Makefile for Linux 64

Jim Li megjim1 at GMAIL.COM
Fri Apr 17 04:11:06 CEST 2009


Dear Guillaume,

That's great! I'm downloading them now. Thanks a lot for your wonderful 
help, :)

Jim

On Wed, 15 Apr 2009 11:27:10 +0100, Guillaume Flandin 
<gflandin at FIL.ION.UCL.AC.UK> wrote:

>Dear Jim,
>
>some 64bit Linux MEX files for SPM2 are available from here:
>ftp://ftp.fil.ion.ucl.ac.uk/spm/spm2_updates/
>
>The website mentioned in previous email is the SPM wikibooks:
>http://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Linux#Compilation_not
es_for_SPM2:
>
>I also attach a SPM2 Makefile that contains instructions for Linux64
>compilation, in case the provided compiled MEX files do not work on your
>platform.
>
>Best regards,
>Guillaume.
>
>
>Jim Li wrote:
>> Dear FTer:
>>
>> We're thinking of buying a 64-bit Quad-core PC w/ big memory(>=16GB), 
then
>> install a Linux OS (CentOS 4) and run Fieldtrip on it. According to the first
>> question asked by Christine below, there seems to be a problem w/ SPM2. 
Is
>> that still an issue or is it solved by now? Are there any other issues to pay
>> attention to w/ 64-bit linux?
>>
>>
>> Thanks a lot,
>>
>> Jim
>>
>> On Tue, 18 Sep 2007 17:03:59 +0200, Christine Tillmann <tillmann at MPIH-
>> FRANKFURT.MPG.DE> wrote:
>>
>>> Hi,
>>>
>>> we are trying to get the fieldtrip beamforming on our linux 64 bit
>>> systems going. As we understand it, there is currently no way around
>>> using spm2. Spm2's mex files however are not compiled for linux 64 bit
>>> and the makefile that's available on the web suffers from the tab/space
>>> delimiter problem.
>>> Does anyone have a makefile for spm2 that works on linux 64 bit?
>>>
>>> Or, else is there a way around spm2? E.g. by using the output of
>>> mriviewer and the localspheres command directly? Or by beamforming in
>>> CTF and feeding its output to sourcestatistics?
>>>
>>> And one last thing: does anyone use the mri files from trhe
>>> CTF-MRIviewer that came with version 5.4.0 yet?
>>>
>>> Thanks,
>>> Christine
>
>
>
>--
>Guillaume Flandin, PhD
>Wellcome Trust Centre for Neuroimaging
>University College London
>12 Queen Square
>London WC1N 3BG
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the 
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and 
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and 
http://www.ru.nl/neuroimaging/fieldtrip.
>
>#!make -f
>#
># @(#)Makefile	2.16 John Ashburner 03/05/12
># Note that changes have been made outside SCCS
># $Id$
>#
>####################################################
###########################
>#
># Suggestions for how to make this file a bit more elegant are welcome.  So 
far
># it works under SunOS and Linux (at the FIL) and some Windows systems
>#
># $Log$
>#
>####################################################
###########################
>
>####################################################
###########################
># Default make
>####################################################
###########################
>unknown:
>	@ make `uname`
>tidy:
>	@ make clean.`uname`
>
>####################################################
###########################
># Architecture specific makes
>####################################################
###########################
>
>MEX = mex -O
>CC  = cc
># mex output object suffix
>MOSUF = o
>CHMODIT = chmod 644
>RANLIB  =
>ADDED_OBS=
>ADDED_MEX=
>
>SunOS:
>	make all SUF=mexsol  CC="cc -xO5"                   MEX="mex 
COPTIMFLAGS=-xO5"
>Linux:
>	make all SUF=mexglx  CC="gcc -O3 -funroll-loops"    MEX="mex 
COPTIMFLAGS='-O3 -funroll-loops'"
>Linux.5:
>	make all SUF=mexlx   CC="gcc -O3 -funroll-loops"    MEX="mex 
COPTIMFLAGS='-O3 -funroll-loops'"
>HP-UX:
>	make all SUF=mexhp7  CC="cc  -O +z -Ae +DAportable" MEX="mex 
COPTIMFLAGS=-O"
>IRIX:
>	make all SUF=mexsg   CC="cc  -O -mips2"             MEX="mex"
>IRIX64:
>	make all SUF=mexsg64 CC="cc  -O -mips4 -64"         MEX="mex"
>AIX:
>	make all SUF=mexrs6
>OSF1:
>	make all SUF=mexaxp
