Hi Christian,
I do not think the problem is restricted to a single node, but I will test for
this in the future (my log files weren't set up in way that allowed me to
easily see where jobs were going when I ran MELODIC originally). The
two errors
are completely random and not reproducible.
Regarding other memory intensive tools: I've ran FLAME1+2 without any
problems.
I have not heard of anyone else on our cluster having trouble with any other
memory intensive FSL tools like Bedpostx.
Thanks,
David
Quoting "Christian F. Beckmann" <[log in to unmask]>:
> Hi,
>
> Does not look like a straight-forward melodic bug to me - I suspect
> that either you have some dodgy RAM on your system somewhere. Can you
> test if the problem always is associated with the same cluster
> node? Also, you might want to try other memory intensive tools to
> see if you can get those to crash. Finally, you might want to
> compile things from scratch
> hth
> christian
>
>
>
>
> On 4 Feb 2008, at 15:46, David V. Smith wrote:
>
>> Hi,
>>
>> I never got a response to this... This looks like a bug with
>> MELODIC. Could this
>> be the result of running on a Sun Grid Engine cluster system? Or is this a
>> memory problem on our end?
>>
>> Thanks,
>> David
>>
>>
>>
>>
>> ----- Forwarded message from [log in to unmask] -----
>> Date: Thu, 17 Jan 2008 20:50:49 -0500
>> From: "David V. Smith" <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Subject: [FSL] MELODIC errors
>> To: [log in to unmask]
>>
>> Hi,
>>
>> I'm getting two random errors when running MELODIC (pasted below).
>> By "random",
>> I mean these errors are not reproducible and do not seem to have
>> anything to do
>> with the data or set up since MELODIC generally works fine if I run
>> it again.
>> Sometimes I'll get one error, and sometimes I'll get the other. When either
>> error arises, the analysis stops after it's estimated the first 1-5ish
>> components (this is when the dimensionality estimate is much higher,
>> usually in
>> the 30s-40s).
>>
>> These errors seems to arise when running system commands like rm or
>> sh, so is
>> this a problem on our end? The data sets aren't really huge
>> (64x64x30x114) and
>> this is only a single run of data/analysis, but could this still be
>> a memory
>> issue?
>>
>> We're running on a 32-processor SGE cluster system, and I'm
>> attaching the output
>> of fslerrorreport so you'll have other system information (*.log files are
>> generated when I get the errors below).
>>
>> Thank you for any help,
>> David
>>
>>
>> ERROR 1:
>>
>> /bin/rm -rf prefiltered_func_data*
>> /bin/sh: line 1: 3707 Segmentation fault /usr/local/fsl/bin/
>> melodic -i
>> filtered_func_data -o filtered_func_data.ica -v --nobet -- bgthreshold=3
>> --tr=2.0 --report --guireport=../../report.html -d 0 --mmthresh=0.5
>> --Ostats
>>
>>
>> ERROR 2:
>>
>> /bin/rm -rf prefiltered_func_data*
>> *** glibc detected *** /usr/local/fsl/bin/melodic: double free or
>> corruption
>> (fasttop): 0x0000000003d3d270 ***
>> ======= Backtrace: =========
>> /lib64/libc.so.6[0x3c89c6ea60]
>> /lib64/libc.so.6(cfree+0x8c)[0x3c89c7217c]
>> /usr/local/fsl/bin/melodic[0x511804]
>> /usr/local/fsl/bin/melodic[0x511a3f]
>> /usr/local/fsl/bin/melodic[0x511d28]
>> /usr/local/fsl/bin/melodic[0x513509]
>> /usr/local/fsl/bin/melodic[0x447f7d]
>> /usr/local/fsl/bin/melodic[0x44ce97]
>> /usr/local/fsl/bin/melodic[0x456a3d]
>> /usr/local/fsl/bin/melodic[0x45b093]
