[Mne_analysis] mne_epochs2mat error

Hari Bharadwaj hari at nmr.mgh.harvard.edu
Wed Jan 25 17:39:45 EST 2012
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Hi Conrad,
    I haven't used mne_epochs2mat much.. I usually use
mne_ex_read_epochs.m in the MATLAB toolbox.. It might be useful to use
that instead to see if your downstream analysis is getting the same
data as with mne_epochs2mat..

Regards,
Hari



On Wed, January 25, 2012 4:15 pm, conrad at nmr.mgh.harvard.edu wrote:
> Paul,
>
> While testing out the process on different machines and in different
> environments I ran across a few new details that may help me figure out
> what is happening.
>
> The machines I run the analysis on are martinos machines 'huygens' and
> 'wittgenstein'. They are both linux computers(CentOS 5.7) and 64 bit. I
> developed a GUI to encompass the analysis in Matlab, so whenever I run a
> terminal command I just do "unix(____)" Sometimes I did not get the error
> when running the command in terminal, but sometimes I still do. Generally,
> Matlab or terminal, mne_epochs2mat does not like my machines.
>
> When I used the machine 'multnomah' (CentOS 4.7) to test the analysis it
> was not happy with matlab7.11 (transcribed):
>
> [Warning: glibc 2.3.4 - Unsupported version.
> [         glibc 2.7 - MATLAB built using this version
> [
> [Your configuration APPEARS to be too OLD to run this MATLAB program!
>
> So I ran it using matlab7.4 on multnomah. From these observations I
> imagine it may have to deal with the glibc version used with the command
> and the configuration of the computer. The program did not make any error
> messages in this environment, however it's hard to read the error messages
> since the program produces so much output so I could have missed it. It
> seems that multnomah ran it fine, huygens and multnomah cannot.
>
> When I run it on matlab7.11 it start with this error message (but still
> proceeds):
>
> [  I18N Runtime Warning:
> [	Missing ICU data file detected while processing $(MATLAB)/bin/$(ARCH).
> [	Hint: Check for a misconfigured environment or installation.
> [
> [  mne_epochs2mat.bin version 1.9 compiled at Jan 25 2012 04:22:57
>
> I was borrowing time on multnomah, it isn't actually my machine, so I
> cannot run my analysis on it. Do you know a way to make it work on my
> primary computers?
>
> Dan,
>
> The stable build produces the same error for me. I usually use the nightly
> build though. However, what is matlab/octave?
>
> Thanks for your input!
> - Conrad
>
>> You fail to state what machine you ran it on.  One likely issue it is
>> too
>> old either via its OS or its processor for running the programs.
>>
>> Have you run the exact same programs and data on another machine
>> where it worked?  If so where?
>>
>> -- Paul Raines (http://help.nmr.mgh.harvard.edu)
>>
>>
>>
>> On Wed, 25 Jan 2012 3:13pm, conrad at nmr.mgh.harvard.edu wrote:
>>
>>> Hey MNE processors & help,
>>>
>>> I am still trying to figure out this error when I run mne_epochs2mat. I
>>> originally had this problem in late October and no one identified the
>>> problem. I'm still able to run my analysis but I'm not sure if it is
>>> secretly corrupted or misaligned or something.
>>>
>>> Does anyone know where this error comes from and how it could affect
>>> the
>>> data?
>>>
>>> I can provide a more full explanation for the environment in which the
>>> error occurs if that would help.
>>>
>>> - Conrad
>>>
>>> *** glibc detected ***
>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin: double
>>> free
>>> or corruption (out): 0x000000000164c500 ***
>>> ======= Backtrace: =========
>>> /lib64/libc.so.6[0x33e6e7245f]
>>> /lib64/libc.so.6(cfree+0x4b)[0x33e6e728bb]
>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin(mne_free_name_list+0x5e)[0x41a60e]
>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin(main+0x19f)[0x40bedf]
>>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x33e6e1d994]
>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat.bin[0x40bbba]
