--- imach/src/Makefile	2015/01/03 16:33:27	1.51
+++ imach/src/Makefile	2015/04/23 12:02:12	1.58
@@ -1,7 +1,7 @@
-VERSION=0.98p
-COPYRIGHT=Copyright (C)  2002-2015 INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)
-#IMACHSETUPVERSION=ilc64
-IMACHSETUPVERSION=mvc
+VERSION=0.98q1
+COPYRIGHT=Copyright (C)  2002-2015 INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121) - Intel Software 2015
+IMACHSETUPVERSION=ilc # This is for Windows only
+#IMACHSETUPVERSION=mvc
 
 #       Linux
 # make _linux=1 imachopt
@@ -20,7 +20,8 @@ IMACHSETUPVERSION=mvc
 #  valgrind  --dsymutil=yes --leak-check=full --show-leak-kinds=all --track-origins=yes ~/Documents/imachcvs/imach/src/imach-1.129cvsmac radlc-1.129.imach
 
 #        Windows
-# make _windowsonosx=1 imachILC64-setup (touch setup.iss.in) #binary should have been compiled on Windows with cl
+# make _windowsonosx=1 imachILC-setup (touch setup.iss.in) #binary should have been compiled on Windows with Intel
+# make _windowsonosx=1 imachILC64-setup (touch setup.iss.in) #binary should have been compiled on Windows with Intel
 # make _windowsonosx=1 imachMVC-setup (touch setup.iss.in) #binary should have been compiled on Windows with cl
 # make _windowsonosx=1 imachMVC-noreg-setup
 #
@@ -42,7 +43,9 @@ IMACHSETUPVERSION=mvc
 ##SETUPCOMP=  "C:\Program Files\Inno Setup 3\Compil32.exe"
 #TESTFILE=$$HOME/Documents/Recherches/REVES/SAITO/Tokyo2014/adlc-test-mac/adecode-1.142c.imach
 #TESTFILE=$(HOME)/Documents/Recherches/REVES/carol/carol-june2014/educadlmwt24.imach
-TESTFILE=$(HOME)/Documents/Recherches/REVES/Biaspar/biaspar-wopowell.imach
+#TESTFILE=$(HOME)/Documents/Recherches/REVES/Biaspar/biaspar-wopowell.imach
+#TESTFILE=$(HOME)/Documents/Recherches/REVES/Biaspar/rbiaspar-098p.imach
+TESTFILE=$(HOME)/Documents/Recherches/REVES/Aaron/brouard/results/COVARAITE_94/rmypar24pis1cov1-age.imach
 #TESTFILE=$(HOME)/Documents/Recherches/REVES/SAITO/Tokyo2014/adlc-test-mac/adecode-1.142c.imach
 #TESTFILE=$(HOME)/Documents/Recherches/REVES/SAITO/Tokyo2014/adlc_test_magei4/radlc_often.imach
 #CC= gcc -v
@@ -52,9 +55,12 @@ GCC= gcc
 ifdef _macosx
 # Mac OS/X version
 LFLAGS= -g -lm 
-CFLAGS= -g -DDEBUG 
+#CFLAGS= -g -DDEBUG 
+CFLAGS= -g 
 LFLAGSOPT= -O3 -lm 
 CFLAGSOPT= -O3 
+CP= cp
+CROSSCOMPILATION= -DCROSS=0
 UNIX2DOS= echo "Unix2dos " 
 DSYMUTIL= dsymutil
 STRIP= strip
@@ -90,6 +96,7 @@ LFLAGS= -g
 CFLAGS= -g
 LFLAGSOPT= -O3 -lm
 CFLAGSOPT= -O3
+CROSSCOMPILATION= -DCROSS=1
 CP= cp
 UNIX2DOS= unix2dos
 SETUPCOMP= wine "C:////Program Files////Inno Setup 4////Compil32.exe"
@@ -105,6 +112,7 @@ LFLAGS= -g
 CFLAGS= -g
 LFLAGSOPT= -O3 -s
 CFLAGSOPT= -O3
+CROSSCOMPILATION= -DCROSS=1
 UNIX2DOS= unix2dos
 SETUPCOMP= ~/bin/InnoSetup5Playonmac
 CP= cp
@@ -118,6 +126,7 @@ LFLAGS= -g
 CFLAGS= -g
 LFLAGSOPT= -O3 -lm -s
 CFLAGSOPT= -O3
+CROSSCOMPILATION= -DCROSS=1
 UNIX2DOS= unix2dos
 SETUPCOMP= ~/bin/InnoSetup5Playonmac
 CP= cp
@@ -134,7 +143,10 @@ ifdef _intel64onosx
 GCC=/opt/intel/bin/icc
 CFLAGS= -m64 -g -std=c99
 LFLAGS= -g -m64
+#CFLAGSOPT= -O3 -m64 -g -std=c99 -no-prec-div idem
+#CFLAGSOPT= -O3 -m64 -g -std=c99 -xSSSE3_ATOM 402
 CFLAGSOPT= -O3 -m64 -g -std=c99
+CROSSCOMPILATION= -DCROSS=0
 IGNORE :=$(shell bash -c "source /opt/intel/bin/iccvars.sh intel64; env | sed 's/=/:=/' | sed 's/^/export /' > makeenv")
 include makeenv
 #lipo -create -arch i386 HelloWorld_32 -arch x86_64 HelloWorld_64 -output HelloWorld
@@ -152,6 +164,7 @@ GCC=/opt/intel/bin/icc
 CFLAGS= -m32 -g -std=c99
 LFLAGS= -g -m32
 CFLAGSOPT= -O3 -m32 -g -std=c99
+CROSSCOMPILATION= -DCROSS=0
 IGNORE :=$(shell bash -c "source /opt/intel/bin/iccvars.sh ia32; env | sed 's/=/:=/' | sed 's/^/export /' > makeenv")
 include makeenv
 #lipo -create -arch i386 HelloWorld_32 -arch x86_64 HelloWorld_64 -output HelloWorld
@@ -187,6 +200,7 @@ LFLAGS= -g
 CFLAGS= -g
 LFLAGSOPT= -O3 -s -lm
 CFLAGSOPT= -O3
+CROSSCOMPILATION= -DCROSS=1
 TAR= /sw/bin/gnutar
 UNIX2DOS= unix2dos
 SETUPCOMP= ~/bin/InnoSetup5Playonmac
@@ -196,7 +210,9 @@ endif
 
