java 8 and OSX
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About a year ago I wrote about Fiji slowing down during use with Java 8
and OSX. http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html As this is still happening, I want to find out if there is any additional information about this. I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). I have 16GB RAM. Wayne had noted that menu updates are problematic, and added a parameter SetMenuBarCount: to follow that. I note problems when this is over 50, but I cannot say when it really becomes unusable and I have to quit and start again. One thing that I noticed -- if I allocate 12GB to Fiji, then the problems will start much sooner than if I allocate 10GB to Fiji. So I suspect that some resource that Fiji uses, which is outside of Fiji, is using up memory (but I dont know how to check this). Do people who are running on high-powered Linux machines have this problem? --aryeh -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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We've been going back and forth on it a bit on the forums too:
http://forum.imagej.net/t/mac-java-speed-issues/304 I think we really need to help pin this down for Chris and Wayne so they can make a change. I've simply not had the time recently to dig further, but I intend to when the field season here settles down. It is absolutely related to the changing of windows, but what exactly is causing it is unclear to me. It does not happen when in batch mode. Only when in interactive mode. On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss <[hidden email]> wrote: > About a year ago I wrote about Fiji slowing down during use with Java 8 > and OSX. > http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html > > As this is still happening, I want to find out if there is any additional > information about this. > > I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). > I have 16GB RAM. > > Wayne had noted that menu updates are problematic, and added a parameter > SetMenuBarCount: to follow that. > I note problems when this is over 50, but I cannot say when it really > becomes unusable and I have to quit and start again. > > One thing that I noticed -- if I allocate 12GB to Fiji, then the problems > will start much sooner than if I allocate 10GB to Fiji. > So I suspect that some resource that Fiji uses, which is outside of Fiji, > is using up memory (but I dont know how to check this). > > Do people who are running on high-powered Linux machines have this problem? > > --aryeh > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Brandon & Aryeh,
I am fairly confident that the cause is attaching AWT menus bars, as I outline here: http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden Someone with a technical background needs to investigate the potential solutions to the issue that I mention in that post. In particular, using the Apple-specific "Application.setDefaultMenuBar" method is highly likely to fix the issue. However, as I outline here: http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden It would be a bit of work to add code to ImageJ2 to hot-translate the ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is that doing this would have multiple advantages: * The "grinding to a halt" performance problem would likely disappear. * We would have a richer menu bar with icons for ImageJ2 commands that provide them. ;-) * The menu bar flashing when you switch windows would no longer happen. The downside is that it is more complex internally, since we would need to keep the JMenuBar internally synchronized with the menu bar that IJ1 believes is its menu bar (but in actuality is now never actually attached to any windows). There might also be unforeseen technical obstacles with my proposed solution here. All in all, it would probably cost me several days to explore and implement this fix, and I currently have other more urgent priorities. But I will try to make time to do this work early this fall. Regards, Curtis -- Curtis Rueden LOCI software architect - http://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr <[hidden email]> wrote: > We've been going back and forth on it a bit on the forums too: > http://forum.imagej.net/t/mac-java-speed-issues/304 > > I think we really need to help pin this down for Chris and Wayne so they > can make a change. I've simply not had the time recently to dig further, > but I intend to when the field season here settles down. > > It is absolutely related to the changing of windows, but what exactly is > causing it is unclear to me. It does not happen when in batch mode. Only > when in interactive mode. > > On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss <[hidden email]> wrote: > > > About a year ago I wrote about Fiji slowing down during use with Java 8 > > and OSX. > > http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html > > > > As this is still happening, I want to find out if there is any additional > > information about this. > > > > I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). > > I have 16GB RAM. > > > > Wayne had noted that menu updates