-2.69 autoconf
${LOCAL}/autotools/bin/autoconf: ${SRC}/autoconf
cd ${SRC}/autoconf && ./configure --prefix=${LOCAL}/autotools && make && make install
${SRC}/automake:
git clone --depth 1 http://git.savannah.gnu.org/r/automake.git
# configure.ac:18: error: Autoconf version 2.69 or higher is required
${LOCAL}/autotools/bin/automake: ${SRC}/automake ${LOCAL}/autotools/bin/autoconf
export PATH="${LOCAL}/autotools/bin:${PATH}"; \
cd ${SRC}/automake && \
./bootstrap.sh && \
./configure --prefix=${LOCAL}/autotools && make && make install
${SRC}/pkgconf:
git clone --depth 1 https://github.com/pkgconf/pkgconf.git
# TODO: review
# Makefile.am:12: error: Libtool library used but 'LIBTOOL' is undefined
${LOCAL}/autotools/bin/pkg-config: ${SRC}/pkgconf ${LOCAL}/autotools/bin/libtool ${LOCAL}/autotools/bin/automake
export PATH="${LOCAL}/autotools/bin:${PATH}"; \
cd ${SRC}/pkgconf && \
./autogen.sh -n && \
./configure --prefix=${LOCAL}/autotools && $(MAKE) && $(MAKE) install && \
ln -sf ${LOCAL}/autotools/bin/pkgconf ${LOCAL}/autotools/bin/pkg-config
${SRC}/gperftools:
git clone --depth 1 https://github.com/gperftools/gperftools.git
# --with-tcmalloc-alignment=8|16
#
# --with-tcmalloc-pagesize=8|32|64 can improve performance 3-5%
# If ___tls_get_addr: symbol not found encountered, remove #define HAVE_TLS
# See "*** TCMALLOC LARGE PAGES: TRADING TIME FOR SPACE" in gpertools INSTALL
#${LIB}/libtcmalloc.so: ${SRC}/gperftools ${BIN}/pkg-config
#
# Upgrade libtool because of the following error:
# ./libtool: line 1304: func_opt_split: command not found
# libtool: error: you must specify a MODE.
#
# autoreconf -i --force because of the following error:
# libtoolize: error: 'm4/ltversion.m4' is newer: use '--force' to overwrite
# libtool: Version mismatch error. This is libtool 2.4.6, but the
# libtool: definition of this LT_INIT comes from libtool 2.2.6b.
# libtool: You should recreate aclocal.m4 with macros from libtool 2.4.6
# libtool: and run autoconf again.
#
# --enable-minimal build only tcmalloc-minimal
# Replaced autoreconf -i --force with ./autogen.sh because something was generating the wrong lib path:
# icpc: error #10236: File not found: '/home/jlt256/src/gperftools/.libs/libtcmalloc_minimal.so'
# libtool: error: cannot find the library '/home/jlt256/local/gperftools/lib/libtcmalloc_minimal.la' or unhandled argument '/home/jlt256/local/gperftools/lib/libtcmalloc_minimal.la'
# The errors are cryptic, but it seems autotools must be updated before gpertools can be
# compiled, however, updating the gperftools autotools files with
# autoconf will also break the build.
# Conclusion: uncertain, but it works
${LOCAL}/gperftools/lib/libtcmalloc_minimal.so: ${SRC}/gperftools ${LOCAL}/autotools/bin/libtool
#export PATH="${LOCAL}/autotools/bin:${PATH}"; \
#cd ${SRC}/gperftools && \
#./autogen.sh && \
#./configure --prefix=${LOCAL}/gperftools --with-tcmalloc-pagesize=32 --enable-minimal && ${MAKE} && ${MAKE} install
# TODO(jtravis): remove jemalloc. I suspect tcmalloc is better.
${SRC}/jemalloc:
git clone --depth 1 https://github.com/jemalloc/jemalloc.git
# make install targets are used directly to avoid compiling
# documentation which depends on Docbook XSL stylesheets
${LOCAL}/jemalloc/lib/libjemalloc.so: ${SRC}/jemalloc
cd ${SRC}/jemalloc && \
sh autogen.sh && ./configure --prefix=${LOCAL}/jemalloc && \
make install_bin install_include install_lib
@echo
@echo '================================================================================'
@echo 'update_paths'
@echo
@echo 'This should update the environment to link all subsequent programs with tcmalloc'
@echo '================================================================================'
@echo
exit 1
${SRC}/pigz:
git clone --depth 1 https://github.com/madler/pigz.git
${BIN}/pigz: ${SRC}/pigz
cd ${SRC}/pigz && \
sed -i 's|^CC=cc||g; s|^CFLAGS=|CFLAGS?=|g; s|LDFLAGS=|LDFLAGS+=|g' Makefile && \
$(MAKE) CFLAGS="$(filter-out -O3,$(CFLAGS))" && \
cp pigz ${BIN} && cp unpigz ${BIN}
${SRC}/gnulib:
