Hi Vy, This is what my 2011 MBP gives: $ glxgears 10235 frames in 5.0 seconds = 2046.978 FPS 10612 frames in 5.0 seconds = 2122.353 FPS 10689 frames in 5.0 seconds = 2137.778 FPS 14639 frames in 5.0 seconds = 2927.775 FPS 14584 frames in 5.0 seconds = 2915.777 FPS 14437 frames in 5.0 seconds = 2885.138 FPS
So yours is quite slow. Did you see the gears move smoothly or where they stuttering? What gives glxgears on your local terminal (without ssh to your server)? You'll probably see the difference... Best, M 2014-06-03 23:39 GMT+02:00 Vy Dinh <vdi...@wisc.edu>: > 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. > >
_______________________________________________ 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.