>MAC:
>	make all SUF=mexmac RANLIB="ranlib spm_vol_utils.mexmac.a"
>
>Linux.A64:
># The '-fPIC' option is nexessary to allow the linking proces to complete.
># '-march=x86-64' provides generic optimisations for both Opteron and 64bit 
Xeon.
># If the code is running on a 64bit Xeon you can change '-march=x86-64' to
># '-march=nocona', when running on an Opteron, change it to '-
march=opteron'.
># Also possibly use '-march=k8' for 64 bit Athlon.
>	make all SUF=mexa64  CC="gcc -O3 -funroll-loops -fPIC -march=x86-
64 -mfpmath=sse"\
>	     MEX="mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86-
64 -mfpmath=sse'"
>
>#windows:
>#	make all  SUF=dll MOSUF=obj CHMODIT="echo > null"  
ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll
>windows:
># Consider adding either of the following, depending on your platform:
>#       -march=pentium3
>#       -march=pentium4
>	make all SUF=dll     CC="gcc -mno-cygwin -O3 -funroll-loops -fomit-
frame-pointer -march=pentium4 -mfpmath=sse -DSPM_WIN32" MEX="mex.bat -
DSPM_WIN32" MOSUF=obj CHMODIT="echo > NUL" 
ADDED_OBS=win32mmap.dll.o ADDED_MEX=spm_win32utils.dll
>
>####################################################
###########################
># Architecture specific cleaning
>####################################################
###########################
>clean.SunOS:
>	make clean SUF=mexsol
>clean.Linux:
>	make clean SUF=mexglx
>clean.Linux.5:
>	make clean SUF=mexlx
>clean.Linux.A64:
>	make clean SUF=mexa64
>clean.HP-UX:
>	make clean SUF=mexhp7
>clean.IRIX:
>	make clean SUF=mexsg
>clean.IRIX64:
>	make clean SUF=mexsg64
>clean.AIX:
>	make clean SUF=mexrs6
>clean.OSF1:
>	make clean SUF=mexaxp
>clean.MAC:
>	make clean SUF=mexmac
>clean.windows:
>	make clean SUF=dll
>
>####################################################
###########################
># Objects to go in the archive and mexfiles
>####################################################
###########################
>
>SUF = unknown
>
>OBS =	utils_uchar.$(SUF).o utils_short.$(SUF).o utils_int.$(SUF).o \
>	utils_schar.$(SUF).o utils_ushort.$(SUF).o utils_uint.$(SUF).o\
>	utils_float.$(SUF).o utils_double.$(SUF).o\
>	utils_short_s.$(SUF).o utils_int_s.$(SUF).o\
>	utils_ushort_s.$(SUF).o utils_uint_s.$(SUF).o\
>	utils_float_s.$(SUF).o utils_double_s.$(SUF).o\
>	spm_make_lookup.$(SUF).o spm_getdata.$(SUF).o 
spm_vol_access.$(SUF).o\
>	spm_mapping.$(SUF).o $(ADDED_OBS)
>
>SPMMEX =\
>	spm_sample_vol.$(SUF) spm_slice_vol.$(SUF) spm_brainwarp.$(SUF)\
>	spm_add.$(SUF) spm_conv_vol.$(SUF) spm_render_vol.$(SUF)\
>	spm_global.$(SUF) spm_resels_vol.$(SUF)\
>	spm_atranspa.$(SUF) spm_list_files.$(SUF) spm_unlink.$(SUF)\
>	spm_krutil.$(SUF) spm_project.$(SUF) spm_hist2.$(SUF) 
spm_max.$(SUF)\
>	spm_clusters.$(SUF) spm_bsplinc.$(SUF) spm_bsplins.$(SUF)\
>	spm_bias_mex.$(SUF) spm_dilate.$(SUF) $(ADDED_MEX)
>
>####################################################
###########################
># The main ways to run make
>####################################################
###########################
>
>all: verb.$(SUF) $(SPMMEX)
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "        FINISHED"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>very_clean: clean
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "        Deleting mex and archive (.a) files"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	rm -f $(SPMMEX) spm_vol_utils.$(SUF).a
>
>clean:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "        Deleting object (.o) files"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	rm -f $(OBS)
>
>archive: spm_vol_utils.$(SUF).a
>
>####################################################
###########################
># Compile spm_vol_utils.c with various flags
>####################################################
###########################
>
>spm_vol_utils.$(SUF).a: $(OBS)
>	rm -f $@
>	ar rcv $@ $(OBS)
>	$(RANLIB)
>	@ $(CHMODIT) $@
>
>UTILS=spm_vol_utils.c spm_sys_deps.h spm_make_lookup.h spm_getdata.h
>