git clone --depth 1 http://git.savannah.gnu.org/r/gnulib.git
${SRC}/lbzip2:
git clone --depth 1 https://github.com/kjn/lbzip2.git
# ./build-aux/autogen.sh: line 48: gnulib-tool: command not found
# configure.ac:27: require Automake 1.14, but have 1.11.1
${BIN}/lbzip2: ${SRC}/lbzip2 ${SRC}/gnulib ${LOCAL}/autotools/bin/automake
cd ${SRC}/lbzip2 && \
PATH=${PATH}:${SRC}/gnulib && \
./build-aux/autogen.sh && \
./configure --prefix=${LOCAL} && make && make install
${SRC}/libevent:
git clone --depth 1 https://github.com/libevent/libevent.git
${LOCAL}/libevent: ${SRC}/libevent
cd ${SRC}/libevent && \
sh autogen.sh && \
./configure --prefix=${LOCAL}/libevent && \
make && make install
${SRC}/tmux:
git clone --depth 1 https://github.com/tmux/tmux.git
# Fixing this error required updating pkgconfig:
# configure.ac:108: error: possibly undefined macro: AC_SEARCH_LIBS
# See https://superuser.com/questions/421396/cant-compile-tmux-with-iterm-support#comment1253220_742095
${LOCAL}/tmux: ${SRC}/tmux ${LOCAL}/libevent
cd ${SRC}/tmux && \
sh autogen.sh && \
./configure --prefix=${LOCAL}/tmux PKG_CONFIG_PATH=${LOCAL}/libevent/lib/pkgconfig && \
make && make install
${SRC}/zlib:
#git clone --depth 1 https://github.com/cloudflare/zlib.git
#sed -i 's:\$\(CC\) \$\(SFLAGS\) -DPIC:\$\(CC\) \$\(SFLAGS\) -xHOST -DPIC:g' Makefile &&
${LOCAL}/zlib: ${SRC}/zlib
#cd ${SRC}/zlib && ./configure --prefix=${LOCAL}/zlib && \
#sed -i 's:\([SC]\)FLAGS=-O3:\1FLAGS=-O3 -xHOST:p' Makefile && \
$(MAKE) && $(MAKE) check && $(MAKE) install
Raw
milc.mk
KS_IMP_RHMC_TARGETS=all: su3_leapfrog su3_omelyan_rhmc su3_rhmd su3_rhmc su3_rhmd_eos su3_rhmc_eos su3_rhmc_susc su3_rhmc_susc_eos su3_rhmc_Nf su3_rhmd_hisq su3_rhmd_hisq_su3 su3_rhmc_hisq_plaq su3_rhmc_hisq_su3 su3_rhmc_hisq_eos su3_rhmd_hisq_eos su3_rhmc_hisq_susc su3_rhmc_hisq_susc_eos
#${SRC}/qip:
# git clone --depth=1 https://github.com/usqcd-software/qio.git
#
#${LOCAL}/qip: ${SRC}/qip ${LOCAL}/scidac/qmp
# BUILD_DIR=${SRC}/qmp/build; \
# mkdir $${BUILD_DIR} && \
# trap "rm -rf $${BUILD_DIR}" EXIT && \
# cd $${BUILD_DIR} && \
# ../configure \
# --prefix=$@ \
# --with-qmp=${LOCAL}/scidac/qmp \
# --disable-qmp-route
# git clone https://github.com/FFTW/fftw3.git
${SRC}/fftw3:
wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.4.tar.gz && \
tar xvf fftw-3.3.4.tar.gz && rm fftw-3.3.4.tar.gz && mv --force fftw-3.3.4 $@
${LOCAL}/fftw3: ${SRC}/fftw3
cd $< && ./configure --prefix=$@ \
--enable-threads \
--enable-openmp \
--enable-mpi \
--enable-fma \
--enable-avx \
&& make && make install
${SRC}/qmp:
git clone --depth=1 https://github.com/usqcd-software/qmp.git
# TODO: review configuration
#./bootstrap.sh &&
#--with-combined-threads \
#--enable-openmp \
#--enable-mpi \
#--enable-avx2 \
#--disable-fortran
${LOCAL}/scidac/qmp: ${SRC}/qmp ${LOCAL}/fftw3
cd $< && \
autoreconf --force --install && \
./configure --prefix=$@ \
make CFLAGS="-std=gnu99 ${CFLAGS}" && make install
${SRC}/qio:
git clone --recursive --depth=1 https://github.com/usqcd-software/qio.git
${LOCAL}/scidac/qio: ${SRC}/qio ${LOCAL}/scidac/qmp
cd $< && ./autogen.sh && \
./configure --prefix=$@ \
--with-qmp=${LOCAL}/scidac/qmp \
--enable-largefile && make CFLAGS="-std=gnu99 ${CFLAGS}" && make install
${SRC}/qla:
git clone --depth=1 https://github.com/usqcd-software/qla.git
#/home/jlt256/src/qla/config/missing: Unknown `--is-lightweight' option
#Try `/home/jlt256/src/qla/config/missing --help' for more information
#configure: WARNING: 'missing' script is too old or missing
${LOCAL}/scidac/qla: ${SRC}/qla
cd $< && \
autoreconf --force --install && \
./configure --prefix=$@ \
--enable-openmp \
--enable-sse3 && make CFLAGS="-std=gnu99 -qopenmp ${CFLAGS}" && make install
${SRC}/qdp:
git clone --depth=1 https://github.com/usqcd-software/qdp.git
${LOCAL}/scidac/qdp: ${SRC}/qdp ${LOCAL}/scidac/qmp ${LOCAL}/scidac/qio ${LOCAL}/scidac/qla
cd $< && autoreconf --force --install && \
./configure --prefix=$@ \
--enable-pthreads \
--with-qmp=${LOCAL}/scidac/qmp \
--with-qio=${LOCAL}/scidac/qio \
