Hi Markus, Thanks for your help!
Here's what I have after typing glxgears: 16523 frames in 5.5 seconds = 3013.267 FPS 362 frames in 5.4 seconds = 66.654 FPS 367 frames in 6.5 seconds = 56.306 FPS 381 frames in 277.1 seconds = 1.375 FPS 16640 frames in 5.2 seconds = 3201.886 FPS 262 frames in 6.1 seconds = 43.029 FPS 372 frames in 5.4 seconds = 69.340 FPS 262 frames in 5.7 seconds = 45.837 FPS 383 frames in 6.4 seconds = 59.809 FPS 382 frames in 6.7 seconds = 56.849 FPS 369 frames in 5.4 seconds = 68.384 FPS 364 frames in 6.4 seconds = 57.207 FPS 370 frames in 5.7 seconds = 65.105 FPS 263 frames in 5.4 seconds = 48.992 FPS 381 frames in 6.4 seconds = 59.994 FPS 381 frames in 5.7 seconds = 67.056 FPS 253 frames in 5.3 seconds = 47.457 FPS 383 frames in 6.3 seconds = 60.355 FPS 383 frames in 6.7 seconds = 57.111 FPS 394 frames in 6.3 seconds = 62.099 FPS 385 frames in 6.7 seconds = 57.298 FPS 325 frames in 5.4 seconds = 59.984 FPS 372 frames in 6.7 seconds = 55.758 FPS 408 frames in 6.4 seconds = 64.083 FPS 391 frames in 6.7 seconds = 58.364 FPS 340 frames in 5.4 seconds = 63.223 FPS 374 frames in 6.3 seconds = 58.905 FPS Best, Vy On Tue, Jun 3, 2014 at 4:27 PM, Markus Gschwind <markus.gschw...@gmail.com> wrote: > 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. > > -- 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.