>>> ======= Memory map: ========
>>> 00400000-004b3000 r-xp 00000000 00:1c 23226731
>>> /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/mne/nightly_build/bin/mne_epochs2mat.bin
>>> 005b2000-005b5000 rw-p 000b2000 00:1c 23226731
>>> /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/mne/nightly_build/bin/mne_epochs2mat.bin
>>> 005b5000-005c8000 rw-p 005b5000 00:00 0
>>> 01585000-019a8000 rw-p 01585000 00:00 0
>>> [heap]
>>> 33e6a00000-33e6a1c000 r-xp 00000000 08:02 782032
>>> /lib64/ld-2.5.so
>>> 33e6c1c000-33e6c1d000 r--p 0001c000 08:02 782032
>>> /lib64/ld-2.5.so
>>> 33e6c1d000-33e6c1e000 rw-p 0001d000 08:02 782032
>>> /lib64/ld-2.5.so
>>> 33e6e00000-33e6f4e000 r-xp 00000000 08:02 782036
>>> /lib64/libc-2.5.so
>>> 33e6f4e000-33e714e000 ---p 0014e000 08:02 782036
>>> /lib64/libc-2.5.so
>>> 33e714e000-33e7152000 r--p 0014e000 08:02 782036
>>> /lib64/libc-2.5.so
>>> 33e7152000-33e7153000 rw-p 00152000 08:02 782036
>>> /lib64/libc-2.5.so
>>> 33e7153000-33e7158000 rw-p 33e7153000 00:00 0
>>> 33e7200000-33e7282000 r-xp 00000000 08:02 782071
>>> /lib64/libm-2.5.so
>>> 33e7282000-33e7481000 ---p 00082000 08:02 782071
>>> /lib64/libm-2.5.so
>>> 33e7481000-33e7482000 r--p 00081000 08:02 782071
>>> /lib64/libm-2.5.so
>>> 33e7482000-33e7483000 rw-p 00082000 08:02 782071
>>> /lib64/libm-2.5.so
>>> 33e7600000-33e7602000 r-xp 00000000 08:02 782081
>>> /lib64/libdl-2.5.so
>>> 33e7602000-33e7802000 ---p 00002000 08:02 782081
>>> /lib64/libdl-2.5.so
>>> 33e7802000-33e7803000 r--p 00002000 08:02 782081
>>> /lib64/libdl-2.5.so
>>> 33e7803000-33e7804000 rw-p 00003000 08:02 782081
>>> /lib64/libdl-2.5.so
>>> 33e7a00000-33e7a16000 r-xp 00000000 08:02 782231
>>> /lib64/libpthread-2.5.so
>>> 33e7a16000-33e7c15000 ---p 00016000 08:02 782231
>>> /lib64/libpthread-2.5.so
>>> 33e7c15000-33e7c16000 r--p 00015000 08:02 782231
>>> /lib64/libpthread-2.5.so
>>> 33e7c16000-33e7c17000 rw-p 00016000 08:02 782231
>>> /lib64/libpthread-2.5.so
>>> 33e7c17000-33e7c1b000 rw-p 33e7c17000 00:00 0
>>> 33eb600000-33eb607000 r-xp 00000000 08:02 782232
>>> /lib64/librt-2.5.so
>>> 33eb607000-33eb807000 ---p 00007000 08:02 782232
>>> /lib64/librt-2.5.so
>>> 33eb807000-33eb808000 r--p 00007000 08:02 782232
>>> /lib64/librt-2.5.so
>>> 33eb808000-33eb809000 rw-p 00008000 08:02 782232
>>> /lib64/librt-2.5.so
>>> 2b924bd5e000-2b924bd61000 rw-p 2b924bd5e000 00:00 0
>>> 2b924bd8c000-2b924bd8d000 rw-p 2b924bd8c000 00:00 0
>>> 2b924bd8d000-2b924bda6000 r-xp 00000000 00:1c 4787101
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmat.so
>>> 2b924bda6000-2b924bea6000 ---p 00019000 00:1c 4787101
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmat.so
>>> 2b924bea6000-2b924beab000 rw-p 00019000 00:1c 4787101
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmat.so
>>> 2b924beab000-2b924bf01000 r-xp 00000000 00:1c 5841980
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmx.so
>>> 2b924bf01000-2b924c000000 ---p 00056000 00:1c 5841980
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmx.so
>>> 2b924c000000-2b924c00f000 rw-p 00055000 00:1c 5841980
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libmx.so
>>> 2b924c00f000-2b924c09f000 r-xp 00000000 00:1c 5842005
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libut.so
>>> 2b924c09f000-2b924c19f000 ---p 00090000 00:1c 5842005
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libut.so
>>> 2b924c19f000-2b924c1c2000 rw-p 00090000 00:1c 5842005
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libut.so
>>> 2b924c1c2000-2b924c4d8000 rw-p 2b924c1c2000 00:00 0
>>> 2b924c4d8000-2b924c56e000 r-xp 00000000 08:02 1736152
>>> /usr/lib64/libgfortran.so.1.0.0
>>> 2b924c56e000-2b924c76d000 ---p 00096000 08:02 1736152
>>> /usr/lib64/libgfortran.so.1.0.0
>>> 2b924c76d000-2b924c76f000 rw-p 00095000 08:02 1736152
>>> /usr/lib64/libgfortran.so.1.0.0
>>> 2b924c76f000-2b924c770000 rw-p 2b924c76f000 00:00 0
>>> 2b924c770000-2b924c87d000 r-xp 00000000 00:1c 4787093
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libhdf5.so.0.0.0