--with-qla=${LOCAL}/scidac/qla && make CFLAGS="-std=gnu99 ${CFLAGS}" && make install
${SRC}/qopqdp:
git clone --depth=1 https://github.com/usqcd-software/qopqdp.git
# TODO: configure with blas and lapack (see configure)
# qll library not found
#--with-qll=${LOCAL}/scidac/qll
${LOCAL}/scidac/qopqdp: ${SRC}/qopqdp ${LOCAL}/scidac/qdp ${LOCAL}/scidac/qla ${LOCAL}/scidac/qio ${LOCAL}/scidac/qio ${LOCAL}/scidac/qmp
cd $< && autoreconf --force --install && \
./configure --prefix=${LOCAL}/scidac/qopqdp \
--with-qdp=${LOCAL}/scidac/qdp \
--with-qla=${LOCAL}/scidac/qla \
--with-qio=${LOCAL}/scidac/qio \
--with-qmp=${LOCAL}/scidac/qmp && make CFLAGS="-std=gnu99 ${CFLAGS}" && make install
${SRC}/MILC_SC15:
tar xvf /scratch/apps/src/MILC_SC15.tgz
${LOCAL}/milc: ${SRC}/MILC_SC15 ${LOCAL}/scidac/qopqdp
cd $< && \
find . -type f -exec sed -i 's:CC *= *gcc:CC = icc:g; s:#MPP = true:MPP = true:g; s:^\(OMP\|WANTQOPo\|WANTQIO\|WANTFFTW\) = #true:\1 = true:g; s:-openmp:-qopenmp:g; s:^CFLAGS *= :CFLAGS = -parallel -xHOST :g; s:INLINEOPT = -DC_GLOBAL_INLINE:INLINEOPT = -DSSE_GLOBAL_INLINE:g' {} + && \
cd $</ks_imp_rhmc && \
grep -q -F "${KS_IMP_RHMC_TARGETS}" Make_template || echo "${KS_IMP_RHMC_TARGETS}" >> Make_template && \
${MAKE} all && cp -r $< $@
#sed -i 's:CC *= *gcc:CC = icc:g; s:#MPP = true:MPP = true:g; s:^\(OMP\|WANTQOPo\|WANTQIO\|WANTFFTW\) = #true:\1 = true:g; s:-openmp:-qopenmp:g; s:^CFLAGS *= :CFLAGS = -parallel -xHOST :g; s:INLINEOPT = -DC_GLOBAL_INLINE:INLINEOPT = -DSSE_GLOBAL_INLINE:g' $</ks_imp_rhmc/Makefile &&
${LOCAL}/milc.vanilla: ${SRC}/MILC_SC15
cd $< && \
cd $</ks_imp_rhmc && \
grep -q -F "${KS_IMP_RHMC_TARGETS}" Make_template || echo "${KS_IMP_RHMC_TARGETS}" >> Make_template && \
${MAKE} all && \
cp -r $< $@
${LOCAL}/milc.fftw3: ${SRC}/MILC_SC15 ${LOCAL}/fftw3
cd $< && \
find . -type f -exec sed -i 's:CC *= *gcc:CC = icc:g; s:AR = ar::g; s:FFTW=$${HOME}/fftw/build-gcc:FFTW=$${LOCAL}/fftw3:g' {} + && \
sed -i 's:^\(WANTFFTW\) = #true:\1 = true:g' $</ks_imp_rhmc/Makefile && \
cd $</ks_imp_rhmc && \
grep -q -F "${KS_IMP_RHMC_TARGETS}" Make_template || echo "${KS_IMP_RHMC_TARGETS}" >> Make_template && \
${MAKE} all && \
cp -r $< $@
${LOCAL}/milc.mpi: ${SRC}/MILC_SC15 ${LOCAL}/fftw3
cd $< && \
find . -type f -exec sed -i 's:CC *= *gcc:CC = icc:g; s:AR = ar::g; s:FFTW=$${HOME}/fftw/build-gcc:FFTW=$${LOCAL}/fftw3:g' {} + && \
sed -i 's:#MPP = true:MPP = true:g; s:-openmp:-qopenmp:g; s:^\(OMP\|WANTFFTW\) = #true:\1 = true:g' $</ks_imp_rhmc/Makefile && \
cd $</ks_imp_rhmc && \
grep -q -F "${KS_IMP_RHMC_TARGETS}" Make_template || echo "${KS_IMP_RHMC_TARGETS}" >> Make_template && \
${MAKE} all && \
cp -r $< $@
${LOCAL}/milc.qio: ${SRC}/MILC_SC15 ${LOCAL}/fftw3 ${LOCAL}/scidac/qio
cd $< && \
find . -type f -exec sed -i 's:CC *= *gcc:CC = icc:g; s:AR = ar::g; s:FFTW=$${HOME}/fftw/build-gcc:FFTW=$${LOCAL}/fftw3:g' {} + && \
sed -i 's:SCIDAC = $${HOME}/scidac/install:SCIDAC = $${LOCAL}/scidac:g; s:#MPP = true:MPP = true:g; s:-openmp:-qopenmp:g; s:^\(OMP\|WANTFFTW\|WANTQIO\) = #true:\1 = true:g' $</ks_imp_rhmc/Makefile && \
cd $</ks_imp_rhmc && \
grep -q -F "${KS_IMP_RHMC_TARGETS}" Make_template || echo "${KS_IMP_RHMC_TARGETS}" >> Make_template && \
${MAKE} all && \
cp -r $< $@
Raw
profile
################################################################################
# LOCAL is the path prefix where user compiled programs are installed
################################################################################
if [[ -z "$LOCAL" ]]; then
2>&1 echo "ERROR: LOCAL environment variable undefined"
2>&1 echo "LOCAL=<install_path> source $BASH_SOURCE"
return 1
fi
################################################################################
# Create mpd.hosts if it does not exist
# https://software.intel.com/sites/products/documentation/hpc/mpi/linux/getting_started.pdf
################################################################################
if [[ -f ${HOME}/mpd.hosts ]]; then
NODES=$(cat ${HOME}/mpd.hosts | tr '\n' ' ')
