corburn/Makefile

## 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


## 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

## 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

## 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 $< $@

## 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

## 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' $< $@


## 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

## 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
	${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
	${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
	# 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
	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 $< $@
	################################################################################
	# LOCAL is the path prefix where user compiled programs are installed
	################################################################################
	if [[ -z "$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
	.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' $< $@
	${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
	${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