 ifdef _linux
 #CFLAGS= -g -DUNIX -DDEBUGHESS
-CFLAGS= -g -DDEBUG
+#CFLAGS= -g -DDEBUG -DFIXMNBRAK
+#CFLAGS= -g -DDEBUG 
+CFLAGS= -g
 LFLAGS= -g -lm
 IGSL= -I/usr/include/gsl
 LGSL= -lgsl -lgslcblas
@@ -204,6 +220,7 @@ INLOPT= -I/usr/local/include
 LNLOPT= -lm -L/usr/local/lib -lnlopt
 CFLAGSOPT= -O3 -g
 LFLAGSOPT= -O3 -g -lm
+CROSSCOMPILATION= -DCROSS=0
 UNIX2DOS= unix2dos
 SETUPCOMP= wine "C:////Program Files////Inno Setup 4////Compil32.exe"
 BINVERSION=LINUXnative
@@ -220,7 +237,8 @@ TMPNOREGSETUPSCRIPT=noreg-setup.iss
 TMPSCRIPTIN=setup.iss.in
 APPLICATION=IMaCh
 APPNAME=$(APPLICATION)-$(VERSION)
-GNUPLOTVERSION=4.0
+APPCOMPILATIONMODE=$(IMACHSETUPVERSION)
+GNUPLOTVERSION=4.6
 LICENSE=Copying
 TMPSETUPEXE=imach-$(VERSION)-$(IMACHSETUPVERSION)-setup.exe
 TMPNOREGSETUPEXE=imach-$(VERSION)-$(IMACHSETUPVERSION)-noreg-setup.exe
@@ -232,6 +250,7 @@ setup.iss: setup.iss.in
 		s/@NOTINNOREG@//g; \
 		s/@NOREG@//g; \
 		s/@IMACHSETUPVERSION@/$(IMACHSETUPVERSION)/g; \
+		s/@APPCOMPILATIONMODE@/$(APPCOMPILATIONMODE)/g; \
 		s/@VERSION@/$(VERSION)/g; \
 		s/@GNUPLOTVERSION@/$(GNUPLOTVERSION)/g; \
 		s/@INFOBEFOREFILE@/$(INFOBEFOREFILE)/g; \
@@ -281,21 +300,26 @@ imachcyg-noreg-setup: imachcygopt.exe no
 	$(SETUPCOMP) /cc $(TMPNOREGSETUPSCRIPT)
 	cp Output/$(TMPNOREGSETUPEXE) imachcyg-noreg-setup
 