else
# The default value of NODES is a list such as node1 node2 node3...
NODES=$(echo icnode{1..6}) ichn1
echo ${NODES// /$'\n'} > ${HOME}/mpd.hosts
echo "Created default ~/mpd.hosts file"
fi
################################################################################
# Add ~/.ssh/config rule to disable host key checking on the nodes
################################################################################
grep -q -F "HOST $NODES" ${HOME}/.ssh/config ||
{ cat << EOF >> ${HOME}/.ssh/config && echo "Added rule to ~/.ssh/config to disable host key checking on the nodes"
HOST $NODES
StrictHostKeyChecking no
EOF
}
PATHRC=${LOCAL}/path.rc
grep "export LOCAL=" $PATHRC || echo "export LOCAL=$LOCAL" >> $PATHRC
# Initialize *PATH variables
source $PATHRC
################################################################################
# Compiler Vars
################################################################################
export CFLAGS="-xCORE_AVX2 -ip -std=gnu99"
#export CXXFLAGS="-xCORE_AVX2 -ip -std=c++11"
export BOOST_ROOT=${LOCAL}/boost
export NETCDF=${LOCAL}
export DISTCC_POTENTIAL_HOSTS="localhost $NODES"
export DISTCC_ARGS="--allow 192.168.0.0/24"
# WCOLL is a file with a list of hosts for pdsh to target
# https://code.google.com/p/pdsh/wiki/UsingPDSH
export WCOLL=${HOME}/mpd.hosts
export PDSH_RCMD_TYPE=ssh
################################################################################
# tcmalloc is supposed to be a faster implementation of the default memory
# allocation library (malloc, calloc, etc)
################################################################################
malloc_cflags="-fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free"
malloc_ldflags="-ltcmalloc_minimal"
malloc_preload="${LOCAL}/gperftools/lib/libtcmalloc_minimal.so"
enable_malloc() {
if pkg-config --exists libtcmalloc_minimal; then
if [[ ! "$CFLAGS" =~ "$malloc_cflags" ]]; then
export CFLAGS="$malloc_cflags $CFLAGS"
fi
if [[ ! "$LDFLAGS" =~ "$malloc_ldflags" ]]; then
export LDFLAGS="$malloc_ldflags ${LDFLAGS}"
fi
if [[ ! "$LD_PRELOAD" =~ "$malloc_preload" ]]; then
export LD_PRELOAD="$malloc_preload $LD_PRELOAD"
fi
else
2>&1 echo "WARNING: pkg-config could not find tc/jemalloc. Programs will link against the default malloc"
if [[ -z "$PKG_CONFIG_PATH" ]]; then
2>&1 echo "WARNING: The PKG_CONFIG_PATH variable is empty"
fi
fi
}
disable_malloc() {
export CFLAGS="${CFLAGS/$malloc_cflags }"
export LDFLAGS="${LDFLAGS/$malloc_ldflags }"
export LD_PRELOAD="${LD_PRELOAD/$malloc_preload }"
}
which_profile() {
echo $(readlink -e $BASH_SOURCE)
}
enable_malloc
Raw
repast.mk
.PHONY: SCC15Programs
SCC15Programs: ${BIN}/python
#SCC15Programs: ${BIN}/tmux ${BIN}/repast ${BIN}/python
${SRC}/Python-2.7.10:
cd ${SRC} && \
tar -xvf Python-2.7.10.tgz
${BIN}/python: ${SRC}/Python-2.7.10
cd ${SRC}/Python-2.7.10 && \
./configure --prefix=${LOCAL} && \
make && make install
${SRC}/curl:
cd ${SRC} && \
git clone https://github.com/bagder/curl.git
${BIN}/curl: ${SRC}/curl
cd ${SRC}/curl && \
./buildconf && \
./configure --prefix=${LOCAL} && \
make && make install
#${SRC}/hdf5:
# cd ${SRC} && \
# tar -xvf hdf5-1.8.15-patch1.tar && \
# mv hdf5-1.8.15-patch1 hdf5
#${LIB}/libhdf5.so: ${SRC}/hdf5
# cd ${SRC}/hdf5 && \
# CC=mpicc CXX=mpicxx FC=mpif90 CFLAGS="" CXXFLAGS="" LDFLAGS="-L/packages/parallel_studio_xe/2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib" ./configure --enable-parallel --prefix=${LOCAL} && \
# make -j 4 && make install
#${SRC}/netcdf:
# cd ${SRC} && \
# tar -xvf netcdf-4.2.1.1.tar.gz && \
# mv netcdf-4.2.1.1 netcdf
#${LIB}/libnetcdf.so: ${SRC}/netcdf
# cd ${SRC}/netcdf && \
# ./configure --prefix=${LOCAL} --disable-netcdf-4 && make && make install
#${SRC}/netcdf-cxx:
# cd ${SRC} && \
# tar -xvf netcdf-cxx-4.2.tar.gz && \
# mv netcdf-cxx-4.2 netcdf-cxx
#${LIB}/libnetcdf_c++.so: ${SRC}/netcdf-cxx ${LIB}/libnetcdf.so
# cd ${SRC}/netcdf-cxx && \
# ./configure --prefix=${LOCAL} && make && make install
${SRC}/repast:
cp -rv /scratch/apps/src/SCC15HPCRepast ./repast
#make CXX="mpicxx" CXXLD="mpicxx -L/usr/lib64 -L/usr/lib/x86_64-redhat-linux5E/lib64 -L/packages/parallel_studio_xe/2016/compilers_and_libraries_2016.0.109/linux/mpi/intel64/lib" BOOST_INCLUDE_DIR=${LOCAL}/boost/include BOOST_LIB_DIR="${LOCAL}/boost/lib" BOOST_INFIX=-mt-s NETCDF_INCLUDE_DIR=${LOCAL}/netcdf/include NETCDF_LIB_DIR=${LOCAL}/netcdf/lib HDF5_INCLUDE_DIR=${LOCAL}/hdf5/include HDF5_LIB_DIR=${LOCAL}/hdf5/lib CURL_LIB_DIR=${LIB} CURL_INCLUDE_DIR=${INCLUDE} Z_LIB_DIR=${LOCAL}/zlib/lib && \
