Dear Victoria,
it seems that your compilation went fine but something goes wrong at
runtime with the dynamically linked libraries (ie it uses a different
libmx library during compilation and at runtime).
Something similar is described here:
http://www.mathworks.com/matlabcentral/newsreader/view_thread/241326
Do you have only one Matlab version installed on your computer?
Also, could you indicate what is returned when you type the following in
a shell window:
ldd /media/IOMEGA_HDD/spm5_32bits/spm5/spm_slice_vol.mexglx
echo $PATH
echo $LD_LIBRARY_PATH
which mex
and the same from the Matlab command line, by adding a "!" at the
beginning of the line (ie !ldd ...)
All the best,
Guillaume.
Victoria Gradin wrote:
> Hi
>
> I am having problems trying to run SPM 5 in linux.
> The available updates for spm5 have been installed and I am using Matlab
> R2008a and Ubuntu 8.10.
>
> If I try a slice timing I get the following error:
>
>
> Running "Slice Timing"
>
> SPM5: spm_slice_timing (v$Rev: 112 $) 11:22:18 - 17/04/2009
> ========================================================================
> Your TR is 2.5
> Error running job:
> Invalid MEX-file '/media/IOMEGA_HDD/spm5_32bits/spm5/spm_slice_vol.mexglx':
> /media/IOMEGA_HDD/spm5_32bits/spm5/spm_slice_vol.mexglx: symbol
> mxGetNumberOfDimensions, version libmx.INTERNAL not defined in file libmx.so
> with link time reference.
> --------------------------
> Done.
>
>
>
> Following the advice I found in another message I tried re-compiling the
> mexglx files typing "make install" in the command line. This didn't fix the
> error I was getting with the slice timing and gives me the following message
> in the command line:
>
>
>
> victoria@thinkpadusuario:/media/IOMEGA_HDD/scripts_spm5/spm5/spm5/src$ make
> install
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_uchar.mexglx.o
> spm_vol_utils.c -DSPM_UNSIGNED_CHAR
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_short.mexglx.o
> spm_vol_utils.c -DSPM_SIGNED_SHORT
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_int.mexglx.o
> spm_vol_utils.c -DSPM_SIGNED_INT
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_schar.mexglx.o
> spm_vol_utils.c -DSPM_SIGNED_CHAR
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_ushort.mexglx.o
> spm_vol_utils.c -DSPM_UNSIGNED_SHORT
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_uint.mexglx.o
> spm_vol_utils.c -DSPM_UNSIGNED_INT
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_float.mexglx.o
> spm_vol_utils.c -DSPM_FLOAT
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_double.mexglx.o
> spm_vol_utils.c -DSPM_DOUBLE
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_short_s.mexglx.o
> spm_vol_utils.c -DSPM_SIGNED_SHORT -DSPM_BYTESWAP
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_int_s.mexglx.o
> spm_vol_utils.c -DSPM_SIGNED_INT -DSPM_BYTESWAP
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_ushort_s.mexglx.o
> spm_vol_utils.c -DSPM_UNSIGNED_SHORT -DSPM_BYTESWAP
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_uint_s.mexglx.o
> spm_vol_utils.c -DSPM_UNSIGNED_INT -DSPM_BYTESWAP
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_float_s.mexglx.o
> spm_vol_utils.c -DSPM_FLOAT -DSPM_BYTESWAP
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o utils_double_s.mexglx.o
> spm_vol_utils.c -DSPM_DOUBLE -DSPM_BYTESWAP
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o spm_make_lookup.mexglx.o
> spm_make_lookup.c
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o spm_getdata.mexglx.o
> spm_getdata.c
> gcc -c -O3 -funroll-loops -fPIC -fexceptions -o spm_vol_access.mexglx.o
> spm_vol_access.c
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' -c spm_mapping.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mv -f spm_mapping.o spm_mapping.mexglx.o
> rm -f spm_vol_utils.mexglx.a
> ar rcs spm_vol_utils.mexglx.a utils_uchar.mexglx.o utils_short.mexglx.o
> utils_int.mexglx.o utils_schar.mexglx.o utils_ushort.mexglx.o
> utils_uint.mexglx.o utils_float.mexglx.o utils_double.mexglx.o
> utils_short_s.mexglx.o utils_int_s.mexglx.o utils_ushort_s.mexglx.o
> utils_uint_s.mexglx.o utils_float_s.mexglx.o utils_double_s.mexglx.o
> spm_make_lookup.mexglx.o spm_getdata.mexglx.o spm_vol_access.mexglx.o
> spm_mapping.mexglx.o
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_sample_vol.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_slice_vol.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_brainwarp.c
> spm_vol_utils.mexglx.a spm_matfuns.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_add.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_conv_vol.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_render_vol.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_global.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_resels_vol.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_bsplinc.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_bsplins.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_bias_mex.c
> spm_vol_utils.mexglx.a
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_atranspa.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_unlink.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_hist.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_krutil.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_project.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_hist2.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_dilate_erode.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_bwlabel.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_get_lm.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_digamma.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' mat2file.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' file2mat.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> mex COPTIMFLAGS='-O3 -funroll-loops -fexceptions' spm_invdef.c
>
> Warning: You are using gcc version "4.3.2-1ubuntu11)". The earliest gcc
> version supported
> with mex is "4.0.0". The latest version tested for use with mex is
> "4.2.0".
> To download a different version of gcc, visit http://gcc.gnu.org
>
> _____________________________________________________________
>
> Installing mex files
> _____________________________________________________________
>
> cp -f spm_sample_vol.mexglx spm_slice_vol.mexglx spm_brainwarp.mexglx
> spm_add.mexglx spm_conv_vol.mexglx spm_render_vol.mexglx spm_global.mexglx
> spm_resels_vol.mexglx spm_bsplinc.mexglx spm_bsplins.mexglx
> spm_bias_mex.mexglx spm_atranspa.mexglx spm_unlink.mexglx spm_hist.mexglx
> spm_krutil.mexglx spm_project.mexglx spm_hist2.mexglx
> spm_dilate_erode.mexglx spm_bwlabel.mexglx spm_get_lm.mexglx
> spm_digamma.mexglx mat2file.mexglx file2mat.mexglx spm_invdef.mexglx ..
>
>
>
>
> I have not experience using linux and I would appreciate any kind of help
> with this problem.
>
> Thanks very much
> Regards
>
> Victoria
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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