Hi - it seem like possibly you have a file system problem - like one
of the nodes maybe temporarily can't see the file system? There should
be no problem in theory in having many nodes access the same file
system (we have about 16 nodes, 100 cores), but yes this is the kind
of thing we've seen when we've had file server problems in the past.
Cheers.
On 11 Nov 2008, at 14:52, Guido Biele wrote:
> Hi,
>
> I am running a first level analysis with feat. for some subjects
> contrast_mgr is aborted with an uncaught exception. (as far as i can
> tell
> from the log, film was successfully completed).
> However, if i run the contrast_mgr command from the terminal, it is
> completed successfully.
> I also could not figure out why the probem appears for some subjects
> and not
> for others.
>
> RAM should not be an issue, as thre are 8GB RAM.
> Can it be a problem that I am running around 1 analysis in parallel
> (on 15
> machines), which all access the same HD?
>
> Does anybody have an idea?
>
> Attached is the report_log.html file.
>
>
> Thank in advance!
> Best Guido
> Progress Report / LogStarted at Tue Nov 11 12:08:19 CET 2008
> Feat main script
>
> /bin/cp /gridwork1/Studien/MML/feat/3/design_2_r3.fsf design.fsf
>
> /programs/fsl/bin/feat_model design
>
> /programs/fsl/bin/fsl_sub -T 50 -l logs -N feat2_pre /programs/fsl/
> bin/feat /gridwork1/Studien/MML/MML2/mri/func/r3/
> HP160_SM8_NC_model2.feat/design.fsf -D /gridwork1/Studien/MML/MML2/
> mri/func/r3/HP160_SM8_NC_model2.feat -I 1 -prestats
> 12988
>
> /programs/fsl/bin/fsl_sub -T 1313 -l logs -N feat3_film -j 12988 /
> programs/fsl/bin/feat /gridwork1/Studien/MML/MML2/mri/func/r3/
> HP160_SM8_NC_model2.feat/design.fsf -D /gridwork1/Studien/MML/MML2/
> mri/func/r3/HP160_SM8_NC_model2.feat -film
> 13576
>
> /programs/fsl/bin/fsl_sub -T 84 -l logs -N feat4_post -j 13576 /
> programs/fsl/bin/feat /gridwork1/Studien/MML/MML2/mri/func/r3/
> HP160_SM8_NC_model2.feat/design.fsf -D /gridwork1/Studien/MML/MML2/
> mri/func/r3/HP160_SM8_NC_model2.feat -poststats 0 0
> 14887
>
> /programs/fsl/bin/fsl_sub -T 30 -l logs -N feat5_reg -j 12988 /
> programs/fsl/bin/feat /gridwork1/Studien/MML/MML2/mri/func/r3/
> HP160_SM8_NC_model2.feat/design.fsf -D /gridwork1/Studien/MML/MML2/
> mri/func/r3/HP160_SM8_NC_model2.feat -I 1 -reg
> 14988
>
> /programs/fsl/bin/fsl_sub -T 15 -l logs -N feat4_post -j
> 14887,14988 /programs/fsl/bin/feat /gridwork1/Studien/MML/MML2/mri/
> func/r3/HP160_SM8_NC_model2.feat/design.fsf -D /gridwork1/Studien/
> MML/MML2/mri/func/r3/HP160_SM8_NC_model2.feat -poststats 1 0
> 15261
>
> /programs/fsl/bin/fsl_sub -T 1 -l logs -N feat5_stop -j
> 12988,13576,15261,14988 /programs/fsl/bin/feat /gridwork1/Studien/
> MML/MML2/mri/func/r3/HP160_SM8_NC_model2.feat/design.fsf -D /
> gridwork1/Studien/MML/MML2/mri/func/r3/HP160_SM8_NC_model2.feat -stop
> Prestats
> /programs/fsl/bin/fslmaths /gridwork1/Studien/MML/MML2/mri/func/r3/
> func_data_b prefiltered_func_data
> Total original volumes = 505
> Deleting 5 volume(s) - BE WARNED for future analysis!
