 |
 |
Dear Hedok, Darren and others, I promise to provide some numbers as soon as I have some time. But a few thougths on your observations: Neither a simple file transfer nor a benchmark on SPM segmentation are a good stress test for filesystem performance in SPM, because - file transfer only tests _either_ read _or_ write performance - segmentation loads data once and does a lengthy computation before writing once. A more realistic test is e.g. realignment, writing normalised images, smoothing or running a fMRI first level stats estimation, where you have lots of data to read, less data to write (and to different files than the originals). On Fri, 6 Apr 2007, Hedok Lee wrote: > Dear Darren and SPMers. > > There are only two computers in my set up, and there is no NAS. One computer > for running SPM analyses and another one for storage. I've been considering > NAS, but it was difficult to find the ones which support NFS. NFS and FTP > are the only servers that I'm currently running. > > As for performance improvements, exporting NFS as "async" has improved > transfer rate by 300%. Also, people use "Jumbo" frame by changing packet > size from 1024 to 8192. I ran some testing to see the differences in > performance under different conditions. > > This link may help you about "async" > http://www.mythtv.org/wiki/index.php/Optimizing_Performance > > I'm no IT guru, but try to provide some information that may be useful. > > Computers > Intel P4(3.0Gx2) Non-RAID SCSI 10000rpm built-in gigabit card by DELL. > running RH4 WS with ext3 partition > Intel P3(1.0x2) Non-RAID IDE 7200rpm PCI gigabit card. running CentOS4 > with ext3 partition > Router: Linksys 5ports gigabit with full duplex support. > Note: Not sure if these cards support jumbo frame. > > Files to transfer > 167MB(1297 DICOM files by Siemens) x5=835MB > > Total time it took to copy 835MB from P4->P3 > 216sec(3.9MB/sec) default setting > 74sec(11.3MB/sec) async turned on > 63sec(13MB/sec) async+Jumbo frame turned on > > Total time it took to copy 835MB from P3->P4 > 29sec(29MB/sec) default setting > 30sec(28MB/sec) async turned on > 36sec(23MB/sec) async+Jumbo frame turned on > Note: I have no idea why it's so much faster when I transfer P3->P4. Perhaps > it has to with writing speed in SCSI? > > SPM test > Default SPM5 segmentation of 3 high resolution anatomical images, SPGR > (1.0x1.0x1.5) > Total time to complete the segmentation > Local storage (SCSI): 25minutes > Remote storage (NFS): 25minutes > > Conclusion: > I'm beginning to think that SPM over NFS may be ok as total time it took to > complete segmentation was the same. > > I'm still curious if I can improve the performance. > > Hedok > > > [log in to unmask] wrote: >> Dear Hedok, Volkmar, >> >> I'd be interested in hearing about (on or off list) what file systems >> (nfs, samba, etc) you are >> using to enable higher performance data transfers on linux systems for mri >> data analysis. Are you >> using NAS-type of data storage? >> >> thanks >> darren >> >> ==============Original message text=============== >> On Thu, 05 Apr 2007 1:26:23 pm CDT Hedok Lee wrote: >> >> Dear Volkmar and SPMers >> >> Regarding this post, >> >> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0704&L=SPM&P=R3600&I=-3 >> >> > I've just investigated this because I am doing a transition of our >> > network filesystem away from >> > >> NFS and had to resolve some performance issues as well. >> >> As our data continue to grow, I was thinking about having a storage server >> and mount the data >> through NFS. This way, I can keep adding more hard drives onto a storage >> server if necessary. I >> was wondering if there is any particular reason why you decided to move >> away from NFS. If you have a better solution to manage storage server, >> please let me know. All of our machines are linux >> based, and they are connected through gigabit but my experience with NFS >> has been pretty slow >> ~ 15MB/sec. I tried jumbo frame and etc, but had not luck to reach >> ~ ~40MB/sec. >> >> This is probably too slow to carry out SPM analysis over NFS isn't it? >> >> With regards, >> >> Hedok >> >> >> >> >> ----- Original Message ----- >> From: Volkmar Glauche <[log in to unmask]> >> Date: Thursday, April 5, 2007 3:42 am >> Subject: Re: SPM5 slower with 4D files >> To: [log in to unmask] >> >> >> > Hi Jerome, >> > >> > yes, SPM will probably slower on 4D files than on 3D files. Also it will >> > be slower on .nii files than on .hdr/.img pairs. The reason is, that for >> > combined header and data files (as in 3D .nii and 4D cases) SPM needs >> > something like random-write-access to your file to store small bits of >> > information. This is more expensive in terms of I/O time (especially on >> > large disks/RAID systems/network file storage) than storing 3D data with >> > separate .hdr/.img files. However, storing one large file is more >> > efficient in terms of disk usage (if you have partitioned/formatted your >> > disk to efficiently store large files). In short, there is no free >> > lunch, and you have to decide what is more important to you: saving time >> > or saving disk space... >> > I've just investigated this because I am doing a transition of our >> > network filesystem away from NFS and had to resolve some performance >> > issues as well. >> > >> > Volkmar >> > >> > On Wed, 4 Apr 2007, Paul Macey wrote: >> > >> > >> > > Hi Jérôme >> > > >> > > I just wrote something to split 4D to 3D; run the attached >> > > >> > script >> > >> > > (cspm_im_4Dto3D, from SPM5 only) and it will prompt for a 4D >> > > >> > file to split. >> > >> > > You can also use it in batch mode with a couple more options >> > > >> > (see help). The >> > >> > > 3D files should be the same as in the 4D file, so I don't think >> > > >> > you will >> > >> > > loose anything by converting. >> > > >> > > Best wishes, >> > > Paul >> > > >> > > Jérôme Redouté wrote: >> > > >> > > > Dear SPMers, >> > > > My parameters estimation process is extremely slow. Could >> > > > >> > this slowness >> > >> > > > be due to using a 4D-Niftii dataset? >> > > > In order to check that, I would like to convert my sw_xxxx.nii >> > > > >> > 4D files >> > >> > > > into a set of 3D files. >> > > > My questions are: >> > > > -SPM has a function to convert 3D -> 4D , but is the reverse >> > > > >> > function>> available? Where can I find such a converter? >> > >> > > > -These images are preprocessed (realignment, normalisation, >> > > > >> > smoothing), do >> > >> > > > I risk to lose these parameters by converting to 4D to 3D? >> > > > Thanks for your help >> > > > Jerome >> > > > >> > > > >> > -- >> > Volkmar Glauche >> > - >> > Department of Neurology [log in to unmask] >> > Universitaetsklinikum Freiburg Phone 49(0)761-270-5331 >> > Breisacher Str. 64 Fax 49(0)761-270-5416 >> > 79106 Freiburg >> > http://fbi.uniklinik-freiburg.de/===========End of original message >> > text=========== >> > >> >> >> >> -------------------------------- >> Darren R. Gitelman, M.D. >> Department of Neurology >> 710 N. Lake Shore Dr. #1122 >> Chicago, IL 60611 >> Voice: (312) 908-8614 >> Fax: (312) 908-5073 >> -------------------------------- >> >> >> > > -- Volkmar Glauche - Department of Neurology [log in to unmask] Universitaetsklinikum Freiburg Phone 49(0)761-270-5331 Breisacher Str. 64 Fax 49(0)761-270-5416 79106 Freiburg http://fbi.uniklinik-freiburg.de/