#${BIN}/repast: ${SRC}/repast ${BIN}/curl ${LOCAL}/boost ${LIB}/libnetcdf_c++.so ${LIB}/libnetcdf.so ${LIB}/libhdf5.so
#${LOCAL}/repast: ${SRC}/repast ${LOCAL}/boost ${LOCAL}/netcdf/netcdf-cxx ${LOCAL}/netcdf/netcdf-c ${LOCAL}/hdf5 ${LOCAL}/zlib
${LOCAL}/repast: ${SRC}/repast ${LOCAL}/netcdf/netcdf-cxx ${LOCAL}/netcdf/netcdf-c ${LOCAL}/hdf5 ${LOCAL}/zlib
cd $</INSTALLATION && \
make \
CXX="mpicxx" \
CXXLD="mpicxx" \
BOOST_INCLUDE_DIR=${LOCAL}/boost/include \
BOOST_LIB_DIR=${LOCAL}/boost/lib \
BOOST_INFIX=-mt-s \
NETCDF_INCLUDE_DIR=${LOCAL}/netcdf/include \
NETCDF_LIB_DIR=${LOCAL}/netcdf/lib \
CURL_INCLUDE_DIR=/usr/include/curl \
CURL_LIB_DIR=/usr/lib64 \
HDF5_INCLUDE_DIR=${LOCAL}/hdf5/include \
HDF5_LIB_DIR=${LOCAL}/hdf5/lib \
Z_LIB_DIR=${LOCAL}/zlib/lib && \
rsync -av --exclude='INSTALLATION' $< $@
Raw
trinityrnaseq.mk
${SRC}/htslib:
git clone --depth 1 https://github.com/samtools/htslib.git
${SRC}/samtools:
git clone --depth 1 https://github.com/samtools/samtools.git
# With the gcc compiler:
# undefined reference to `gzopen64'
# Use sed to delete CC and LDFLAGS variables so the environment CC (icc) and LDFLAGS (ltcmalloc)
# will be used
#make prefix=${LOCAL}/samtools install HTSDIR=${SRC}/htslib install-htslib
#mkdir -pv $@/lib && cp libbam.a $@/samtools/lib
#${LOCAL}/samtools: ${SRC}/samtools ${SRC}/htslib ${LOCAL}/zlib ${LOCAL}/perl
${LOCAL}/samtools: ${SRC}/samtools ${SRC}/htslib ${LOCAL}/zlib
cd $< && \
sed -i 's:^\(CC\|AR\|CFLAGS\|LDFLAGS\)\s*=.*$$::g' ${SRC}/htslib/Makefile && \
sed -i 's:^\(CC\|LDFLAGS\)\s*=.*$$::g; s/-D_CURSES_LIB=1/-D_CURSES_LIB=0/g; s|$$(CC) -pthread|$$(CC) -qopenmp -pthread|g; s|$$(CC) $$(LDFLAGS)|$$(CC) -qopenmp $$(LDFLAGS)|g' Makefile && \
$(MAKE) all CFLAGS="-parallel -qopenmp ${CFLAGS}" LDFLAGS="${LDFLAGS}" && $(MAKE) prefix=$@ install
# FIXME: tbb does not have a make install and the generated tbbvars.sh initialization script assumes everything is in the source folder
#${SRC}/tbb:
${LOCAL}/tbb:
wget https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20150728oss_src.tgz && \
tar xvf tbb44_20150728oss_src.tgz && \
rm tbb44_20150728oss_src.tgz && \
mv tbb44_20150728oss $@
# cp ${SRC}/tbb/build/linux_intel64_icc_cc4.4.7_libc2.12_kernel2.6.32_release/{libtbbmalloc_proxy,libtbbmalloc,libtbb}.so.2 ${LIB} && \
# cp -rv ${SRC}/tbb/include/tbb/* ${INCLUDE} && \
# ln -sf ${LIB}/libtbbmalloc_proxy.so.2 ${LIB}/libtbbmalloc_proxy.so
${LOCAL}/tbb/build/linux_intel64_${CC}_cc4.4.7_libc2.12_kernel2.6.32_release/tbbvars.sh: ${LOCAL}/tbb
cd ${LOCAL}/tbb && $(MAKE) compiler=${CC}
${SRC}/bowtie:
git clone --depth 1 --depth 1 https://github.com/BenLangmead/bowtie.git
# sed replaces the prefix with $LOCAL and removes the compiler variables
#
#sed -i "s:^prefix *=.*:prefix = ${LOCAL}:; \
#s:^CPP = .*::; \
#s:^CXX = .*::; \
#s:^CC = .*::" Makefile
# TODO: review
#sed -i "s:^prefix *=.*:prefix = $@:; s:^\(CPP\|CXX\|CC\)\s*=.*::g" Makefile && \
#sed -i "s:__cpuid((void \*):__cpuid((int \*):g" processor_support.h &&
#${LOCAL}/bowtie: ${SRC}/bowtie ${LOCAL}/tbb/build/linux_intel64_${CC}_cc4.4.7_libc2.12_kernel2.6.32_release/tbbvars.sh
# export LIBRARY_PATH="${LOCAL}/tbb/build/linux_intel64_icc_cc4.4.7_libc2.12_kernel2.6.32_release/:${LIBRARY_PATH}"; \
# cd $< && \
# sed -i "s:^prefix *=.*:prefix = $@:" Makefile && \
# source ${LOCAL}/tbb/build/linux_intel64_${CC}_cc4.4.7_libc2.12_kernel2.6.32_release/tbbvars.sh && \
# $(MAKE) clean && $(MAKE) CFLAGS="" WITH_TBB=1 && $(MAKE) install
${LOCAL}/bowtie: ${SRC}/bowtie
cd $< && \
sed -i "s:^prefix *=.*:prefix = $@:" Makefile && \
$(MAKE) clean && $(MAKE) CFLAGS="" CXXFLAGS="" LDFLAGS="" && $(MAKE) install
${SRC}/bowtie2:
git clone --branch v2.2.6 --depth 1 https://github.com/BenLangmead/bowtie2.git
# sed -i "s:__cpuid((void \*):__cpuid((int \*):g" processor_support.h fixes:
# error: argument of type "void *" is incompatible with parameter of type "int *"
${LOCAL}/bowtie2: ${SRC}/bowtie2 ${LOCAL}/tbb/build/linux_intel64_${CC}_cc4.4.7_libc2.12_kernel2.6.32_release/tbbvars.sh
export LIBRARY_PATH="${LOCAL}/tbb/build/linux_intel64_icc_cc4.4.7_libc2.12_kernel2.6.32_release/:${LIBRARY_PATH}"; \
cd $< && \
sed -i "s:^prefix *=.*:prefix = $@:" Makefile && \
sed -i "s:__cpuid((void \*):__cpuid((int \*):g" processor_support.h && \
source ${LOCAL}/tbb/build/linux_intel64_${CC}_cc4.4.7_libc2.12_kernel2.6.32_release/tbbvars.sh && \
$(MAKE) clean && CFLAGS="" CXXFLAGS="" $(MAKE) WITH_TBB=1 && $(MAKE) install
${SRC}/protobuf:
git clone --branch v3.0.0-beta-1 --depth 1 https://github.com/google/protobuf.git
