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Old 01-29-2009, 11:52 AM   #1
zest n zeal
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Registered: May 2007
Posts: 18

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Error compiling mex files for matlab using make.


Hi I'm having problems compiling some files (mex files for matlab).

In the makefile they use "uname -m" to determine the HARDWARE and do not give an option for my output (i686), The nearest option is (i386)
PHP Code:
    HARDWARE  = $(shell uname -m)
    
ifeq (i386,$(HARDWARE))
      
SUF     mexglx
      CC      
gcc
      CFLAGS  
= -O3 -funroll-loops -fPIC -fexceptions
      MEXOPTS 
COPTIMFLAGS='-O3 -funroll-loops -fexceptions'
    
endif 
The variables SUF and CC look appropriate, I have no idea about CFLAGS and MEXOPTS but I tried just substituting i386 for i686 instead and ran make...

PHP Code:
am0032@linux-vvi7:~/spm5/srcmake && make install
_____________________________________________________________

        Linux compilation 
(x86-32) - using gcc
_____________________________________________________________

gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_uchar.mexglx.o spm_vol_utils.-DSPM_UNSIGNED_CHAR
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_short.mexglx.o spm_vol_utils.-DSPM_SIGNED_SHORT
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_int.mexglx.o spm_vol_utils.-DSPM_SIGNED_INT
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_schar.mexglx.o spm_vol_utils.-DSPM_SIGNED_CHAR
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_ushort.mexglx.o spm_vol_utils.-DSPM_UNSIGNED_SHORT
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_uint.mexglx.o spm_vol_utils.-DSPM_UNSIGNED_INT
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_float.mexglx.o spm_vol_utils.-DSPM_FLOAT
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_double.mexglx.o spm_vol_utils.-DSPM_DOUBLE
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_short_s.mexglx.o spm_vol_utils.-DSPM_SIGNED_SHORT -DSPM_BYTESWAP
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_int_s.mexglx.o spm_vol_utils.-DSPM_SIGNED_INT -DSPM_BYTESWAP
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_ushort_s.mexglx.o spm_vol_utils.-DSPM_UNSIGNED_SHORT -DSPM_BYTESWAP
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_uint_s.mexglx.o spm_vol_utils.-DSPM_UNSIGNED_INT -DSPM_BYTESWAP
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_float_s.mexglx.o spm_vol_utils.-DSPM_FLOAT -DSPM_BYTESWAP
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o utils_double_s.mexglx.o spm_vol_utils.-DSPM_DOUBLE -DSPM_BYTESWAP
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o spm_make_lookup.mexglx.o spm_make_lookup.c
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o spm_getdata.mexglx.o spm_getdata.c
gcc 
--O3 -funroll-loops -fPIC -fexceptions -o spm_vol_access.mexglx.o spm_vol_access.c
mex COPTIMFLAGS
='-O3 -funroll-loops -fexceptions' -c spm_mapping.
make
mexCommand not found
make
: *** [spm_mapping.mexglx.oError 127 

I understand that this mex function cannot be found, albeit that grepping the c files indicates multiple files with the line

PHP Code:
#include "mex.h" 

When I run 'make -d && make install' in debug mode I get the following as the last few lines of output.

PHP Code:
      Trying pattern rule with stem `spm_mapping'.
         Rejecting impossible implicit prerequisite 
`spm_mapping.w'.
         No implicit rule found for `spm_mapping.c'
.
         
Finished prerequisites of target file `spm_mapping.c'.
        No need to remake target 
`spm_mapping.c'.
        Considering target file `spm_mapping.h'
.
         
Looking for an implicit rule for `spm_mapping.h'.
         Trying pattern rule with stem 
`spm_mapping.h'.
         Trying implicit prerequisite `spm_mapping.h,v'
.
         
Trying pattern rule with stem `spm_mapping.h'.
         Trying implicit prerequisite 
`RCS/spm_mapping.h,v'.
         Trying pattern rule with stem `spm_mapping.h'
.
         
Trying implicit prerequisite `RCS/spm_mapping.h'.
         Trying pattern rule with stem 
`spm_mapping.h'.
         Trying implicit prerequisite `s.spm_mapping.h'
.
         
Trying pattern rule with stem `spm_mapping.h'.
         Trying implicit prerequisite 
`SCCS/s.spm_mapping.h'.
         No implicit rule found for `spm_mapping.h'
.
         
Finished prerequisites of target file `spm_mapping.h'.
        No need to remake target 
`spm_mapping.h'.
        Pruning file `spm_vol_access.h'
.
        
Pruning file `spm_datatypes.h'.
       Finished prerequisites of target file 
`spm_mapping.mexglx.o'.
      Must remake target `spm_mapping.mexglx.o'
.
mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' -c spm_mapping.
make
mexCommand not found
Putting child 0x0808a070 
(spm_mapping.mexglx.oPID 11002 on the chain.
Live child 0x0808a070 (spm_mapping.mexglx.oPID 11002 
Reaping losing child 0x0808a070 PID 11002 
make
: *** [spm_mapping.mexglx.oError 127
Removing child 0x0808a070 PID 11002 from chain
.
am0032@linux-vvi7:~/spm5/src

Does any kind soul have an idea what is going wrong? I am sure the source files are fine so I am just being a newbie-muppet.

Zest
 
Old 01-30-2009, 02:50 PM   #2
knudfl
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/usr/bin/mex ? You will have to 'buy' a Matlab licence
to get it, I think.
They have a 15 day trial for some applications too.
I don't think, that anyting else will substitute the genuine mex.

Files, you probably have it all ....

MEX Required
Mex (Matlab EXecutibles) are required to compile SPM. :

http://en.wikibooks.org/wiki/SPM/Ins...x#MEX_Required

files.c , files.h , Makefile ....
http://www.umich.edu/~fmri/course/2005/files/spm2/

mex.h
http://www.princeton.edu/~rvdb/matlab/mex.h
....

Last edited by knudfl; 01-30-2009 at 02:51 PM.
 
  


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