>>> 2b924c87d000-2b924c97c000 ---p 0010d000 00:1c 4787093
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libhdf5.so.0.0.0
>>> 2b924c97c000-2b924c98e000 rw-p 0010c000 00:1c 4787093
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libhdf5.so.0.0.0
>>> 2b924c98e000-2b924c98f000 rw-p 2b924c98e000 00:00 0
>>> 2b924c98f000-2b924ca5c000 r-xp 00000000 00:1c 4542391
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libstdc++.so.6.0.8
>>> 2b924ca5c000-2b924cb5c000 ---p 000cd000 00:1c 4542391
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libstdc++.so.6.0.8
>>> 2b924cb5c000-2b924cb7d000 rw-p 000cd000 00:1c 4542391
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libstdc++.so.6.0.8
>>> 2b924cb7d000-2b924cb90000 rw-p 2b924cb7d000 00:00 0
>>> 2b924cb90000-2b924cb9c000 r-xp 00000000 00:1c 4542388
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1
>>> 2b924cb9c000-2b924cc9b000 ---p 0000c000 00:1c 4542388
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1
>>> 2b924cc9b000-2b924cc9d000 rw-p 0000b000 00:1c 4542388
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/sys/os/glnxa64/libgcc_s.so.1
>>> 2b924cc9d000-2b924cc9e000 rw-p 2b924cc9d000 00:00 0
>>> 2b924cc9e000-2b924cc9f000 r-xp 00000000 00:1c 4787095
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicudata.so.32.0
>>> 2b924cc9f000-2b924cd9e000 ---p 00001000 00:1c 4787095
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicudata.so.32.0
>>> 2b924cd9e000-2b924cd9f000 rw-p 00000000 00:1c 4787095
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicudata.so.32.0
>>> 2b924cd9f000-2b924ce7f000 r-xp 00000000 00:1c 4787098
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuuc.so.32.0
>>> 2b924ce7f000-2b924cf7e000 ---p 000e0000 00:1c 4787098
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuuc.so.32.0
>>> 2b924cf7e000-2b924cf8b000 rw-p 000df000 00:1c 4787098
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuuc.so.32.0
>>> 2b924cf8b000-2b924cf8d000 rw-p 2b924cf8b000 00:00 0
>>> 2b924cf8d000-2b924d0ae000 r-xp 00000000 00:1c 4787096
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicui18n.so.32.0
>>> 2b924d0ae000-2b924d1ad000 ---p 00121000 00:1c 4787096
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicui18n.so.32.0
>>> 2b924d1ad000-2b924d1b6000 rw-p 00120000 00:1c 4787096
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicui18n.so.32.0
>>> 2b924d1b6000-2b924d1c0000 r-xp 00000000 00:1c 4787097
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuio.so.32.0
>>> 2b924d1c0000-2b924d2c0000 ---p 0000a000 00:1c 4787097
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuio.so.32.0
>>> 2b924d2c0000-2b924d2c2000 rw-p 0000a000 00:1c 4787097
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libicuio.so.32.0
>>> 2b924d2c2000-2b924d2ce000 r-xp 00000000 00:1c 5842011
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libz.so.1.1.4
>>> 2b924d2ce000-2b924d3ce000 ---p 0000c000 00:1c 5842011
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libz.so.1.1.4
>>> 2b924d3ce000-2b924d3d1000 rw-p 0000c000 00:1c 5842011
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/libz.so.1.1.4
>>> 2b924d3d1000-2b924d3d5000 rw-p 2b924d3d1000 00:00 0
>>> 2b924d3d5000-2b924dd27000 r--s 00000000 00:1c 4787071
>>> /autofs/cluster/pubsw/2/pubsw/common/matlab/7.4/bin/glnxa64/icudt32l.dat
>>> 2b924dd27000-2b924de68000 rw-p 2b924dd27000 00:00 0
>>> 2b927275e000-2b9275d2b000 r--p 00000000 08:02 1748532
>>> /usr/lib/locale/locale-archive
>>> 7fff81478000-7fff8148c000 rwxp 7ffffffe8000 00:00 0
>>> [stack]
>>> 7fff8148c000-7fff8148e000 rw-p 7fffffffd000 00:00 0
>>> 7fff8153d000-7fff81540000 r-xp 7fff8153d000 00:00 0
>>> [vdso]
>>> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
>>> [vsyscall]
>>> /usr/pubsw/packages/mne/nightly_build/bin/mne_epochs2mat: line 68:
>>> 15797
>>> Aborted
>>>
>>>
>>>
>>
>>
>>
>
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>


-- 
Hari Bharadwaj



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