[Mne_analysis] mne_epochs2mat error

Wed Jan 25 16:15:41 EST 2012

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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>
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