Makefile for building INLA in Debian:Stretch

Makefile

## Makefile for downloading the source code and building
## a binary package of R-INLA on Debian:Stretch
## using a custom version of R and Intel MKL
## Intended for use by : Institute for Health Metrics and Evaluation
##
## Maintained by : Nafis Sadat, [email protected]
##


#### 2018/01/28 Update: removing r-mathlib and adding metis5
#### 2018/03/23 Update: update path to new MKL version installation
#### 2018/04/25 Update: remove metis installs (pointing to Metis 5.1.0 instead) 
#### 2018/05/03 Update: pointing to custom Metis install 
#### 2018/05/13 Update: remove Metis pointer, and update MKL paths (also remove mkldnn)
#### 2018/05/22 Update: Point to older branch (18.05.08)
#### 2018/05/23 Update: Use own forked version with Pardiso linked in 'inla' Makefile
#### 2018/06/10 Update: INLA main repo fixed Pardiso issue, reverting to that; x11 fmesher
#### 2018/06/11 Update: Untagging hg clone, and cleaning up some flags so that fmesher actually builds
#### 2018/06/15 Update: New MKL build (3.222)
#### 2018/07/16 Update: Add bunch more flags to the other Intel products
#### 2018/07/18 Update: AVX2 is not recommended
#### 2018/10/02 Update: Rename explicit folder names from 2018 MKL reference to generic path

#### NOTE: -I/opt/R/lib/R/include/ MUST be included explicitly in the FLAGS variable

## NOTE: Changes to the Makefile should be made as needed for compilers and flags
SHELL = /bin/bash

## This Makefile is only supported for platform 'linux':
PLATFORM = linux
## Must match the machine architecture (32 or 64):
BITS = 64
## Compiler flags

## Set up the flags for MKL bindings 
MKLROOT=/opt/intel/compilers_and_libraries/linux/mkl
MKL=-L/opt/intel/compilers_and_libraries/linux/mkl/lib/intel64_lin -lRmath -Wl,--no-as-needed -lmkl_gf_lp64 -Wl,--start-group -lmkl_gnu_thread -lmkl_core -Wl,--end-group -fopenmp  -dl -lpthread -lm

## Point to the R headers
INLA_LIBR="/opt/R/lib/R/lib -I/opt/R/lib/R/include/"

## Common compile flags

## Common compile flags
FLAGS = -m64 -w -g -O3 -mtune=generic -mavx -msse2 -msse3 -msse4.1 -msse4.2 -mfpmath=sse \
	-msse2 -L/opt/R/lib/R/lib -lR -lRmath \
	-I/opt/R/lib/R/include/ \
	-L/usr/local/lib64/ \
	-funroll-loops -fPIC -ftracer -pipe \
	-I/usr/include -I${MKLROOT}/include \
	-L/usr/local/lib -L/usr/lib -L${MKLROOT}/lib/intel64_lin \
	-L/opt/intel/tbb/lib/intel64_lin/gcc4.7 -L/opt/intel/daal/lib/intel64_lin
	 


FLAGS_INLA = $(FLAGS) -std=gnu99 -fopenmp
FLAGS_FMESHER = $(FLAGS) -std=c++11

## For Debian or Ubuntu package installation in lib-install:
APT=aptitude

## Path configuration:
MAINDIR=$(PWD)
PREFIX = $(MAINDIR)/local
BINPREFIX = $(PREFIX)/bin/$(PLATFORM)
LIBPREFIX = $(PREFIX)/lib
INCPREFIX = $(PREFIX)/include

## Compiler options:
#CC=mpicc
#CXX=mpic++
#FC=mpifort

CC=gcc
CXX=g++
FC=gfortran
LD=$(CXX)
ARGS = CC="$(CC)" CXX="$(CXX)" FC="$(FC)" LD="$(LD)"

all :;
	@(echo "";\
	echo "Edit this Makefile, especially the 'FLAGS_COMMON' variable,";\
	echo "check if you need to run 'sudo $(MAKE) lib-install', then do";\
	echo "";\
	echo "	$(MAKE) lib-install";\
	echo "	$(MAKE) download";\
	echo "	$(MAKE) bin";\
	echo "	$(MAKE) package";\
	echo "";\
	echo "If all goes well, you should have binaries for inla and fmesher at";\
	echo "";\
	echo "	$(BINPREFIX)";\
	echo "";\
	echo "and an INLA_*.tgz binary R package in your working directory.";\
	echo "";\
	echo "To later download and build an updated package, do";\
	echo "";\
	echo "	$(MAKE) update";\
	echo "";\
	echo "To build a package for the JSS 2015 paper, do";\
	echo "";\
	echo "	$(MAKE) download-jss2014 && $(MAKE) bin && $(MAKE) package";\
	echo "";\
	echo "Note: Not all lapack versions contain all the needed routines,";\
	echo "so make sure that /usr/lib/lapack/liblapack.so is selected in";\
	echo "";\
	echo "	sudo update-alternatives --config liblapack.so";\
	echo "";\
	echo "It's possible to link to both lapack and lapack_atlas.";\
	echo "";\
	echo "For x11 enabled fmesher, use lib-install-x11 and bin-x11.";\
	echo "";\
	echo "To deactivate the use of libR, use '$(MAKE) bin INLA_WITHOUT_LIBR=1'.";\
	echo "";)

