Diff for "TestsNewConfigJuly2009" - MRC CBU Imaging Wiki
location: Diff for "TestsNewConfigJuly2009"
Differences between revisions 11 and 12
Revision 11 as of 2009-08-04 09:40:39
Size: 6954
Editor: RhodriCusack
Comment:
Revision 12 as of 2009-11-09 14:33:24
Size: 7046
Editor: MartinMonti
Comment:
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
Rob installed Matlab R2006b (7.3) R2008b and R2009a I think this should
be enough version wise hopefully.
Rob installed Matlab R2006b (7.3) R2008b and R2009a I think this should be enough version wise hopefully.
Line 7: Line 6:
L43 / L44 = CentOS 5.3 x86-64
L45/ L46 = CentOS 5.3 i386
L43 / L44 = CentOS 5.3 x86-64 L45/ L46 = CentOS 5.3 i386
Line 10: Line 8:
All systems have a 80GB /scratch partition to testing using local disc
during the analyses.
All systems have a 80GB /scratch partition to testing using local disc during the analyses.
Line 19: Line 16:
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 32bit (FSL4.1.4) 2221.62user 51.34system 45:29.18elapsed 83%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (41major+16526197minor)pagefaults 0swaps
Line 23: Line 18:
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
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
Line 29: Line 22:
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
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
Line 40: Line 30:
Tested by Jason Taylor/ Daniel Mitchell
.mex64 required recompile (got spurious "out of memory" error in filearray access) but then appears to work fine
Tested by Jason Taylor/ Daniel Mitchell .mex64 required recompile (got spurious "out of memory" error in filearray access) but then appears to work fine
Line 44: Line 33:
aa version 3 test script, all stages up to and including smoothing
Runs fine on 32 & 64 bit machines
aa version 3 test script, all stages up to and including smoothing Runs fine on 32 & 64 bit machines
Line 81: Line 69:
STAGES NOT COMPLETED: 0 TOTAL TIME SO FAR: 7847.129752    STAGES NOT COMPLETED: 0 TOTAL TIME SO FAR: 7847.129752
Line 86: Line 72:
Line 92: Line 77:
||FSL ||<style="vertical-align: top;"> ||<style="vertical-align: top;">Martin Monti ||<style="vertical-align: top;">Martin Monti ||<style="vertical-align: top;"> || ||FSL ||<style="vertical-align: top;">FSL FEEDS
[javascript:void(0);/*1257777180331*/ http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html]||<style="vertical-align: top;">Martin Monti ||<style="vertical-align: top;">Martin Monti ||<style="vertical-align: top;">Martin
Monti||

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

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

139.64137

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

1004.43418

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 ||<style="vertical-align: top;">FSL FEEDS [javascript:void(0);/*1257777180331*/ http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html]||<style="vertical-align: top;">Martin Monti ||<style="vertical-align: top;">Martin Monti ||<style="vertical-align: top;">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

CbuImaging: TestsNewConfigJuly2009 (last edited 2013-03-07 21:22:56 by localhost)