Add some compilation options to the Makefile.

It is now possible to use an external lapack version. If using
directly the Makefile, use
   make pybinding USE_MKL=1 LINKER_FLAGS=-L$(MKLROOT) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential
If using the install script, you can choose to edit each option of the compilation

src/install.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/bash
 # vim: set ts=4 sw=4 sts noet mouse=a fdm=indent:
 
 BYPASS="n"
@@ -10,6 +10,13 @@ DATE=$(date +%Y%m%d_%H%M%S)
 LOGFILE="${HOME}/msspec_install_${DATE}.log"
 GETOUTFILE=$(mktemp)
 
+USE_MKL=0
+LINKER_FLAGS=""
+COMP=gfortran
+COMP_OPTS="-O2 -ffast-math -fno-automatic"
+DEBUG_MODE=0
+
+
 trap "abort_install" INT
 trap "error_exit" HUP QUIT ILL ABRT
 
@@ -101,6 +108,7 @@ wrap () {
 	log_message "================================================================================"
 	log_message "$2"
 	log_message "================================================================================"
+	log_message "$1"
 	if [ "$DEBUG" = y ]; then
 		printf "%s...\n" "$2"
 		(eval "$1" || echo $? >"${GETOUTFILE}") | tee -a "${LOGFILE}"
@@ -211,9 +219,38 @@ local_install () {
 	# check dependencies
 	wrap "check_dependencies" "Checking dependencies"
 
-	# build the Fortran code
+	# Do we have Lapack.
-	wrap "make pybinding VERBOSE=1" "Building Phagen and Spec Python dynamic library"
+	log_message "Checking if lapack is installed..."
+	pkg-config --exists lapack
+	if test "$?" -ne 0; then
+		HAS_LAPACK="n"
+		log_message "No, will use included routines\n"
+	else
+		HAS_LAPACK="y"
+		log_message "Ok\n"
+	fi
 
+	if [ x"${HAS_LAPACK}" = xy ]; then
+		read_yes_no "You have Lapack. Do you wish to link with installed lapack" "y"
+		if [ x"${ANSWER}" = xy ]; then
+			USE_MKL=1
+			LINKER_FLAGS=`pkg-config --libs lapack`
+		fi
+	fi
+
+	# ask for expert options
+	read_yes_no "Do you wish to edit compilation options" "n"
+	if [ x"${ANSWER}" = xy ]; then
+		read -ep "FORTRAN COMPILER...................> " -i "${COMP}" COMP
+		read -ep "COMPILER OPTIONS...................> " -i "${COMP_OPTS}" COMP_OPTS
+		read -ep "USE EXTERNAL LAPACK (0:no, 1:yes)..> " -i "${USE_MKL}" USE_MKL
+		read -ep "LINKER FLAGS.......................> " -i "${LINKER_FLAGS}" LINKER_FLAGS
+		read -ep "INCLUDE DEBUG SYMBOLS (0:no, 1:yes)> " -i "${DEBUG_MODE}" DEBUG_MODE
+	fi
+
+	# build the Fortran code
+	wrap "make pybinding VERBOSE=1 USE_MKL=${USE_MKL} LINKER_FLAGS=\"${LINKER_FLAGS}\" COMP=\"${COMP}\" COMP_OPTS=\"${COMP_OPTS}\" DEBUG=\"${DEBUG_MODE}\"" "Building Phagen and Spec Python dynamic library"
+	exit
 	# build the source distribution
 	wrap "make sdist VERBOSE=1" "Building msspec python package"
 

src/msspec/spec/fortran/Makefile

@@ -1,46 +1,52 @@
 COMP:=gfortran
 F2PY:=f2py3
 
-COMP_OPTS:= -O2 -ffast-math
+COMP_OPTS:= -O2 -ffast-math -fno-automatic
+LINKER_FLAGS:=
 F2PY_OPTS:=
 