## Package list updated 2017-12-01
LIBPKG = libgsl0-dev zlib1g-dev \
	 libsuitesparse-dev \
	 libxdmcp-dev libx11-dev libc6-dev \
	 libmuparser-dev \
	 libmetis-dev libmetis5-dbg libmetis5
LIBPKGX = $(LIBPKG) libx11-dev
 
lib-install :
	$(APT) install -y $(LIBPKG)

lib-install-x11 :
	$(APT) install $(LIBPKGX)

init :
	@mkdir -p $(LIBPREFIX)
	@mkdir -p $(BINPREFIX)
	@mkdir -p $(INCPREFIX)

download : init
	@( test -d inla && $(MAKE) download-update ) || \
	( rm -rf inla && hg clone https://bitbucket.org/hrue/r-inla inla )
	@ln -sTf $(PREFIX) inla/local

download-update : init
	@cd inla ; hg pull ; hg update
	@ln -sTf $(PREFIX) inla/local

download-jss2014 :
	@$(MAKE) download
	@cd inla ; hg update -r jss2014
	@ln -sTf $(PREFIX) inla/local

bin :
	$(MAKE) taucs
	$(MAKE) fmesher
	$(MAKE) GMRFLib
	$(MAKE) inla
	
bin-x11 :
	$(MAKE) taucs
	$(MAKE) fmesher-x11
	$(MAKE) GMRFLib
	$(MAKE) inla
	
update :
	$(MAKE) download-update
	$(MAKE) bin
	$(MAKE) package

fmesher-x11:
	$(MAKE) -C inla/fmesher PREFIX=$(PREFIX) $(ARGS) -k clean
	$(MAKE) -C inla/fmesher PREFIX=$(PREFIX) FMESHER_USE_X=1  FLAGS="$(FLAGS) -I/usr/include -I/usr/include/gsl -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS) EXTLIBS="-lX11 -lgsl -lgslcblas -lxcb -lpthread -lXau -lXdmcp"
	$(MAKE) -C inla/fmesher PREFIX=$(PREFIX) $(ARGS) install
	@rsync -a $(PREFIX)/bin/fmesher $(BINPREFIX)/fmesher$(BITS)
	@rm $(PREFIX)/bin/fmesher

fmesher :
	$(MAKE) -C inla/fmesher PREFIX=$(PREFIX) $(ARGS) -k clean
	$(MAKE) -C inla/fmesher PREFIX=$(PREFIX) FLAGS="$(FLAGS) -I/usr/include -I/usr/include/gsl -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS) EXTLIBS="-lX11 -lgsl -lgslcblas -lxcb -lpthread -lXau -lXdmcp"
	$(MAKE) -C inla/fmesher PREFIX=$(PREFIX) $(ARGS) install
	@rsync -a $(PREFIX)/bin/fmesher $(BINPREFIX)/fmesher$(BITS)
	@rm $(PREFIX)/bin/fmesher

inla :
	ln -sTf /usr/include $(INCPREFIX)/muParser
	$(MAKE) -C inla/inlaprog PREFIX=$(PREFIX) FLAGS="-lRmath  $(FLAGS) -I/usr/include -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS) -k clean 
	$(MAKE) -C inla/inlaprog PREFIX=$(PREFIX) FLAGS="-lRmath  $(FLAGS) -I/usr/include -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS)
	$(MAKE) -C inla/inlaprog PREFIX=$(PREFIX) FLAGS="-lRmath  $(FLAGS) -I/usr/include -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS) install
	@rsync -a $(PREFIX)/bin/inla $(BINPREFIX)/inla$(BITS)
	@rm $(PREFIX)/bin/inla $(PREFIX)/bin/inla-snapshot

GMRFLib :
	$(MAKE) -C inla/gmrflib PREFIX=$(PREFIX) FLAGS="$(FLAGS) -lRmath -I/usr/include -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS) -k clean
	$(MAKE) -C inla/gmrflib PREFIX=$(PREFIX) FLAGS="$(FLAGS) -lRmath -I/usr/include -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS)
	$(MAKE) -C inla/gmrflib PREFIX=$(PREFIX) FLAGS="$(FLAGS) -lRmath -I/usr/include -I/opt/R/lib/R/include/ -I${MKLROOT}/include ${MKL}" $(ARGS) install

sync-taucs :
	mkdir -p $(MAINDIR)/tmp
	-rm -rf $(MAINDIR)/tmp/taucs-2.2--my-fix
	cp inla/extlibs/taucs-2.2--my-fix.tgz $(MAINDIR)/tmp/
	cd $(MAINDIR)/tmp ; tar -zxf taucs-2.2--my-fix.tgz

taucs : sync-taucs
	$(MAKE) -C $(MAINDIR)/tmp/taucs-2.2--my-fix CFLAGS="$(FLAGS)" FFLAGS="$(FLAGS)" $(ARGS) -k clean
	$(MAKE) -C $(MAINDIR)/tmp/taucs-2.2--my-fix CFLAGS="$(FLAGS)" FFLAGS="$(FLAGS)" $(ARGS)
	@cp -v -f $(MAINDIR)/tmp/taucs-2.2--my-fix/lib/linux/libtaucs.a $(PREFIX)/lib

package :
	@rm -f inla/INLA_*.tgz
	cd inla ; utils/build-package-bin $(PREFIX)/bin $(MAINDIR)/tmp

clean :
	rm -rf inla

.PHONY: all inla GMRFLib taucs download download-update update fmesher bin init download-jss2014 sync-taucs package clean