-imachILC64-setup: IMaCh-ilc64.exe setup.iss
+# both 32 and 64 executables should have been built on Windows with Intel compiler.
+imachILC-setup: IMaCh-ilc64-$(VERSION).exe IMaCh-ilc32-$(VERSION).exe setup.iss
+	pwd
+	$(SETUPCOMP) /cc setup.iss
+	$(CP) Output/$(TMPSETUPEXE) imachILC-setup
+
+imachILC64-setup: IMaCh-ilc64-$(VERSION).exe setup.iss
 	pwd
-	$(CP) IMaCh-ilc64.exe imach.exe
+	$(CP) IMaCh-ilc64-$(VERSION).exe imach.exe
 	$(SETUPCOMP) /cc setup.iss
 	$(CP) Output/$(TMPSETUPEXE) imachILC64-setup
 
-imachILC64-noreg-setup: IMaCh-ilc64.exe noreg-setup.iss
+imachILC64-noreg-setup: IMaCh-ilc64-$(VERSION).exe noreg-setup.iss
 	touch setup.iss.in
-	$(CP) IMaCh-ilc64.exe imach.exe
 	$(SETUPCOMP) /cc $(TMPNOREGSETUPSCRIPT)
 	$(CP) Output/$(TMPSETUPEXE) imachILC64-noreg-setup
 
-imachILC32-setup: IMaCh-ilc32.exe setup.iss
+imachILC32-setup: IMaCh-ilc32-$(VERSION).exe setup.iss
 	touch setup.iss.in
-	$(CP) IMaCh-ilc32.exe imach.exe
+	$(CP) IMaCh-ilc32-$(VERSION).exe imach.exe
 	$(SETUPCOMP) /cc setup.iss
 	$(CP) Output/$(TMPSETUPEXE) imachILC32-setup
 
@@ -309,7 +333,7 @@ imachMVC-setup: imachMVC.exe setup.iss
 	touch setup.iss.in
 	$(CP) imachMVC.exe imach.exe
 	$(SETUPCOMP) /cc setup.iss
-	$(CP) Output/$(TMPSETUPEXE) imachcyg-setup
+	$(CP) Output/$(TMPSETUPEXE) imachMVC-setup
 
 # imachcyg-noreg-setup : imachcygopt imachcygopt.o setup.iss.in noreg-setup.iss $(TMPNOREGSETUPEXE)
 imachMVC-noreg-setup: imachMVC.exe noreg-setup.iss
@@ -323,14 +347,26 @@ simach : simach.o
 simach.o : simach.c 
 	$(CC) $(CFLAGS) -DGSL -c simach.c
 
-imach : imach.o 
+imachtest: imachtest.o 
+	$(CC) $(LFLAGS) -o imachtest imachtest.o
+ifdef _macosx
+	$(DSYMUTIL) imachtest
+endif
+
+imach: imach.o 
 	$(CC) $(LFLAGS) -o imach imach.o
 ifdef _macosx
 	$(DSYMUTIL) imach
 endif
 
 imach.o : imach.c 
-	 $(CC) $(CFLAGS) -DPOWELL -c imach.c
+	 $(CC) $(CFLAGS) $(CROSSCOMPILATION)  -c imach.c
+#	 $(CC) $(CFLAGS) $(CROSSCOMPILATION) -DDEBUGBRENT -c imach.c
+
+imachtest.o : imach.c 
+	 $(CC) $(CFLAGS) $(CROSSCOMPILATION) -DPOWELLORIGINAL -DNRCORIGINAL -DINFINITYORIGINAL -DDEBUGBRENT -o imachtest.o -c imach.c
+
+#	 $(CC) $(CFLAGS) $(CROSSCOMPILATION)  -DFIXMNBRAK -o imachtest.o -c imach.c
 
 # http://msdn.microsoft.com/en-us/library/abx4dbyh%28v=vs.100%29.aspx
 imachcl: imach.c
@@ -365,7 +401,7 @@ imachBOBYQAopt.o : imach.c
 
 imachopt : imachopt.o 
 	$(CC) $(LFLAGSOPT) -o imachopt imachopt.o
-	ln -f imachopt imach
+#	ln -f imachopt imach
 	$(CP) imachopt Output/imachopt$(VERSION)-$(BINVERSION)
 	$(CP) -f imach ../bin
 ifdef _intel64onosx
@@ -421,8 +457,9 @@ imachdmg : imachopt.o create-dmg applet
 #	./create-dmg --volname "IMaCh $(VERSION)" imach$(VERSION).dmg imach$(VERSION).app
 #	./createdmg2.sh --volname "IMaCh $(VERSION)" imach$(VERSION).dmg imach$(VERSION)
 
-upload:
+md5:
 	ls Output/* | xargs md5sum
+upload:
 	rsync -v Output/* brouard@henry.ined.fr:/home/euroreves/html/imach/
 
 imachcyg : imachcyg.o