are problematic, and added a parameter > > SetMenuBarCount: to follow that. > > I note problems when this is over 50, but I cannot say when it really > > becomes unusable and I have to quit and start again. > > > > One thing that I noticed -- if I allocate 12GB to Fiji, then the problems > > will start much sooner than if I allocate 10GB to Fiji. > > So I suspect that some resource that Fiji uses, which is outside of Fiji, > > is using up memory (but I dont know how to check this). > > > > Do people who are running on high-powered Linux machines have this > problem? > > > > --aryeh > > > > -- > > Aryeh Weiss > > Faculty of Engineering > > Bar Ilan University > > Ramat Gan 52900 Israel > > > > Ph: 972-3-5317638 > > FAX: 972-3-7384051 > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Curtis
Thank you for your reply. It is good to know that there is hope... Is there anything that I can do in either my Fiji configuration or my Java configuration to improve performance? Best regards --aryeh On 11/07/2016 1:25 AM, Curtis Rueden wrote: > Hi Brandon & Aryeh, > > I am fairly confident that the cause is attaching AWT menus bars, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden > > Someone with a technical background needs to investigate the potential > solutions to the issue that I mention in that post. > > In particular, using the Apple-specific "Application.setDefaultMenuBar" > method is highly likely to fix the issue. However, as I outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden > > It would be a bit of work to add code to ImageJ2 to hot-translate the > ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is that doing > this would have multiple advantages: > > * The "grinding to a halt" performance problem would likely disappear. > * We would have a richer menu bar with icons for ImageJ2 commands that > provide them. ;-) > * The menu bar flashing when you switch windows would no longer happen. > > The downside is that it is more complex internally, since we would need to > keep the JMenuBar internally synchronized with the menu bar that IJ1 > believes is its menu bar (but in actuality is now never actually attached > to any windows). > > There might also be unforeseen technical obstacles with my proposed > solution here. All in all, it would probably cost me several days to > explore and implement this fix, and I currently have other more urgent > priorities. But I will try to make time to do this work early this fall. > > Regards, > Curtis > > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr <[hidden email]> > wrote: > >> We've been going back and forth on it a bit on the forums too: >> http://forum.imagej.net/t/mac-java-speed-issues/304 >> >> I think we really need to help pin this down for Chris and Wayne so they >> can make a change. I've simply not had the time recently to dig further, >> but I intend to when the field season here settles down. >> >> It is absolutely related to the changing of windows, but what exactly is >> causing it is unclear to me. It does not happen when in batch mode. Only >> when in interactive mode. >> >> On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss <[hidden email]> wrote: >> >>> About a year ago I wrote about Fiji slowing down during use with Java 8 >>> and OSX. >>> http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html >>> >>> As this is still happening, I want to find out if there is any additional >>> information about this. >>> >>> I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). >>> I have 16GB RAM. >>> >>> Wayne had noted that menu updates are problematic, and added a parameter >>> SetMenuBarCount: to follow that. >>> I note problems when this is over 50, but I cannot say when it really >>> becomes unusable and I have to quit and start again. >>> >>> One thing that I noticed -- if I allocate 12GB to Fiji, then the problems >>> will start much sooner than if I allocate 10GB to Fiji. >>> So I suspect that some resource that Fiji uses, which is outside of Fiji, >>> is using up memory (but I dont know how to check this). >>> >>> Do people who are running on high-powered Linux machines have this >> problem? >>> --aryeh >>> >>> -- >>> -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Aryeh,
> Is there anything that I can do in either my Fiji configuration or my > Java configuration to improve performance? The only workarounds I know of right now: - On OS X, use Apple Java 6 - Use Linux instead of OS X - Do not open and close many windows -- Of course, if you are doing exploratory viz and processing, you can't avoid it - Restart ImageJ after opening and closing many windows Regards, Curtis -- Curtis Rueden LOCI software architect - http://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email]> wrote: > Hi Curtis > > Thank you for your reply. It is good to know that there is hope... > > Is there anything that I can do in either my Fiji configuration or my Java > configuration to improve performance? > > Best regards > --aryeh > > > > On 11/07/2016 1:25 AM, Curtis Rueden wrote: > >> Hi Brandon & Aryeh, >> >> I am fairly confident that the cause is attaching AWT menus bars, as I >> outline