# TODO: verify protobuf.so exists
# make check
${LOCAL}/protobuf: ${SRC}/protobuf
cd $< && ./autogen.sh && ./configure --prefix=$@ && $(MAKE) && $(MAKE) install
# Configure enable plugins? weak-threads?
${SRC}/libicu:
svn export https://ssl.icu-project.org/repos/icu/icu/trunk/source/ libicu
# The build fails if it does not find a license.html in the parent directory
# TODO: review remove CFLAGS and CXXFLAGS
# TODO: update prefix and target
${LOCAL}/libicu/lib/libicudata.so: ${SRC}/libicu
cd $< && \
touch ../license.html && \
trap "rm ../license.html" EXIT && \
./runConfigureICU Linux/ICC --prefix=${LOCAL}/libicu && \
$(MAKE) VERBOSE=1 && $(MAKE) install
#git clone --depth 1 --recursive https://github.com/boostorg/boost.git
#wget http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.gz &&
${SRC}/boost:
wget http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.bz2 && \
tar xvf boost_1_58_0.tar.gz && rm boost_1_58_0.tar.gz && mv boost_1_58_0 $@
# TODO: requires libicu?
#./b2 --build-dir=$${BOOST_BUILD_PATH} --prefix=$@ cflags="-parallel -qopenmp ${CFLAGS}" cxxflags="-parallel -qopenmp ${CFLAGS}" linkflags="${LDFLAGS}" address-model=64 toolset=intel install
${LOCAL}/boost: ${SRC}/boost ${LOCAL}/libicu/lib/libicudata.so
cd $< && \
./bootstrap.sh --prefix=$@ --with-toolset=intel-linux && \
export BOOST_BUILD_PATH=$(shell mktemp --directory --tmpdir=${SRC} --suffix=boost) && \
trap "rm -rf $${BOOST_BUILD_PATH}" EXIT && \
printf "using mpi : : <find-shared-library>mpi ;" > $${BOOST_BUILD_PATH}/user-config.jam && \
./b2 -q -d+2 --build-dir=$${BOOST_BUILD_PATH} --prefix=$@ cxxflags="-parallel -qopenmp -xCORE-AVX2 ${CXXFLAGS}" address-model=64 toolset=intel install
${SRC}/bamtools:
git clone --depth 1 https://github.com/pezmaster31/bamtools.git
# https://software.intel.com/en-us/forums/intel-c-compiler/topic/477556
${LOCAL}/bamtools: ${SRC}/bamtools
BUILD_DIR=$(shell mktemp --directory --tmpdir=${SRC} --suffix=.bamtools) && \
export CFLAGS="$(filter-out -std=gnu11,$(CFLAGS))"; \
export CXXFLAGS="$(filter-out -ipo,$(filter-out -std=c++11,$(CXXFLAGS)))"; \
trap "rm -rf $${BUILD_DIR}" EXIT && \
cd $${BUILD_DIR} && \
cmake -DCMAKE_INSTALL_PREFIX=$@ $< && \
make && make install
touch ${LOCAL}/bamtools
${SRC}/eXpress:
git clone --depth 1 https://github.com/adarob/eXpress.git
#
# No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the
# directory containing Boost libraries or BOOST_ROOT to the location of
# Boost.
#
# -lrt is required because the installed clib (ldd --version) 2.12 is less than 2.17
# where it was included inherently.
# See http://stackoverflow.com/a/32649327
#
# Add -qopenmp to resolve the following error:
# undefined reference tp __kmpc_begin
#${LOCAL}/express: ${SRC}/eXpress ${LOCAL}/bamtools ${LOCAL}/zlib ${LOCAL}/boost ${LOCAL}/protobuf
${LOCAL}/express: ${SRC}/eXpress ${LOCAL}/bamtools ${LOCAL}/zlib ${LOCAL}/protobuf
BUILD_DIR=$(shell mktemp --directory --tmpdir=$< --suffix=.express) && \
cd $${BUILD_DIR} && \
trap "rm -rf $${BUILD_DIR}" EXIT && \
sed -i 's:"$${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a":"$$ENV{LOCAL}/bamtools/lib/bamtools/libbamtools.a" "rt":g' $</src/CMakeLists.txt && \
sed -i 's:set(CMAKE_CXX_FLAGS ":set(CMAKE_CXX_FLAGS "-qopenmp :g' $</src/CMakeLists.txt && \
cmake -DCMAKE_C_FLAGS="-qopenmp" -DCMAKE_CXX_FLAGS="-qopenmp" -DCMAKE_INSTALL_PREFIX=$@ -DZLIB_ROOT=${LOCAL}/zlib -DPROTOBUF_LIBRARY=${LOCAL}/protobuf/lib/libprotobuf.a -DPROTOBUF_INCLUDE_DIR=${LOCAL}/protobuf/include -DGPERFTOOLS_TCMALLOC_LIB=${LOCAL}/gperftools/lib .. && \
make CFLAGS="-qopenmp ${CFLAGS}" CXXFLAGS="-qopenmp ${CXXFLAGS}" CPATH="${LOCAL}/bamtools/include/bamtools:${CPATH}" && make install
${SRC}/R:
wget https://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz && \
tar xvf R-3.2.2.tar.gz && rm R-3.2.2.tar.gz && \
mv R-3.2.2 R
#CFLAGS="${CFLAGS} -O3 -ipo -qopenmp -xHost" \
#CXXFLAGS="${CXXFLAGS} -O3 -ipo -openmp -xHost" \
#--with-blas="-lmkl_gf_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread" \
#--with-lapack \
# https://software.intel.com/en-us/articles/build-r-301-with-intel-c-compiler-and-intel-mkl-on-linux
${LOCAL}/R: ${SRC}/R
cd $< && ./tools/rsync-recommended && ./tools/rsync-recommended && \
./configure --prefix=$@ \
AR=ar LD=ld CC=gcc CXX=g++ CFLAGS="" CXXFLAGS="" LDFLAGS="" \
&& make && make install
${SRC}/RSEM:
git clone --depth=1 https://github.com/deweylab/RSEM.git
#sed -i '/:.*/ s/sam\/.*\b//g; s:sam/::g; s:libbam.a:-lbam:g' Makefile &&
${LOCAL}/RSEM: ${SRC}/RSEM ${LOCAL}/samtools
cd $< && \
find . -type f -exec sed -i 's/^\(CC\|CFLAGS\|AR\|LDFLAGS\)\s*=.*$$//g; s/-D_CURSES_LIB=1/-D_CURSES_LIB=0/g' {} + && \
sed -i 's:^CC = g++::g; s:^CFLAGS=.*:CFLAGS += -fast -c -I.:g; s:^COFLAGS.*:COFLAGS = -fast -c -I.:g; s:\$$(CC):\$${CC} $${CFLAGS}:g' Makefile && \
$(MAKE) && \
mkdir -p $@/bin && cp rsem-* $@/bin && \
cp rsem_perl_utils.pm $@/bin && cp WHAT_IS_NEW $@/bin
${SRC}/kallisto:
git clone --depth=1 https://github.com/pachterlab/kallisto.git
# FIXME: undeclared tcmalloc requirement
${LOCAL}/kallisto: ${SRC}/kallisto ${LOCAL}/zlib ${LOCAL}/hdf5
BUILD_DIR=$(shell mktemp --directory --tmpdir=$< --suffix=.kallisto) && \
cd $${BUILD_DIR} && \
cmake -DCMAKE_INSTALL_PREFIX=$@ -DHDF5_tcmalloc_minimal_LIBRARY_RELEASE=${LOCAL}/gperftools/lib/libtcmalloc_minimal.so -DZLIB_ROOT=${LOCAL}/zlib .. && \
make CXXFLAGS="$(filter-out -std=c++11,$(CXXFLAGS))" && make install
${LOCAL}/trimmomatic:
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.33.zip && \
unzip Trimmomatic-Src-0.33.zip && rm Trimmomatic-Src-0.33.zip && \
mv trimmomatic-0.33 $@ && \
cd $@ && ant
${SRC}/perl5:
git clone --depth=1 https://github.com/Perl/perl5.git
# http://www.gossamer-threads.com/lists/modperl/modperl/97948
#./Configure -Duse64bitall -Dusethreads -Dcc=icc -Dprefix=${LOCAL} -Dusedevel -Accflags='-fPIC -xHOST -fast' -de &&
${LOCAL}/perl: ${SRC}/perl5
cd $< && \
./Configure -Duse64bitall -Dusethreads -Dcc=icc -Dprefix=$@ -Dusedevel -Accflags='-fPIC -xHOST -O3' -de && \
$(MAKE) && $(MAKE) test; $(MAKE) install
${SRC}/trinityrnaseq:
git clone --depth 1 https://github.com/trinityrnaseq/trinityrnaseq.git
# express is an alternative dependency to RSEM
# http://trinityrnaseq.sourceforge.net/analysis/abundance_estimation.html
#
# bowtie2 supersedes bowtie, but some scripts still depend on bowtie
#cp -rv ${SRC}/trinityrnaseq ${BIN}
# TODO: restore express dependency
$ #$(MAKE) plugins
#${LOCAL}/trinityrnaseq: ${SRC}/trinityrnaseq ${LOCAL}/bowtie ${LOCAL}/bowtie2 ${LOCAL}/samtools ${LOCAL}/trimmomatic ${LOCAL}/RSEM ${LOCAL}/perl