>utils_uchar.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_CHAR
>	@ $(CHMODIT) $@
>
>utils_short.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT
>	@ $(CHMODIT) $@
>
>utils_int.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT
>	@ $(CHMODIT) $@
>
>utils_schar.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_CHAR
>	@ $(CHMODIT) $@
>
>utils_ushort.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT
>	@ $(CHMODIT) $@
>
>utils_uint.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT
>	@ $(CHMODIT) $@
>
>utils_float.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT
>	@ $(CHMODIT) $@
>
>utils_double.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE
>	@ $(CHMODIT) $@
>
>utils_short_s.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_SHORT -
DSPM_BYTESWAP
>	@ $(CHMODIT) $@
>
>utils_int_s.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_SIGNED_INT -
DSPM_BYTESWAP
>	@ $(CHMODIT) $@
>
>utils_ushort_s.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_SHORT -
DSPM_BYTESWAP
>	@ $(CHMODIT) $@
>
>utils_uint_s.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_UNSIGNED_INT -
DSPM_BYTESWAP
>	@ $(CHMODIT) $@
>
>utils_float_s.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_FLOAT -DSPM_BYTESWAP
>	@ $(CHMODIT) $@
>
>utils_double_s.$(SUF).o: $(UTILS)
>	$(CC) -c -o $@ spm_vol_utils.c -DSPM_DOUBLE -DSPM_BYTESWAP
>	@ $(CHMODIT) $@
>
>####################################################
###########################
># Compile a few additional C routines for linking
>####################################################
###########################
>
>%.$(SUF).o : %.c spm_sys_deps.h
>	$(CC) -c -o $@ $<
>	@ $(CHMODIT) $@
>
>spm_getdata.$(SUF).o: spm_getdata.c spm_sys_deps.h
>
>spm_vol_access.$(SUF).o:  spm_vol_access.c spm_vol_access.h 
spm_datatypes.h
>
>spm_make_lookup.$(SUF).o: spm_make_lookup.c spm_sys_deps.h
>
>spm_getdata.$(SUF).o: spm_getdata.c
>
>spm_mapping.$(SUF).o:     spm_mapping.c spm_sys_deps.h spm_mapping.h 
spm_datatypes.h
>	$(MEX) -c spm_mapping.c
>	mv spm_mapping.$(MOSUF) $@
>	@ $(CHMODIT) $@
>
>win32mmap.$(SUF).o: win32mmap.c win32mmap.h
>	$(CC) -c -o $@ win32mmap.c
>	@ $(CHMODIT) $@
>
>####################################################
###########################
># Compile the mex files themselves
>####################################################
###########################
>
>%.$(SUF) : %.c spm_sys_deps.h
>	$(MEX) $<
>	@ $(CHMODIT) $@
>
>spm_add.$(SUF): spm_add.c spm_vol_utils.$(SUF).a\
>		spm_sys_deps.h spm_mapping.h
>	$(MEX) spm_add.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_brainwarp.$(SUF): spm_brainwarp.c  spm_vol_utils.$(SUF).a 
spm_matfuns.c\
>		spm_sys_deps.h spm_mapping.h
>	$(MEX) spm_brainwarp.c spm_vol_utils.$(SUF).a spm_matfuns.c
>	@ $(CHMODIT) $@
>
>spm_bsplinc.$(SUF): spm_bsplinc.c spm_vol_utils.$(SUF).a\
>		spm_sys_deps.h spm_mapping.h spm_datatypes.h
>	$(MEX) spm_bsplinc.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_bsplins.$(SUF): spm_bsplins.c spm_sys_deps.h
>	$(MEX) spm_bsplins.c
>	@ $(CHMODIT) $@
>
>spm_conv_vol.$(SUF): spm_conv_vol.c spm_vol_utils.$(SUF).a\
>		spm_sys_deps.h spm_mapping.h spm_datatypes.h
>	$(MEX) spm_conv_vol.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_global.$(SUF): spm_global.c spm_vol_utils.$(SUF).a\
>		spm_sys_deps.h spm_mapping.h
>	$(MEX) spm_global.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_atranspa.$(SUF): spm_atranspa.c spm_sys_deps.h
>
>spm_unlink.$(SUF): spm_unlink.c spm_sys_deps.h
>
>spm_max.$(SUF): spm_max.c spm_sys_deps.h
>
>spm_clusters.$(SUF): spm_clusters.c spm_sys_deps.h
>
>spm_hist2.$(SUF):      spm_hist2.c spm_sys_deps.h
>
>spm_krutil.$(SUF): spm_krutil.c spm_sys_deps.h
>
>spm_dilate.$(SUF): spm_dilate.c
>
>spm_list_files.$(SUF): spm_list_files.c spm_sys_deps.h
>
>spm_project.$(SUF): spm_project.c spm_sys_deps.h
>
>spm_render_vol.$(SUF): spm_render_vol.c spm_vol_utils.$(SUF).a\
>		spm_sys_deps.h spm_mapping.h
>	$(MEX) spm_render_vol.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_resels_vol.$(SUF): spm_resels_vol.c spm_vol_utils.$(SUF).a\