here: >> http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden >> >> Someone with a technical background needs to investigate the potential >> solutions to the issue that I mention in that post. >> >> In particular, using the Apple-specific "Application.setDefaultMenuBar" >> method is highly likely to fix the issue. However, as I outline here: >> http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden >> >> It would be a bit of work to add code to ImageJ2 to hot-translate the >> ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is that doing >> this would have multiple advantages: >> >> * The "grinding to a halt" performance problem would likely disappear. >> * We would have a richer menu bar with icons for ImageJ2 commands that >> provide them. ;-) >> * The menu bar flashing when you switch windows would no longer happen. >> >> The downside is that it is more complex internally, since we would need to >> keep the JMenuBar internally synchronized with the menu bar that IJ1 >> believes is its menu bar (but in actuality is now never actually attached >> to any windows). >> >> There might also be unforeseen technical obstacles with my proposed >> solution here. All in all, it would probably cost me several days to >> explore and implement this fix, and I currently have other more urgent >> priorities. But I will try to make time to do this work early this fall. >> >> Regards, >> Curtis >> >> >> -- >> Curtis Rueden >> LOCI software architect - http://loci.wisc.edu/software >> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden >> Did you know ImageJ has a forum? http://forum.imagej.net/ >> >> >> On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr <[hidden email]> >> wrote: >> >> We've been going back and forth on it a bit on the forums too: >>> http://forum.imagej.net/t/mac-java-speed-issues/304 >>> >>> I think we really need to help pin this down for Chris and Wayne so they >>> can make a change. I've simply not had the time recently to dig further, >>> but I intend to when the field season here settles down. >>> >>> It is absolutely related to the changing of windows, but what exactly is >>> causing it is unclear to me. It does not happen when in batch mode. Only >>> when in interactive mode. >>> >>> On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss <[hidden email]> >>> wrote: >>> >>> About a year ago I wrote about Fiji slowing down during use with Java 8 >>>> and OSX. >>>> http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html >>>> >>>> As this is still happening, I want to find out if there is any >>>> additional >>>> information about this. >>>> >>>> I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). >>>> I have 16GB RAM. >>>> >>>> Wayne had noted that menu updates are problematic, and added a parameter >>>> SetMenuBarCount: to follow that. >>>> I note problems when this is over 50, but I cannot say when it really >>>> becomes unusable and I have to quit and start again. >>>> >>>> One thing that I noticed -- if I allocate 12GB to Fiji, then the >>>> problems >>>> will start much sooner than if I allocate 10GB to Fiji. >>>> So I suspect that some resource that Fiji uses, which is outside of >>>> Fiji, >>>> is using up memory (but I dont know how to check this). >>>> >>>> Do people who are running on high-powered Linux machines have this >>>> >>> problem? >>> >>>> --aryeh >>>> >>>> -- >>>> >>>> > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On 11/07/2016 10:29 AM, Curtis Rueden wrote:
> Hi Aryeh, > > > Is there anything that I can do in either my Fiji configuration or my > > Java configuration to improve performance? > > The only workarounds I know of right now: > > - On OS X, use Apple Java 6 I am using some plugins that require Java 7 or higher, so that is no longer an option. > - Use Linux instead of OS X I am seriously considering that, but it will require new laptop because switching to Linux on a macbook pro is not for the faint of heart. For those who wish to try, this is relevant: http://www.makeuseof.com/tag/install-linux-macbook-pro/ > - Do not open and close many windows I will try to use batch mode as much as possible, and it buys some time. > -- Of course, if you are doing exploratory viz and processing, you > can't avoid it > - Restart ImageJ after opening and closing many windows yes -- I have been doing a lot of that. I will add the one other thing that I found -- reducing ImageJ's memory appears to buy some time. > > Regards, > Curtis > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 > > On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email] > <mailto:[hidden email]>> wrote: > > Hi Curtis > > Thank you for your reply. It is good to know that there is hope... > > Is there anything that I can do in either my Fiji configuration or > my Java configuration to improve performance? > > Best regards > --aryeh > > > > On 11/07/2016 1:25 AM, Curtis Rueden wrote: > > Hi Brandon & Aryeh, > > I am fairly confident that the cause is attaching AWT menus > bars, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden > > Someone with a technical background needs to investigate the > potential > solutions to the