>
> /programs/fsl/bin/fslroi prefiltered_func_data prefiltered_func_data
> 5 500
>
> /programs/fsl/bin/fslroi prefiltered_func_data example_func 250 1
>
> /programs/fsl/bin/mcflirt -in prefiltered_func_data -out
> prefiltered_func_data_mcf -mats -plots -refvol 250 -rmsrel -rmsabs
>
> /bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat
> prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms
> prefiltered_func_data_mcf_abs_mean.rms
> prefiltered_func_data_mcf_rel.rms
> prefiltered_func_data_mcf_rel_mean.rms mc
>
> /programs/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t
> 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a
> x,y,z -w 640 -h 144 -o rot.png
>
> /programs/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t
> 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a
> x,y,z -w 640 -h 144 -o trans.png
>
> /programs/fsl/bin/fsl_tsplot -i
> prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -
> t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a
> absolute,relative -o disp.png
>
> /programs/fsl/bin/bet prefiltered_func_data_mcf
> prefiltered_func_data_bet -F
>
> /programs/fsl/bin/fslmaths prefiltered_func_data_bet -thrp 10 -Tmin -
> bin mask -odt char
>
> /programs/fsl/bin/fslmaths prefiltered_func_data_bet -mas mask
> prefiltered_func_data_bet
>
> /programs/fsl/bin/fslmaths mask -kernel gauss 3.39702760085 -fmean
> mask_weight -odt float
>
> /programs/fsl/bin/fslmaths prefiltered_func_data_bet -kernel gauss
> 3.39702760085 -fmean -div mask_weight -mas mask filtered_func_data -
> odt float
>
> /programs/fsl/bin/fslmaths filtered_func_data -ing 10000
> filtered_func_data -odt float
>
> /programs/fsl/bin/fslmaths filtered_func_data -bptf 25.0 -1
> filtered_func_data -odt float
>
> /programs/fsl/bin/fslhd -x filtered_func_data | sed 's/ dt = .*/
> dt = '2.0'/g' | /programs/fsl/bin/fslcreatehd - filtered_func_data
>
> /programs/fsl/bin/fslmaths filtered_func_data -Tmean mean_func
>
> /bin/rm -rf prefiltered_func_data*
> Stats
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_choicesEXPECT_m2.foe custom_timing_files/ev1.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_choicesEXPECTcbl_m2.foe custom_timing_files/ev2.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_fb_pos.foe custom_timing_files/ev3.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_fb_neg.foe custom_timing_files/ev4.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_PE_m2.foe custom_timing_files/ev5.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_PEcbl_m2.foe custom_timing_files/ev6.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_WEIGHTcbl_m2.foe custom_timing_files/ev7.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_alphas_m2.foe custom_timing_files/ev8.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_alphascbl_m2.foe custom_timing_files/ev9.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_choiceMISSED.foe custom_timing_files/ev10.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_fb_missed.foe custom_timing_files/ev11.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_choice_bs.foe custom_timing_files/ev12.txt
>
> mkdir -p custom_timing_files ; /bin/cp /gridwork1/Studien/MML/MML2/
> foe/r3/m5tr_fb_bs.foe custom_timing_files/ev13.txt
>
> /programs/fsl/bin/feat_model design mc/prefiltered_func_data_mcf.par
>
> /programs/fsl/bin/film_gls -rn stats -sa -ms 5 -sp /programs/fsl/bin/
> susan_smooth filtered_func_data design.mat 1000.0
> Log directory is: stats
> parad.getDesignMatrix().Nrows()=500
> parad.getDesignMatrix().Ncols()=32
> sizeTS=500
> numTS=95271
> Calculating residuals...
> Completed
> Estimating residual autocorrelation...
> Calculating raw AutoCorrs... Completed
> mode = 10519
> sig = 1029
> Spatially smoothing auto corr estimates
> .....................
> Completed
> Tukey M = 22
> Tukey estimates... Completed
> Completed
> Prewhitening and Computing PEs...
