Hi Volkmar,
Thanks for your help with this!
> libmx.so is a MathWorks supplied library - at least it should be. What does
>
> ldd /depot7/LocalMatlab/spm5/spm_bsplinc.mexa64
>
> in a shell terminal tell you? Any undefined symbols, libmx.so pointing
> to somewhere else than to the Matlab binary directory for R14SP3? Maybe
> during making of your mex files you have picked up a mex from a
> different Matlab version. I have two different sets of mex files around
> for running either R14SP3 and 2007a - they are source compatible, but
> not binary.
I'm not used to looking at these library files, so it took me a while to
realise that I needed to run the ldd command **whilst matlab was running**!
(as they are dynamically loaded) Doh! :-)
Anyway, the output is shown below.
On our system, the 64-bit machines use the /depot64 and /lib64 mounts for
libraries, binaries etc. SPM etc is stored in /depot7 which contains both
the 32bit and 64bit SPM mex files.
It looks like a lot of the lib files used are those in the /lib64 directory,
but there are some (e.g. libm.so.6) which are pointing to the version in /lib
(presumably a 32bit version). Could this be the problem, and how would I fix it?
Many thanks,
M@
>> !ldd -v /depot7/LocalMatlab/spm5/spm_bsplinc.mexa64 > ldd_output_matlabrunning.txt
libmx.so => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so (0x00002af69f383000)
libmex.so => /depot64/matlab.7.0.3/bin/glnxa64/libmex.so (0x00002af69f4cf000)
libmat.so => /depot64/matlab.7.0.3/bin/glnxa64/libmat.so (0x00002af69f5dc000)
libm.so.6 => /lib/libm.so.6 (0x00002af69f6f5000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00002af69f877000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00002af69fa75000)
libc.so.6 => /lib/libc.so.6 (0x00002af69fb8b000)
libut.so => /depot64/matlab.7.0.3/bin/glnxa64/libut.so (0x00002af69fdc8000)
libicudata.so.32 => /depot64/matlab.7.0.3/bin/glnxa64/libicudata.so.32 (0x00002af6a0065000)
libicuuc.so.32 => /depot64/matlab.7.0.3/bin/glnxa64/libicuuc.so.32 (0x00002af6a0167000)
libicui18n.so.32 => /depot64/matlab.7.0.3/bin/glnxa64/libicui18n.so.32 (0x00002af6a035b000)
libicuio.so.32 => /depot64/matlab.7.0.3/bin/glnxa64/libicuio.so.32 (0x00002af6a0576000)
libz.so => /depot64/matlab.7.0.3/bin/glnxa64/libz.so (0x00002af6a0683000)
libstdc++.so.5 => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5 (0x00002af6a0791000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00002af6a096e000)
libmwmvalue.so => /depot64/matlab.7.0.3/bin/glnxa64/libmwmvalue.so (0x00002af6a0a7c000)
libmwservices.so => /depot64/matlab.7.0.3/bin/glnxa64/libmwservices.so (0x00002af6a0b90000)
libmwmpath.so => /depot64/matlab.7.0.3/bin/glnxa64/libmwmpath.so (0x00002af6a0d8c000)
libmwm_dispatcher.so => /depot64/matlab.7.0.3/bin/glnxa64/libmwm_dispatcher.so (0x00002af6a0ea6000)
/lib64/ld-linux-x86-64.so.2 (0x0000555555554000)
librt.so.1 => /lib/librt.so.1 (0x00002af6a104b000)
libMTwister.so => /depot64/matlab.7.0.3/bin/glnxa64/libMTwister.so (0x00002af6a1155000)
libdl.so.2 => /lib/libdl.so.2 (0x00002af6a1258000)
libncurses.so.5 => /lib/libncurses.so.5 (0x00002af6a135c000)
libmwdatasvcs.so => /depot64/matlab.7.0.3/bin/glnxa64/libmwdatasvcs.so (0x00002af6a14b7000)
libxerces-c.so.26 => /depot64/matlab.7.0.3/bin/glnxa64/libxerces-c.so.26 (0x00002af6a15d9000)
Version information:
/depot7/LocalMatlab/spm5/spm_bsplinc.mexa64:
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libmex.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmex.so
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libmx.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libmx.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
/depot64/matlab.7.0.3/bin/glnxa64/libmex.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libmwmpath.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwmpath.so
libmwservices.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwservices.so
libmwmvalue.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwmvalue.so
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libmx.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so
libmwm_dispatcher.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwm_dispatcher.so
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
/depot64/matlab.7.0.3/bin/glnxa64/libmat.so:
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libmx.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so
/lib/libm.so.6:
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/usr/lib/libstdc++.so.6:
libgcc_s.so.1 (GCC_3.3) => /lib/libgcc_s.so.1
libgcc_s.so.1 (GCC_4.2.0) => /lib/libgcc_s.so.1
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/lib/libpthread.so.0:
ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6
libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/lib/libc.so.6:
ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
/depot64/matlab.7.0.3/bin/glnxa64/libut.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
librt.so.1 (GLIBC_2.2.5) => /lib/librt.so.1
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libdl.so.2 (GLIBC_2.2.5) => /lib/libdl.so.2
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libpthread.so.0 (GLIBC_2.3.2) => /lib/libpthread.so.0
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libicudata.so.32:
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libicuuc.so.32:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libicui18n.so.32:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
/depot64/matlab.7.0.3/bin/glnxa64/libicuio.so.32:
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libz.so:
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5:
libgcc_s.so.1 (GCC_3.3) => /lib/libgcc_s.so.1
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/lib/libgcc_s.so.1:
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libmwmvalue.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
libmx.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libmwservices.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libmwmpath.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwmpath.so
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libpthread.so.0 (GLIBC_2.3.2) => /lib/libpthread.so.0
libmx.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
/depot64/matlab.7.0.3/bin/glnxa64/libmwmpath.so:
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
/depot64/matlab.7.0.3/bin/glnxa64/libmwm_dispatcher.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libm.so.6 (GLIBC_2.2.5) => /lib/libm.so.6
libmwmvalue.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwmvalue.so
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libmwservices.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwservices.so
libmx.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmx.so
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libmwmpath.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libmwmpath.so
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
/lib/librt.so.1:
ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libpthread.so.0 (GLIBC_PRIVATE) => /lib/libpthread.so.0
libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libMTwister.so:
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
/lib/libdl.so.2:
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6
ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
/lib/libncurses.so.5:
libdl.so.2 (GLIBC_2.2.5) => /lib/libdl.so.2
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libmwdatasvcs.so:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libut.so (v7.0) => /depot64/matlab.7.0.3/bin/glnxa64/libut.so
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
/depot64/matlab.7.0.3/bin/glnxa64/libxerces-c.so.26:
libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
libpthread.so.0 (GLIBC_2.2.5) => /lib/libpthread.so.0
libstdc++.so.5 (CXXABI_1.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libstdc++.so.5 (GLIBCPP_3.2) => /depot64/matlab.7.0.3/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.5
libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
libc.so.6 (GLIBC_2.2.5) => /lib/libc.so.6
--------------------------------------------------------------------------------------------------
>> I need some help getting a 64-bit Linux (Debian) SPM5 (latest patches)
>> installation to behave.
>>
>> The compilation went smoothly, (make && make install), and SPM5 starts
>> without problems.
>> However, when trying to do a reslice of some data, one of the MEX
>> files seems to have a problem:
>>
>> --------------------------
>> Running "Realign: Estimate & Reslice"
>> ??? Invalid MEX-file '/depot7/LocalMatlab/spm5/spm_bsplinc.mexa64':
>> /depot7/LocalMatlab/spm5/spm_bsplinc.mexa64:
>> symbol mxCreateNumericArray_700,
>> version v7.0 not defined in file libmx.so with
>> link time reference.
>>
>> ??? Error while evaluating uicontrol Callback.
>>
>> Some technical details are given below.
>> Any help would be much appreciated!
>>
>> Cheers,
>>
>> M@
>>
>> Technical stuff:
>>
>> > > ver
>> MATLAB Version 7.1.0.183 (R14) Service Pack 3
>> Operating System: Linux 2.6.18-4-amd64 #1 SMP Wed Feb 21 14:29:38 UTC
>> 2007 x86_64
>> Java VM Version: Java 1.4.2 with Blackdown Java-Linux Team Java
>> HotSpot(TM) 64-Bit Server VM mixed mode
>>
>>
>> Feedback from 'make':
>>
>> goedel:/depot7/LocalMatlab/spm5/src# make && make install
>> _____________________________________________________________
>>
>> Linux compilation (x86-64) - using gcc
>> _____________________________________________________________
>>
>> _____________________________________________________________
>>
>> FINISHED
>> _____________________________________________________________
>>
>> _____________________________________________________________
>>
>> Installing mex files
>> _____________________________________________________________
>>
>> cp -f spm_sample_vol.mexa64 spm_slice_vol.mexa64 spm_brainwarp.mexa64
>> spm_add.mexa64 spm_conv_vol.mexa64 spm_render_vol.mexa64
>> spm_global.mexa64
>> spm_resels_vol.mexa64 spm_bsplinc.mexa64 spm_bsplins.mexa64
>> spm_bias_mex.mexa64
>> spm_atranspa.mexa64 spm_unlink.mexa64 spm_hist.mexa64
>> spm_krutil.mexa64
>> spm_project.mexa64 spm_hist2.mexa64 spm_dilate_erode.mexa64
>> spm_bwlabel.mexa64
>> spm_get_lm.mexa64 spm_digamma.mexa64 mat2file.mexa64 file2mat.mexa64
>> spm_invdef.mexa64 ..
>> goedel:/depot7/LocalMatlab/spm5/src#
>>
>>
>
--
Matthew Liptrot
Biomedical Research Engineer
Danish Research Centre for Magnetic Resonance, DRCMR
MR Dept. 340B
Copenhagen University Hospital
Kettegaard Alle 30
DK-2650 Hvidovre
DENMARK
www.drcmr.dk
Tel: +45 36 32 62 03
Email: [log in to unmask]
(Alternative email: [log in to unmask])
|