Dear All.
I'm trying to run a randomise_parallel job on an SGE cluster. The job is taking a long time to finish and I was beginning to wonder why.
I have looked in the log folders and at the specific log files for the fragments, and I wonder if you can let me know if there is anything wrong with what they contain:
randomise options: -i all_FA_skeletonised -o ./slope10 -m mean_FA_skeleton_mask -d slopes.mat -t slopes.con -n 10000 --T2 -n 11 -o ./slope10_SEED680 --seed=680
Seeding with 680
Loading Data:
Data loaded
1.5207e+64 permutations required for exhaustive test of t-test 1
Doing 11 random permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Starting permutation 3
Starting permutation 4
Starting permutation 5
Starting permutation 6
Starting permutation 7
Starting permutation 8
Starting permutation 9
Starting permutation 10
Starting permutation 11
1.5207e+64 permutations required for exhaustive test of t-test 2
Doing 11 random permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Starting permutation 3
Starting permutation 4
......
......
Can there really be 10^64 permutations for my model? I'm attaching the model and contrast files below....
The other thing that's worrying me is that when I look at the individual nodes in the cluster for the randomise process, I see the following:
[mt1005@auba neuro_sky]$ ps -edaf | grep rand
mt1005 9047 9046 0 14:58 ? 00:00:00 /bin/sh -c FSLOUTPUTTYPE=NIFTI_GZ; sleep 3445 ; /usr/local/fsl//bin/randomise -i all_FA_skeletonised -o ./slope10 -m mean_FA_skeleton_mask -d slopes.mat -t slopes.con -n 10000 --T2 -n 11 -o ./slope10_SEED689 --seed=689
mt1005 13275 13274 0 15:39 ? 00:00:00 /bin/sh -c FSLOUTPUTTYPE=NIFTI_GZ; sleep 3520 ; /usr/local/fsl//bin/randomise -i all_FA_skeletonised -o ./slope10 -m mean_FA_skeleton_mask -d slopes.mat -t slopes.con -n 10000 --T2 -n 11 -o ./slope10_SEED704 --seed=704
The node is not overloaded, but each randomise job is being set to sleep for about 1 hour before being run!
With 910 fragments I'm not hopeful that I'll live long enough to see the end of my job :-)
/ContrastName1 "group mean"
/ContrastName2 ""
/ContrastName3 ""
/ContrastName4 ""
/ContrastName5 ""
/ContrastName6 ""
/ContrastName7 ""
/ContrastName8 ""
/ContrastName9 ""
/ContrastName10 ""
/ContrastName11 ""
/ContrastName12 ""
/ContrastName13 ""
/ContrastName14 ""
/ContrastName15 ""
/ContrastName16 ""
/ContrastName17 ""
/ContrastName18 ""
/NumWaves 10
/NumContrasts 18
/PPheights 3.850658e+00 3.850658e+00 1.109141e+01 1.109141e+01 2.520255e+00 2.520255e+00 4.906752e+00 4.906752e+00 6.691092e+00 6.691092e+00 2.415261e+00 2.415261e+00 1.730678e+00 1.730678e+00 4.191010e+00 4.191010e+00 1.294439e+00 1.294439e+00
/RequiredEffect 2.919 2.919 3.731 3.731 3.389 3.389 4.296 4.296 4.228 4.228 4.070 4.070 3.456 3.456 3.969 3.969 3.431 3.431
/Matrix
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/NumWaves 10
/NumPoints 50
/PPheights 1.000000e+00 4.630000e+00 6.050000e+00 1.000000e+00 7.300000e+00 1.113000e+01 1.000000e+00 4.120000e+00 7.840000e+00 3.160000e+02
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Apologies for the long e-mail, thank you for your help,
Regards,
Maria Tziraki
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