issue that I mention in that post. > > In particular, using the Apple-specific > "Application.setDefaultMenuBar" > method is highly likely to fix the issue. However, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden > > It would be a bit of work to add code to ImageJ2 to > hot-translate the > ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is > that doing > this would have multiple advantages: > > * The "grinding to a halt" performance problem would likely > disappear. > * We would have a richer menu bar with icons for ImageJ2 > commands that > provide them. ;-) > * The menu bar flashing when you switch windows would no > longer happen. > > The downside is that it is more complex internally, since we > would need to > keep the JMenuBar internally synchronized with the menu bar > that IJ1 > believes is its menu bar (but in actuality is now never > actually attached > to any windows). > > There might also be unforeseen technical obstacles with my > proposed > solution here. All in all, it would probably cost me several > days to > explore and implement this fix, and I currently have other > more urgent > priorities. But I will try to make time to do this work early > this fall. > > Regards, > Curtis > > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr > <[hidden email] <mailto:[hidden email]>> > wrote: > > We've been going back and forth on it a bit on the forums too: > http://forum.imagej.net/t/mac-java-speed-issues/304 > > I think we really need to help pin this down for Chris and > Wayne so they > can make a change. I've simply not had the time recently > to dig further, > but I intend to when the field season here settles down. > > It is absolutely related to the changing of windows, but > what exactly is > causing it is unclear to me. It does not happen when in > batch mode. Only > when in interactive mode. > > On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss > <[hidden email] <mailto:[hidden email]>> wrote: > > About a year ago I wrote about Fiji slowing down > during use with Java 8 > and OSX. > http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html > > As this is still happening, I want to find out if > there is any additional > information about this. > > I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). > I have 16GB RAM. > > Wayne had noted that menu updates are problematic, and > added a parameter > SetMenuBarCount: to follow that. > I note problems when this is over 50, but I cannot say > when it really > becomes unusable and I have to quit and start again. > > One thing that I noticed -- if I allocate 12GB to > Fiji, then the problems > will start much sooner than if I allocate 10GB to Fiji. > So I suspect that some resource that Fiji uses, which > is outside of Fiji, > is using up memory (but I dont know how to check this). > > Do people who are running on high-powered Linux > machines have this > > problem? > > --aryeh > > -- > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Aryeh,
I have used linux in macbook pros since 2005. Works better than MacOSX itself, and by better I mean better wifi, same battery life, same programs run faster, no swapping. The main motivation was the same issue you are experiencing now: Java never worked as well in macosx as it did in other operating systems. The best guide for installing Ubuntu in a MacBook Pro, better than my own guides, is this one: http://heeris.id.au/2014/ubuntu-plus-mac-pure-efi-boot/ Make sure to read the whole thing before you start. You can also dual-boot easily. Best, Albert 2016-07-11 3:39 GMT-04:00 Aryeh Weiss <[hidden email]>: > On 11/07/2016 10:29 AM, Curtis Rueden wrote: > >> Hi Aryeh, >> >> > Is there anything that I can do in either my Fiji configuration or my >> > Java configuration to improve performance? >> >> The only workarounds I know of right now: >> >> - On OS X, use Apple Java 6 >> > I am using some plugins that require Java 7 or higher, so that is no > longer an option. > >> - Use Linux instead of OS X >> > I am seriously considering that, but it will require new laptop because > switching to Linux on a macbook pro is not for the faint of heart. For > those who wish to try, this is relevant: > http://www.makeuseof.com/tag/install-linux-macbook-pro/ > >> - Do not open and close many windows >> > I will try to use batch mode as much as possible, and it buys some time. > >> -- Of course, if you are doing exploratory viz and processing, you can't >> avoid it >> - Restart ImageJ after opening and closing many windows >> > yes -- I have been doing a lot of that. > I will add the one other thing that I found -- reducing ImageJ's memory > appears to buy some time. > >> >> Regards, >> Curtis >> >> -- >> Curtis Rueden >> LOCI software architect - http://loci.wisc.edu/software >> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden >> Did you know ImageJ has a forum? http://forum.imagej.net/ >> >> Best regards > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > > > > >> On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email] >> <mailto:[hidden email]>> wrote: >> >> Hi Curtis >> >> Thank you for your reply. It is good to know that there is hope... >> >> Is