#${LOCAL}/trinityrnaseq: ${SRC}/trinityrnaseq ${LOCAL}/bowtie ${LOCAL}/bowtie2 ${LOCAL}/samtools ${LOCAL}/trimmomatic ${LOCAL}/RSEM
${LOCAL}/trinityrnaseq: ${SRC}/trinityrnaseq ${LOCAL}/bowtie ${LOCAL}/bowtie2 ${LOCAL}/samtools
cd $< && \
sed -i 's|CC=gcc CXX=g++||g; s|\(^trinity_essentials: .*\)samtools|\1|g' $</trinity-plugins/Makefile && \
replace 'cd htslib && $$(MAKE)' 'cd htslib && sed -i "s/^\(CC\|CFLAGS\|AR\|LDFLAGS\)\s*=.*//g" Makefile && $(MAKE)' -- $</trinity-plugins/Makefile && \
find $< -type f -exec sed -i 's/^\(CC\|CXX\)\s*=.*//g; s/-openmp/-qopenmp/g' {} + && \
sed -i 's|-DMAKE_DATE=\x27"$$(DATE)"\x27 |-DMAKE_DATE=\x27"Fri Oct 23 18:07:50 CDT 2015"\x27 |g' Chrysalis/Makefile && \
$(MAKE) TRINITY_COMPILER=intel && cp -rv $< $@ && \
find $@/sample_data -type f -exec sed -i 's:./Trinity :./Trinity --grid_conf $@/hpc_conf/SLURM.test.conf :g' {} + && \
sed -i 's/queue_name/all/g' $@/hpc_conf/SLURM.test.conf
Raw
wrf.mk
${SRC}/hdf5:
wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.15-patch1.tar.bz2 && \
tar xvf hdf5-1.8.15-patch1.tar.bz2 && \
rm hdf5-1.8.15-patch1.tar.bz2 && \
mv hdf5-1.8.15-patch1 hdf5
# TODO: are cxx and fortran required
${LOCAL}/hdf5: ${SRC}/hdf5 ${LOCAL}/zlib
cd $< && \
CC=mpicc ./configure --prefix=$@ \
--enable-parallel \
--enable-cxx \
--enable-fortran \
--with-zlib=${LOCAL}/zlib && \
make && make test; make install
${SRC}/netcdf-c:
git clone --depth=1 https://github.com/Unidata/netcdf-c.git
# cmake did not respond to setting -DZLIB_ROOT
# hdf5 must be in PATH for cmake to find it
${LOCAL}/netcdf/lib64/libnetcdf.so: ${SRC}/netcdf-c ${LOCAL}/hdf5 ${LOCAL}/zlib
@PATH="${LOCAL}/hdf5:${PATH}"; \
BUILD_DIR=$(shell mktemp --directory --tmpdir=$< --suffix=.netcdf-c) && \
cd $${BUILD_DIR} && \
trap "rm -rf $${BUILD_DIR}" EXIT && \
cmake -DCMAKE_INSTALL_PREFIX=${LOCAL}/netcdf \
-DCMAKE_C_COMPILER=mpiicc \
-DZLIB_INCLUDE_DIR=${LOCAL}/zlib/include \
-DZLIB_LIBRARY=${LOCAL}/zlib/lib/libz.so $< && \
make && make install
${SRC}/netcdf-fortran:
git clone --depth=1 https://github.com/Unidata/netcdf-fortran.git
#trap "rm -rf $${BUILD_DIR}" EXIT &&
${LOCAL}/netcdf/netcdf-fortran: ${SRC}/netcdf-fortran ${LOCAL}/netcdf/lib64/libnetcdf.so
BUILD_DIR=${SRC}/netcdf-fortran/build; \
mkdir $${BUILD_DIR} && \
cd $${BUILD_DIR} && \
cmake -DCMAKE_INSTALL_PREFIX=${LOCAL}/netcdf --config Release .. && \
make FC=mpif90 F77=mpif90 CXX=mpicxx CC=mpicc && make install
#${SRC}/netcdf-cxx:
# git clone --depth=1 https://github.com/Unidata/netcdf-cxx4.git netcdf-cxx
#
#${LOCAL}/netcdf/lib64/netcdf-cxx4.so: ${SRC}/netcdf-cxx ${LOCAL}/netcdf/lib64/libnetcdf.so
# BUILD_DIR=$</build; \
# mkdir $${BUILD_DIR} && \
# trap "rm -rf $${BUILD_DIR}" EXIT && \
# cd $${BUILD_DIR} && \
# cmake -DCMAKE_INSTALL_PREFIX=${LOCAL}/netcdf --config Release .. && \
# make && make install
${SRC}/jasper:
wget https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip && \
unzip jasper-1.900.1.zip && \
rm jasper-1.900.1.zip && \
mv jasper-1.900.1 jasper
${LOCAL}/jasper: ${SRC}/jasper
cd $< && \
./configure --prefix=$@ && \
make && make install
${SRC}/WPS:
wget http://www2.mmm.ucar.edu/wrf/src/WPSV3.7.1.TAR.gz && \
tar xvf WPSV3.7.1.TAR.gz && \
rm WPSV3.7.1.TAR.gz
${SRC}/WRFV3:
wget http://www2.mmm.ucar.edu/wrf/src/WRFV3.7.1.TAR.gz && \
tar xvf WRFV3.7.1.TAR.gz && \
rm WRFV3.7.1.TAR.gz
# https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11504.html
# The netcdf-fortran interface provides netcdf.inc
${LOCAL}/wrf: ${SRC}/WRFV3 ${LOCAL}/netcdf/lib64/libnetcdf.so ${LOCAL}/netcdf/netcdf-fortran
cd $< && \
expect -c 'spawn ./configure; \
expect "Enter selection \\\[1-63\\\] :"; \
send "21\r"; \
expect "Compile for nesting? \\\(1=basic, 2=preset moves, 3=vortex following\\\) \\\[default 1\\\]: "; \
send "1\r"; \
expect eof' && \
sed -i 's|-xAVX|-xCORE-AVX2|; s|-openmp|-qopenmp|g' configure.wrf && \
./compile em_real
# Error : Not building geogrid. Check whether WRF is compiled in /home/jlt256/local/src/WPS/../WRFV3
${LOCAL}/wps: ${SRC}/WPS ${LOCAL}/wrf ${LOCAL}/netcdf/lib64/libnetcdf.so ${LOCAL}/jasper
cd $< && \
expect -c 'spawn ./configure; \
expect "Enter selection \\\[1-40\\\] :"; \
send "22\r"; \
expect eof' && \
./compile
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