> Percentage done:
> 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,Completed
> Saving results...
> Completed
>
> /programs/fsl/bin/smoothest -d 468 -m mask -r stats/res4d > stats/
> smoothness
> Post-stats
> /programs/fsl/bin/contrast_mgr stats design.con
> Uncaught exception!
> Rendering using zmin=2.3 zmax=8
> couldn't open "tmpreport_poststats.html": no such file or directory
> while executing
> "open tmp${pagename} r "
> (procedure "feat5:report_insert_stop" line 4)
> invoked from within
> "feat5:report_insert_stop report_poststats.html poststatspics"
> (procedure "feat5:proc_poststats" line 384)
> invoked from within
> "feat5:proc_poststats $RERUNNING $STDSPACE "
> ("-poststats" arm line 6)
> invoked from within
> "switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set session [ lindex $argv $argindex ]
> }
>
> -D {
> incr argindex 1
> set..."
> ("for" body line 2)
> invoked from within
> "for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set ses..."
> (file "/programs/fsl/bin/feat" line 137)
> Registration
> /bin/mkdir -p reg
> Warning - registration to initial_highres turned on but
> no initial_highres image specified in setup file or in
> FEAT directory! Will not register to initial_highres.
> Warning - registration to highres turned on but
> no highres image specified in setup file or in
> FEAT directory! Will not register to highres.
>
> /programs/fsl/bin/flirt -ref standard -in example_func -out
> example_func2standard -omat example_func2standard.mat -cost corratio
> -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp
> trilinear
> ** ERROR (nifti_image_read): failed to find header file for 'standard'
> ** ERROR: nifti_image_open(standard): bad header info
> Error: failed to open file standard
> ERROR: Could not open image standard
> Image Exception : #22 :: Failed to read volume standard
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
>
> /programs/fsl/bin/convert_xfm -inverse -omat
> standard2example_func.mat example_func2standard.mat
> Could not open matrix file example_func2standard.mat
> Cannot read input-matrix
>
> /programs/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35
> sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35
> sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35
> sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /programs/
> fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png +
> slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png
> example_func2standard1.png ; /programs/fsl/bin/slicer standard
> example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55
> slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55
> slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
> slk.png -z 0.65 sll.png ; /programs/fsl/bin/pngappend sla.png +
> slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png
> + sli.png + slj.png + slk.png + sll.png
> example_func2standard2.png ; /programs/fsl/bin/pngappend
> example_func2standard1.png - example_func2standard2.png
> example_func2standard.png; /bin/rm -f sl?.png
> ** ERROR (nifti_image_read): failed to find header file for
> 'example_func2standard'
> ** ERROR: nifti_image_open(example_func2standard): bad header info
> Error: failed to open file example_func2standard
> ERROR: Could not open image example_func2standard
> Image Exception : #22 :: Failed to read volume example_func2standard
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> sh: line 1: 15245 Aborted /programs/fsl/bin/slicer
> example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -
> x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
> 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
> slk.png -z 0.65 sll.png
>
> Cannot open sla.png for reading
> sh: line 1: 15246 Segmentation fault /programs/fsl/bin/
> pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png
> + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png
> example_func2standard1.png
> ** ERROR (nifti_image_read): failed to find header file for 'standard'
> ** ERROR: nifti_image_open(standard): bad header info
> Error: failed to open file standard
> ERROR: Could not open image standard
> Image Exception : #22 :: Failed to read volume standard
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> sh: line 1: 15247 Aborted /programs/fsl/bin/slicer
> standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -
> x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y
> 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55
> slk.png -z 0.65 sll.png
>
> Cannot open sla.png for reading
> sh: line 1: 15248 Segmentation fault /programs/fsl/bin/
> pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png
> + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png
> example_func2standard2.png
>
> Cannot open example_func2standard1.png for reading
> sh: line 1: 15249 Segmentation fault /programs/fsl/bin/
> pngappend example_func2standard1.png - example_func2standard2.png
> example_func2standard.png
>
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---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------
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