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>
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