Hi! Can the connection be slow?
Can you type in your local terminal and also in the ssh remote terminal the following: glxgears and let it run a while and past here the output. Cheers! Markus 2014-06-03 23:16 GMT+02:00 Vy Dinh <vdi...@wisc.edu>: > Hi, > > I discovered that installing Freesurfer onto my local workstation and > running Tkmedit from there has resolved my issue. It doesn't explain why > tkmedit is so slow when run from our server, so if you have some ideas > please let me know. Thank you all for your help. > > Best, > > Vy > > > On Tue, Jun 3, 2014 at 12:39 PM, Vy Dinh <vydi...@gmail.com> wrote: > >> Thank you for your reply. All of our Freesurfer commands, including >> Tkmedit are run from the servers on the RedHat Machine. We use the ssh -Y >> syntax (not -X), and when I tried using -X instead, it doesn't change the >> speed of tkmedit. >> >> Additionally, I tried copying my data to another (department's) server at >> our institution and running tkmedit from there. We didn't experience any >> lag here, so this suggests that our department's dedicated server is >> somehow dealing with tkmedit differently. However, when our server expert >> checked the CPU usage, it appears that OUR department's server is using >> less RAM overall (so it if anything, our data should process more >> quickly.). In other words, we can't figure out how Tkmedit is utilized by >> the servers differently. >> >> -Vy >> >> >> On Tue, Jun 3, 2014 at 11:13 AM, dgw <dgwake...@gmail.com> wrote: >> >>> Hi, >>> >>> What machine are you actually running tkmedit on? >>> >>> more specifically: >>> You appear to be using a mac. Do you run tkmedit directly on the mac? >>> >>> or are you using ssh -X (or something like it to run it) on the Red Hat >>> machines? >>> >>> Thanks, >>> D >>> >>> >>> On Tue, Jun 3, 2014 at 11:55 AM, Vy Dinh <vdi...@wisc.edu> wrote: >>> >>>> >>>> Greetings Freesurfer developers, >>>> >>>> I'm looking for ways to improve the speed of TKMEDIT for Freesurfer >>>> 5.3. Specifically, the GUI interface is abnormally slow; edits made to a >>>> voxel takes 1-2 seconds to show up on the screen. Interesting, the >>>> recon-all doesn't appear to be slow (as each subject has been processed >>>> within a 24 hr period), so I wonder if this problem has something to do >>>> with TKMEDIT's GUI & my current setup. >>>> >>>> Although I SSH into our server for data processing, here are the specs >>>> for my local workstation: >>>> >>>> Mac OSX 10.9.2 >>>> 2.7 GHz Intel Core i5 Determine how many cores (Apple icon >> About >>>> this Mac >> More Info) >>>> 4 GB 1333 MHz DDR3 >>>> >>>> Server Specs: >>>> >>>> Our App servers have 4 Xeon CPUs apiece, each with 8 cores running at >>>> 2.7GHz, for a total of 32 cores (I was told that this shouldn't be the >>>> cause as the point of multi-core and multi-threading is not dependent on >>>> speed only). As well, each server has 94 GB of RAM. >>>> >>>> Our App servers mount shares via NFS from our file servers. All servers >>>> are the same version of Red Hat Linux, so there is no differences >>>> there. According to the server expert at our institution, the tkmedit does >>>> not appear to surpass a CPU *utilization* of 8*%* of a single core, so >>>> the programs running off the server should be able to utilize its maximum >>>> speed. >>>> >>>> I am working closely with our server expert to troubleshoot this issue, >>>> so any insight from the development team will be much appreciated. Thank >>>> you. >>>> >>>> >>>> Best regards, >>>> >>>> Vy Dinh >>>> MD Candidate, Class of 2017 >>>> University of Wisconsin School of Medicine and Public Health >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >> >> >> -- >> Vy T.U. Dinh >> Research Assistant, Neurological Sciences >> Rush University Medical Center >> Phone: (312) 563-3853 >> Fax: (312) 563-4660 >> Email: vy_d...@rush.edu >> >> > > > -- > Vy Dinh > MD Candidate, Class of 2017 > University of Wisconsin School of Medicine and Public Health > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