>> /lib64/libc.so.6(__libc_start_main+0xf4)[0x3c89c1da44]
>> /usr/local/fsl/bin/melodic(__gxx_personality_v0+0xba)[0x404a5a]
>> ======= Memory map: ========
>> 00400000-0063d000 r-xp 00000000 08:01 33915183
>> /usr/local/fsl-4.0.1-centos4_64/bin/melodic
>> 0073d000-0075d000 rw-p 0023d000 08:01 33915183
>> /usr/local/fsl-4.0.1-centos4_64/bin/melodic
>> 0075d000-0528e000 rw-p 0075d000 00:00 0
>> [heap]
>> 3c88c00000-3c88c1a000 r-xp 00000000 08:01 18415962
>> /lib64/ld-2.5.so
>> 3c88e19000-3c88e1a000 r--p 00019000 08:01 18415962
>> /lib64/ld-2.5.so
>> 3c88e1a000-3c88e1b000 rw-p 0001a000 08:01 18415962
>> /lib64/ld-2.5.so
>> 3c89c00000-3c89d44000 r-xp 00000000 08:01 18415963
>> /lib64/libc-2.5.so
>> 3c89d44000-3c89f44000 ---p 00144000 08:01 18415963
>> /lib64/libc-2.5.so
>> 3c89f44000-3c89f48000 r--p 00144000 08:01 18415963
>> /lib64/libc-2.5.so
>> 3c89f48000-3c89f49000 rw-p 00148000 08:01 18415963
>> /lib64/libc-2.5.so
>> 3c89f49000-3c89f4e000 rw-p 3c89f49000 00:00 0
>> 3c8a000000-3c8a082000 r-xp 00000000 08:01 18415964
>> /lib64/libm-2.5.so
>> 3c8a082000-3c8a281000 ---p 00082000 08:01 18415964
>> /lib64/libm-2.5.so
>> 3c8a281000-3c8a282000 r--p 00081000 08:01 18415964
>> /lib64/libm-2.5.so
>> 3c8a282000-3c8a283000 rw-p 00082000 08:01 18415964
>> /lib64/libm-2.5.so
>> 3c8e400000-3c8e40d000 r-xp 00000000 08:01 18415968
>> /lib64/libgcc_s-4.1.1-20061011.so.1
>> 3c8e40d000-3c8e60c000 ---p 0000d000 08:01 18415968
>> /lib64/libgcc_s-4.1.1-20061011.so.1
>> 3c8e60c000-3c8e60d000 rw-p 0000c000 08:01 18415968
>> /lib64/libgcc_s-4.1.1-20061011.so.1
>> 3c8ec00000-3c8ece7000 r-xp 00000000 08:01 25533528
>> /usr/lib64/libstdc++.so.6.0.8
>> 3c8ece7000-3c8eee7000 ---p 000e7000 08:01 25533528
>> /usr/lib64/libstdc++.so.6.0.8
>> 3c8eee7000-3c8eeed000 r--p 000e7000 08:01 25533528
>> /usr/lib64/libstdc++.so.6.0.8
>> 3c8eeed000-3c8eef0000 rw-p 000ed000 08:01 25533528
>> /usr/lib64/libstdc++.so.6.0.8
>> 3c8eef0000-3c8ef02000 rw-p 3c8eef0000 00:00 0
>> 2aaaaaaab000-2aaaaaab0000 rw-p 2aaaaaaab000 00:00 0
>> 2aaaaaaec000-2aaaaab68000 rw-p 2aaaaaaec000 00:00 0
>> 2aaaac000000-2aaaac021000 rw-p 2aaaac000000 00:00 0
>> 2aaaac021000-2aaab0000000 ---p 2aaaac021000 00:00 0
>> 7fff65da3000-7fff65dba000 rw-p 7fff65da3000 00:00 0
>> [stack]
>> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
>> [vdso]
>> /bin/sh: line 1: 1847 Aborted /usr/local/fsl/bin/
>> melodic -i
>> filtered_func_data -o filtered_func_data.ica -v --nobet -- bgthreshold=3
>> --tr=2.0 --report --guireport=../../report.html -d 0 --mmthresh=0.5
>> --Ostats
>>
>>
>>
>>
>> --------------------------------------------------
>> David V. Smith
>> Graduate Student, Huettel Lab
>> Center for Cognitive Neuroscience
>> Duke University
>> Durham, NC 27708
>> www.mind.duke.edu
>> --------------------------------------------------
>>
>> ----- End forwarded message -----
>>
>>
>> --------------------------------------------------
>> David V. Smith
>> Graduate Student, Huettel Lab
>> Center for Cognitive Neuroscience
>> Duke University
>> Durham, NC 27708
>> www.mind.duke.edu
>> --------------------------------------------------
>> <fslerror_report_gen.sh.48664.out>
>
--------------------------------------------------
David V. Smith
Graduate Student, Huettel Lab
Center for Cognitive Neuroscience
Duke University
Durham, NC 27708
www.mind.duke.edu
--------------------------------------------------
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