there anything that I can do in either my Fiji configuration or >> my Java configuration to improve performance? >> >> Best regards >> --aryeh >> >> >> >> On 11/07/2016 1:25 AM, Curtis Rueden wrote: >> >> Hi Brandon & Aryeh, >> >> I am fairly confident that the cause is attaching AWT menus >> bars, as I >> outline here: >> http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden >> >> Someone with a technical background needs to investigate the >> potential >> solutions to the issue that I mention in that post. >> >> In particular, using the Apple-specific >> "Application.setDefaultMenuBar" >> method is highly likely to fix the issue. However, as I >> outline here: >> http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden >> >> It would be a bit of work to add code to ImageJ2 to >> hot-translate the >> ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is >> that doing >> this would have multiple advantages: >> >> * The "grinding to a halt" performance problem would likely >> disappear. >> * We would have a richer menu bar with icons for ImageJ2 >> commands that >> provide them. ;-) >> * The menu bar flashing when you switch windows would no >> longer happen. >> >> The downside is that it is more complex internally, since we >> would need to >> keep the JMenuBar internally synchronized with the menu bar >> that IJ1 >> believes is its menu bar (but in actuality is now never >> actually attached >> to any windows). >> >> There might also be unforeseen technical obstacles with my >> proposed >> solution here. All in all, it would probably cost me several >> days to >> explore and implement this fix, and I currently have other >> more urgent >> priorities. But I will try to make time to do this work early >> this fall. >> >> Regards, >> Curtis >> >> >> -- >> Curtis Rueden >> LOCI software architect - http://loci.wisc.edu/software >> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden >> Did you know ImageJ has a forum? http://forum.imagej.net/ >> >> >> On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr >> <[hidden email] <mailto:[hidden email]>> >> wrote: >> >> We've been going back and forth on it a bit on the forums too: >> http://forum.imagej.net/t/mac-java-speed-issues/304 >> >> I think we really need to help pin this down for Chris and >> Wayne so they >> can make a change. I've simply not had the time recently >> to dig further, >> but I intend to when the field season here settles down. >> >> It is absolutely related to the changing of windows, but >> what exactly is >> causing it is unclear to me. It does not happen when in >> batch mode. Only >> when in interactive mode. >> >> On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss >> <[hidden email] <mailto:[hidden email]>> wrote: >> >> About a year ago I wrote about Fiji slowing down >> during use with Java 8 >> and OSX. >> >> http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html >> >> As this is still happening, I want to find out if >> there is any additional >> information about this. >> >> I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). >> I have 16GB RAM. >> >> Wayne had noted that menu updates are problematic, and >> added a parameter >> SetMenuBarCount: to follow that. >> I note problems when this is over 50, but I cannot say >> when it really >> becomes unusable and I have to quit and start again. >> >> One thing that I noticed -- if I allocate 12GB to >> Fiji, then the problems >> will start much sooner than if I allocate 10GB to Fiji. >> So I suspect that some resource that Fiji uses, which >> is outside of Fiji, >> is using up memory (but I dont know how to check this). >> >> Do people who are running on high-powered Linux >> machines have this >> >> problem? >> >> --aryeh >> >> -- >> >> >> > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- http://albert.rierol.net http://www.janelia.org/lab/cardona-lab http://www.ini.uzh.ch/~acardona/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hello Pioneers and Users,
Is there any progress in resolving this issue? What has been posted are workarounds, but what is needed is a solution. I am experiencing the exact same problem: Mac + ImageJ (1.50b) + Java8 (latest update)—> very long loading times…the Menus appear very late especially with z-stacks. Any help is appreciated. Best Manu ******************************** Manu Tiwari Molekulare Zellbiologie Institut I für Anatomie Universität zu Köln Kerpener Str. 62, Geb.37 D-50937 Köln Germany Tel. +49 - 221 - 478 32655 On 11 Jul 2016, at 19:58, Albert Cardona <[hidden email]<mailto:[hidden email]>> wrote: Hi Aryeh, I have used linux in macbook pros since 2005. Works better than MacOSX itself, and by better I mean better wifi, same battery life, same programs run faster, no swapping. The main motivation was the same issue you are experiencing now: Java never worked as well in macosx as it did in other operating systems. The best guide for installing Ubuntu in a MacBook Pro, better than my own guides, is this one: http://heeris.id.au/2014/ubuntu-plus-mac-pure-efi-boot/ Make sure to read the whole thing before you start. You can also dual-boot easily. Best, Albert 