TestsNewConfigJuly2009 - MRC CBU Imaging Wiki

Revision 9 as of 2009-08-04 09:38:01

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Configuration

Rob installed Matlab R2006b (7.3) R2008b and R2009a I think this should be enough version wise hopefully.

Machines details are as follows

L43 / L44 = CentOS 5.3 x86-64 L45/ L46 = CentOS 5.3 i386

All systems have a 80GB /scratch partition to testing using local disc during the analyses.

EEG Lab

Tested by Jason Taylor - works fine on 32 & 64 bit machines

FSL

Tested by Martin Monti

CentOs 5 32bit (FSL4.1.4) 2221.62user 51.34system 45:29.18elapsed 83%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (41major+16526197minor)pagefaults 0swaps

CentOs 5 64 Bit (FSL4.1.4) 1815.98user 37.20system 32:30.90elapsed 94%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (5major+14040943minor)pagefaults 0swaps

Additional testing by Jonathan Peelle

FSL test suite. 32-bit FSL on l46(i386): 37m16.659s 32-bit FSL on l44(x86-64): 37m23.956s 64-bit FSL on l44(x86-64): 29m38.987s

MNE/Freesurfer

Tested by Dan Wakeman

They seem to be missing some key libraries (or possibly improperly installed) e.g. lapack for lots of software. Will play with 3d stuff once this is sorted.

SPM MEG

Tested by Jason Taylor/ Daniel Mitchell .mex64 required recompile (got spurious "out of memory" error in filearray access) but then appears to work fine

SPM FMRI

aa version 3 test script, all stages up to and including smoothing Runs fine on 32 & 64 bit machines Benchmarks

BENCHMARK TIMINGS IN SECONDS 04-Aug-2009 10:34:30 MACHINE l43 ============================================================= 0.034743 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/done_aamod_converttmaps 77.955775 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/done_aamod_copystructural 102.068164 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/vstm/done_aamod_convert_epis 124.188648 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/esta/done_aamod_convert_epis 854.017165 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/done_aamod_realign 13.004268 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/vstm/done_aamod_tsdiffana 12.437592 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/esta/done_aamod_tsdiffana 122.092428 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/vstm/done_aamod_slicetiming 132.987688 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/esta/done_aamod_slicetiming 25.242228 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/done_aamod_coreg_noss 516.907568 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/done_aamod_norm_noss 211.949091 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/vstm/done_aamod_norm_write 255.698338 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/esta/done_aamod_norm_write 248.993594 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/vstm/done_aamod_smooth 295.791207 taken to complete stage /imaging/rhodri/aa_demo_l43/testdata/CBU090300/esta/done_aamod_smooth STAGES NOT COMPLETED: 0 TOTAL TIME SO FAR: 2993.368497

BENCHMARK TIMINGS IN SECONDS 04-Aug-2009 09:17:44 MACHINE l45 ============================================================= 0.054619 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/done_aamod_converttmaps 79.689526 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/done_aamod_copystructural 528.510791 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/vstm/done_aamod_convert_epis 478.110204 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/esta/done_aamod_convert_epis 2415.385071 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/done_aamod_realign 128.452764 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/vstm/done_aamod_tsdiffana 14.462088 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/esta/done_aamod_tsdiffana 139.641370 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/vstm/done_aamod_slicetiming 142.661687 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/esta/done_aamod_slicetiming 40.816936 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/done_aamod_coreg_noss 871.872395 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/done_aamod_norm_noss 646.672488 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/vstm/done_aamod_norm_write 875.077629 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/esta/done_aamod_norm_write 1004.434180 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/vstm/done_aamod_smooth 481.288004 taken to complete stage /imaging/rhodri/aa_demo_l45/testdata/CBU090300/esta/done_aamod_smooth STAGES NOT COMPLETED: 0 TOTAL TIME SO FAR: 7847.129752

Software maintainers copied from AvailableSoftware

Software

Package

First port of Call (i.e. wiki page)

Manager

Maintainer

Contributors

EEG Lab

Jason Taylor

Jason Taylor

Jason Taylor

Fieldtrip

FieldtripInformation

Jonathan Peelle

Jonathan Peelle

Freesurfer

Daniel Wakeman

Daniel Wakeman

Daniel Wakeman

FSL

Martin Monti

Martin Monti

MNE

http://imaging.mrc-cbu.cam.ac.uk/meg/MneAnalysis

Daniel Wakeman

Daniel Wakeman

Daniel Wakeman

SPM

<style="vertical-align: top;">http://imaging.mrc-cbu.cam.ac.uk/imaging/SpmInformation (FMRI) http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis (MEG/EEG)

Rhodri Cusack

Rhodri Cusack

Daniel Mitchell, Jason Taylor, Rik Henson, Rhodri Cusack