 DEBUG:=0
+USE_MKL:=0
+
+
  
 includes := -I./memalloc/ -I./cluster_gen/ -I./common_sub -I./renormalization 
 includes += -I./phd_se_noso_nosp_nosym 
 includes += -I./eig/common -I./eig/mi -I./eig/pw
 
 memalloc_src:=memalloc/dim_mod.f memalloc/modules.f memalloc/allocation.f 
-memalloc_obj:=$(patsubst %.f,%.o, $(memalloc_src))
-
 cluster_gen_src:=$(wildcard cluster_gen/*.f)
-cluster_gen_obj:=$(patsubst %.f,%.o, $(cluster_gen_src))
-
 common_sub_src:=$(wildcard common_sub/*.f)
-common_sub_obj:=$(patsubst %.f,%.o, $(common_sub_src))
-
 renormalization_src:=$(wildcard renormalization/*.f)
-renormalization_obj:=$(patsubst %.f,%.o, $(renormalization_src))
 
 phd_se_noso_nosp_nosym_src:=$(filter-out phd_se_noso_nosp_nosym/main.f, $(wildcard phd_se_noso_nosp_nosym/*.f))
-phd_se_noso_nosp_nosym_obj:=$(patsubst %.f,%.o, $(phd_se_noso_nosp_nosym_src))
-
 phd_mi_noso_nosp_nosym_src:=$(filter-out phd_mi_noso_nosp_nosym/main.f, $(wildcard phd_mi_noso_nosp_nosym/*.f))
-phd_mi_noso_nosp_nosym_obj:=$(patsubst %.f,%.o, $(phd_mi_noso_nosp_nosym_src))
 
 eig_common_src:=$(wildcard eig/common/*.f)
-eig_common_obj:=$(patsubst %.f,%.o, $(eig_common_src))
-
 eig_mi_src:=$(filter-out eig/mi/main.f, $(wildcard eig/mi/*.f))
-eig_mi_obj:=$(patsubst %.f,%.o, $(eig_mi_src))
-
 eig_pw_src:=$(filter-out eig/pw/main.f, $(wildcard eig/pw/*.f))
-eig_pw_obj:=$(patsubst %.f,%.o, $(eig_pw_src))
+
+ifeq ($(USE_MKL), 1)
+    eig_common_src:=$(filter-out $(wildcard eig/common/lapack*.f), $(eig_common_src))
+    phd_mi_noso_nosp_nosym_src:=$(filter-out $(wildcard phd_mi_noso_nosp_nosym/lapack*.f), $(phd_mi_noso_nosp_nosym))
+    LINKER_FLAGS:=$(shell pkg-config --libs lapack)
+#    MKL:=-L$(MKLROOT) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential
+endif
 
 objects_src := $(memalloc_src) $(cluster_gen_src) $(common_sub_src) 
 objects_src += $(renormalization_src) $(phd_se_noso_nosp_nosym_src)
 objects_src += $(eig_common_src) $(eig_mi_src) $(eig_pw_src)
 objects_src += $(phd_mi_noso_nosp_nosym_src)
+
+memalloc_obj:=$(patsubst %.f,%.o, $(memalloc_src))
+cluster_gen_obj:=$(patsubst %.f,%.o, $(cluster_gen_src))
+common_sub_obj:=$(patsubst %.f,%.o, $(common_sub_src))
+renormalization_obj:=$(patsubst %.f,%.o, $(renormalization_src))
+phd_se_noso_nosp_nosym_obj:=$(patsubst %.f,%.o, $(phd_se_noso_nosp_nosym_src))
+phd_mi_noso_nosp_nosym_obj:=$(patsubst %.f,%.o, $(phd_mi_noso_nosp_nosym_src))
+eig_common_obj:=$(patsubst %.f,%.o, $(eig_common_src))
+eig_mi_obj:=$(patsubst %.f,%.o, $(eig_mi_src))
+eig_pw_obj:=$(patsubst %.f,%.o, $(eig_pw_src))
 objects:=$(patsubst %.f,%.o, $(objects_src))
 
 libs_targets := phd_se_noso_nosp_nosym.target phd_mi_noso_nosp_nosym.target eig_mi.target eig_pw.target
@@ -58,6 +64,8 @@ export COMP_OPTS
 
 .PHONY: clean
 
+truc:
+	@echo $(eig_common_src)
 
 pybinding: $(libs_targets)
 
@@ -68,17 +76,17 @@ phd_se_noso_nosp_nosym.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_o
 
 phd_mi_noso_nosp_nosym.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(phd_mi_noso_nosp_nosym_obj)
 	@echo "building Python binding..."      
-	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) phd_mi_noso_nosp_nosym/main.f
+	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) phd_mi_noso_nosp_nosym/main.f $(LINKER_FLAGS)
 	@touch $@
 
 eig_mi.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_mi_obj)
 	@echo "building Python binding..."      
-	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/mi/main.f
+	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/mi/main.f $(LINKER_FLAGS)
 	@touch $@
 
 eig_pw.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_pw_obj)
 	@echo "building Python binding..."      
-	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/pw/main.f
+	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/pw/main.f $(LINKER_FLAGS)
 	@touch $@
 
 %.o: %.f