2016-07-11 3:39 GMT-04:00 Aryeh Weiss <[hidden email]>: On 11/07/2016 10:29 AM, Curtis Rueden wrote: Hi Aryeh, Is there anything that I can do in either my Fiji configuration or my Java configuration to improve performance? The only workarounds I know of right now: - On OS X, use Apple Java 6 I am using some plugins that require Java 7 or higher, so that is no longer an option. - Use Linux instead of OS X I am seriously considering that, but it will require new laptop because switching to Linux on a macbook pro is not for the faint of heart. For those who wish to try, this is relevant: http://www.makeuseof.com/tag/install-linux-macbook-pro/ - Do not open and close many windows I will try to use batch mode as much as possible, and it buys some time. -- Of course, if you are doing exploratory viz and processing, you can't avoid it - Restart ImageJ after opening and closing many windows yes -- I have been doing a lot of that. I will add the one other thing that I found -- reducing ImageJ's memory appears to buy some time. Regards, Curtis -- Curtis Rueden LOCI software architect - http://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ Best regards -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email] <mailto:[hidden email]>> wrote: Hi Curtis Thank you for your reply. It is good to know that there is hope... Is there anything that I can do in either my Fiji configuration or my Java configuration to improve performance? Best regards --aryeh On 11/07/2016 1:25 AM, Curtis Rueden wrote: Hi Brandon & Aryeh, I am fairly confident that the cause is attaching AWT menus bars, as I outline here: http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden Someone with a technical background needs to investigate the potential solutions to the issue that I mention in that post. In particular, using the Apple-specific "Application.setDefaultMenuBar" method is highly likely to fix the issue. However, as I outline here: http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden It would be a bit of work to add code to ImageJ2 to hot-translate the ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is that doing this would have multiple advantages: * The "grinding to a halt" performance problem would likely disappear. * We would have a richer menu bar with icons for ImageJ2 commands that provide them. ;-) * The menu bar flashing when you switch windows would no longer happen. The downside is that it is more complex internally, since we would need to keep the JMenuBar internally synchronized with the menu bar that IJ1 believes is its menu bar (but in actuality is now never actually attached to any windows). There might also be unforeseen technical obstacles with my proposed solution here. All in all, it would probably cost me several days to explore and implement this fix, and I currently have other more urgent priorities. But I will try to make time to do this work early this fall. Regards, Curtis -- Curtis Rueden LOCI software architect - http://loci.wisc.edu/software ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/ On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr <[hidden email] <mailto:[hidden email]>> wrote: We've been going back and forth on it a bit on the forums too: http://forum.imagej.net/t/mac-java-speed-issues/304 I think we really need to help pin this down for Chris and Wayne so they can make a change. I've simply not had the time recently to dig further, but I intend to when the field season here settles down. It is absolutely related to the changing of windows, but what exactly is causing it is unclear to me. It does not happen when in batch mode. Only when in interactive mode. On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss <[hidden email] <mailto:[hidden email]>> wrote: About a year ago I wrote about Fiji slowing down during use with Java 8 and OSX. http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html As this is still happening, I want to find out if there is any additional information about this. I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). I have 16GB RAM. Wayne had noted that menu updates are problematic, and added a parameter SetMenuBarCount: to follow that. I note problems when this is over 50, but I cannot say when it really becomes unusable and I have to quit and start again. One thing that I noticed -- if I allocate 12GB to Fiji, then the problems will start much sooner than if I allocate 10GB to Fiji. So I suspect that some resource that Fiji uses, which is outside of Fiji, is using up memory (but I dont know how to check this). Do people who are running on high-powered Linux machines have this problem? --aryeh -- -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- http://albert.rierol.net http://www.janelia.org/lab/cardona-lab http://www.ini.uzh.ch/~acardona/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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On 13/07/2016 8:04 PM, Manu Tiwari wrote:
