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
--------------------------------------------------
----JOB [fslerror_report_gen.sh.48664] START [Thu Jan 17 20:30:45 EST 2008] on HOST [node6.biac.duke.edu]----
cat: /mnt/users.q.shares/smith.6u9hUCxLKYZqmHmHaUYu/Analysis/Cluster/PassiveTask/32953/32953_ica_pt00_noBET_8mm/32953_run2.ica/*.log: No such file or directory
######################################################################
#### MACHINE INFORMATION
######################################################################
Uname:
Linux
df:
Filesystem 1K-blocks Used Available Use% Mounted on
//goldman/data 8593612796 8363005136 230607660 98% /mnt/users.q.shares/smith.6u9hUCxLKYZqmHmHaUYu
quota:
Memory and Swap info:
MemTotal: 8160472 kB
MemFree: 7213276 kB
Buffers: 233504 kB
Cached: 335056 kB
SwapCached: 0 kB
Active: 541380 kB
Inactive: 73024 kB
SwapTotal: 0 kB
SwapFree: 0 kB
Dirty: 128 kB
Writeback: 0 kB
AnonPages: 44048 kB
Mapped: 9948 kB
Slab: 305948 kB
SReclaimable: 282924 kB
SUnreclaim: 23024 kB
PageTables: 6052 kB
NFS_Unstable: 0 kB
Bounce: 0 kB
CommitLimit: 4080236 kB
Committed_AS: 102036 kB
VmallocTotal: 34359738367 kB
VmallocUsed: 400 kB
VmallocChunk: 34359737959 kB
HugePages_Total: 0
HugePages_Free: 0
HugePages_Rsvd: 0
Hugepagesize: 2048 kB
######################################################################
#### ENVIRONMENT INFORMATION
######################################################################
FSL_BIN=/usr/local/fsl/bin
FSLMULTIFILEQUIT=TRUE
FSLMACHTYPE=linux_64-gcc4.1
FSLTCLSH=/usr/local/fsl/bin/fsltclsh
FSLMACHINELIST=
FSLREMOTECALL=
FSLWISH=/usr/local/fsl/bin/fslwish
FSLCONFDIR=/usr/local/fsl/config
FSLBROWSER=/usr/local/fsl/tcl/fslwebbrowser
FSLDISPLAY=/usr/bin/display
FSLCONVERT=/usr/bin/convert
FSLDIR=/usr/local/fsl
FSLLOCKDIR=
FSLOUTPUTTYPE=NIFTI_GZ
FSL_DIR=/usr/local/fsl
PATH=/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/tmp/48664.1.users.q:/usr/local/bin:/bin:/usr/bin:/usr/local/fsl/bin:/usr/local/packages/libsvm:/usr/local/freesurfer/bin
SGE_BINARY_PATH=/opt/gridengine/bin/lx24-amd64
SGE_STDERR_PATH=/home/smith/fslerror_report_gen.sh.48664.out
SGE_STDOUT_PATH=/home/smith/fslerror_report_gen.sh.48664.out
SGE_CWD_PATH=/home/smith
SGE_O_PATH=/opt/gridengine/bin/lx24-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/smith/bin
MNI_DATAPATH=/usr/local/freesurfer/mni/data
SGE_STDIN_PATH=/dev/null
######################################################################
#### DIRECTORY INFORMATION
######################################################################
PWD:
/mnt/users.q.shares/smith.6u9hUCxLKYZqmHmHaUYu/Analysis/Cluster/PassiveTask/32953/32953_ica_pt00_noBET_8mm/32953_run2.ica
total 94362
drwx------ 1 smith root 0 Jan 17 11:50 .
drwx------ 1 smith root 0 Jan 16 17:48 ..
-rw------- 1 smith root 10 Jan 6 15:37 absbrainthresh.txt
-rw------- 1 smith root 22230980 Jan 16 18:07 denoised_data_auto3_8mm.nii.gz
-rw------- 1 smith root 22230951 Jan 16 18:07 denoised_data_auto4_8mm.nii.gz
-rw------- 1 smith root 6840 Jan 6 15:33 design.fsf
-rw------- 1 smith root 165887 Jan 6 15:34 example_func.nii.gz
drwx------ 1 smith root 0 Jan 6 15:38 filtered_func_data.ica
-rw------- 1 smith root 51385361 Jan 6 15:37 filtered_func_data.nii.gz
-rw------- 1 smith root 630 Jan 6 15:42 .logC
drwx------ 1 smith root 0 Jan 6 15:42 logs
-rw------- 1 smith root 318 Jan 6 15:35 mask.nii.gz
drwx------ 1 smith root 0 Jan 6 15:34 mc
-rw------- 1 smith root 451087 Jan 6 15:37 mean_func.nii.gz
-rw------- 1 smith root 2775 Jan 17 11:50 new_mean_func_betp0.45_mask.nii.gz
-rw------- 1 smith root 100114 Jan 17 11:50 new_mean_func_betp0.45.nii.gz
drwx------ 1 smith root 0 Jan 6 15:38 reg
-rw------- 1 smith root 965 Jan 6 15:42 report.html
-rw------- 1 smith root 18869 Jan 6 15:42 report_log.html
-rw------- 1 smith root 1403 Jan 6 15:37 report_prestats.html
-rw------- 1 smith root 1630 Jan 6 15:38 report_reg.html
######################################################################
#### MELODIC INFORMATION
######################################################################
Log files:
######################################################################
#### Main directory:
total 94362
drwx------ 1 smith root 0 Jan 17 11:50 .
drwx------ 1 smith root 0 Jan 16 17:48 ..
-rw------- 1 smith root 10 Jan 6 15:37 absbrainthresh.txt
-rw------- 1 smith root 22230980 Jan 16 18:07 denoised_data_auto3_8mm.nii.gz
-rw------- 1 smith root 22230951 Jan 16 18:07 denoised_data_auto4_8mm.nii.gz
-rw------- 1 smith root 6840 Jan 6 15:33 design.fsf
-rw------- 1 smith root 165887 Jan 6 15:34 example_func.nii.gz
drwx------ 1 smith root 0 Jan 6 15:38 filtered_func_data.ica
-rw------- 1 smith root 51385361 Jan 6 15:37 filtered_func_data.nii.gz
-rw------- 1 smith root 630 Jan 6 15:42 .logC
drwx------ 1 smith root 0 Jan 6 15:42 logs
-rw------- 1 smith root 318 Jan 6 15:35 mask.nii.gz
drwx------ 1 smith root 0 Jan 6 15:34 mc
-rw------- 1 smith root 451087 Jan 6 15:37 mean_func.nii.gz
-rw------- 1 smith root 2775 Jan 17 11:50 new_mean_func_betp0.45_mask.nii.gz
-rw------- 1 smith root 100114 Jan 17 11:50 new_mean_func_betp0.45.nii.gz
drwx------ 1 smith root 0 Jan 6 15:38 reg
-rw------- 1 smith root 965 Jan 6 15:42 report.html
-rw------- 1 smith root 18869 Jan 6 15:42 report_log.html
-rw------- 1 smith root 1403 Jan 6 15:37 report_prestats.html
-rw------- 1 smith root 1630 Jan 6 15:38 report_reg.html
This error report is saved in the file: /tmp/fsl_SnGSRW.gz
----JOB [fslerror_report_gen.sh.48664] STOP [Thu Jan 17 20:30:45 EST 2008]----
|