>		spm_sys_deps.h spm_mapping.h
>	$(MEX) spm_resels_vol.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_sample_vol.$(SUF): spm_sample_vol.c spm_vol_utils.$(SUF).a 
spm_mapping.h
>	$(MEX) spm_sample_vol.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_slice_vol.$(SUF): spm_slice_vol.c  spm_vol_utils.$(SUF).a 
spm_mapping.h
>	$(MEX) spm_slice_vol.c  spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_bias_mex.$(SUF): spm_bias_mex.c spm_vol_utils.$(SUF).a 
spm_mapping.h
>	$(MEX) spm_bias_mex.c spm_vol_utils.$(SUF).a
>	@ $(CHMODIT) $@
>
>spm_win32utils.$(SUF): spm_win32utils.c
>	$(MEX) spm_win32utils.c
>	@ $(CHMODIT) $@
>
>####################################################
###########################
># Assorted architecture dependent messages
>####################################################
###########################
>
>verb.unknown:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "PROBLEM: Dont know how to do this."
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexhp7:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "unix compile for hpux cc, and maybe aix cc"
>	@ echo ""
>	@ echo "Under HPUX 10.20 with MATLAB 5.2.1 and gcc, you may 
wish"
>	@ echo "to modify this Makefile to say something like:"
>	@ echo '  CC=gcc -O -fpic'
>	@ echo '  MEX=mex COPTIMFLAGS=-O -f gccopts.sh'
>	@ echo "where the gccopts.sh file is modified to remove the +z"
>	@ echo "(which is used with version 9.0 and possibly also 10.0)."
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexsg:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Feedback from users with R10000 O2 and R10000 Indigo2 
systems"
>	@ echo "running IRIX6.5 suggests that the cmex program with 
Matlab 5.x"
>	@ echo "compiles with the old 32bit (o32) instruction set (MIPS2) 
only,"
>	@ echo "while cc by default compiles with the new32 bit (n32 or 
MIPS4)."
>	@ echo "Matlab 5.x only likes o32 for O2 R10000 systems."
>	@ echo ""
>	@ echo "We also suggest you modify your options file mexopts.sh in"
>	@ echo 'the sgi section: change LD="ld" to LD="ld -o32"'
>	@ echo "this tells the linker to use o32 instead of n32."
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexsg64:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "not optimised sgi 64 bit compile for CC"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.dll:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Windows compile with gcc/mingw"
>	@ echo "see http://www.mrc-
cbu.cam.ac.uk/Imaging/gnumex20.html"
>	@ echo "for instructions about installing gcc/mingw for"
>	@ echo "compiling Mex files."
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexsol:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Unix compile for Sun cc"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexlx:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Linux compilation (Matlab 5.x) - using gcc"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexglx:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Linux compilation (Matlab 6.x) - using gcc"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexaxp:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "keep your fingers crossed"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexmac:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Unix compile for MacOS X"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>verb.mexa64:
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>	@ echo "Unix compile for Linux A64"
>	@ 
echo "_____________________________________________________________
"
>	@ echo ""
>
>
>----------------------------------
>The aim of this list is to facilitate the discussion between users of the 
FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and 
EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and 
http://www.ru.nl/neuroimaging/fieldtrip.
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.



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