> Hello Pioneers and Users, > > Is there any progress in resolving this issue? > What has been posted are workarounds, but what is needed is a solution. > I am experiencing the exact same problem: Mac + ImageJ (1.50b) + Java8 (latest update)—> very long loading times…the Menus appear very late especially with z-stacks. > Any help is appreciated. There is no solution yet. My situation improved a lot when I ran my macros in batch mode, so I recommend you do that when possible. The other action that appears to help is leaving zs much memory available to the OS 9outside of ImageJ, as you can . Since my images are often more than a GB, that can be a problem , but I manage with 10GB in ImageJ out of 16GB. These steps significantly lengthened the intervals between quitting and restarting. Curtiss wrote that he may be able to work on this in the Fall, so there is hope. If you are braver than I, Albert Cardona posted a link (see below) with instructions on how to run Linux on your mac. Best regards --aryeh > Best > Manu > > > > > ******************************** > Manu Tiwari > Molekulare Zellbiologie > Institut I für Anatomie > Universität zu Köln > Kerpener Str. 62, Geb.37 > D-50937 Köln Germany > Tel. +49 - 221 - 478 32655 > > > > > > > On 11 Jul 2016, at 19:58, Albert Cardona <[hidden email]<mailto:[hidden email]>> wrote: > > Hi Aryeh, > > I have used linux in macbook pros since 2005. Works better than MacOSX > itself, and by better I mean better wifi, same battery life, same programs > run faster, no swapping. > > The main motivation was the same issue you are experiencing now: Java never > worked as well in macosx as it did in other operating systems. > > The best guide for installing Ubuntu in a MacBook Pro, better than my own > guides, is this one: > > http://heeris.id.au/2014/ubuntu-plus-mac-pure-efi-boot/ > > Make sure to read the whole thing before you start. You can also dual-boot > easily. > > Best, > > Albert > > 2016-07-11 3:39 GMT-04:00 Aryeh Weiss <[hidden email]>: > > On 11/07/2016 10:29 AM, Curtis Rueden wrote: > > Hi Aryeh, > > Is there anything that I can do in either my Fiji configuration or my > Java configuration to improve performance? > > The only workarounds I know of right now: > > - On OS X, use Apple Java 6 > > I am using some plugins that require Java 7 or higher, so that is no > longer an option. > > - Use Linux instead of OS X > > I am seriously considering that, but it will require new laptop because > switching to Linux on a macbook pro is not for the faint of heart. For > those who wish to try, this is relevant: > http://www.makeuseof.com/tag/install-linux-macbook-pro/ > > - Do not open and close many windows > > I will try to use batch mode as much as possible, and it buys some time. > > -- Of course, if you are doing exploratory viz and processing, you can't > avoid it > - Restart ImageJ after opening and closing many windows > > yes -- I have been doing a lot of that. > I will add the one other thing that I found -- reducing ImageJ's memory > appears to buy some time. > > > Regards, > Curtis > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > Best regards > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > > > > > On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email] > <mailto:[hidden email]>> wrote: > > Hi Curtis > > Thank you for your reply. It is good to know that there is hope... > > Is there anything that I can do in either my Fiji configuration or > my Java configuration to improve performance? > > Best regards > --aryeh > > > > On 11/07/2016 1:25 AM, Curtis Rueden wrote: > > Hi Brandon & Aryeh, > > I am fairly confident that the cause is attaching AWT menus > bars, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden > > Someone with a technical background needs to investigate the > potential > solutions to the issue that I mention in that post. > > In particular, using the Apple-specific > "Application.setDefaultMenuBar" > method is highly likely to fix the issue. However, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden > > It would be a bit of work to add code to ImageJ2 to > hot-translate the > ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is > that doing > this would have multiple advantages: > > * The "grinding to a halt" performance problem would likely > disappear. > * We would have a richer menu bar with icons for ImageJ2 > commands that > provide them. ;-) > * The menu bar flashing when you switch windows would no > longer happen. > > The downside is that it is more complex internally, since we > would need to > keep the JMenuBar internally synchronized with the menu bar > that IJ1 > believes is its menu bar (but in actuality is now never > actually attached > to any windows). > > There might also be unforeseen technical obstacles with my > proposed > solution here. All in all, it would probably cost me several > days to > explore and implement this fix, and I currently have other > more urgent > priorities. But I will try to make time to do this work early > this fall. > > Regards, > Curtis > > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr > <[hidden email] <mailto:[hidden email]>> > wrote: > > We've been going back and forth on it a bit on the forums too: > http://forum.imagej.net/t/mac-java-speed-issues/304 > > I think we really need to help pin this down for Chris and > Wayne so they > can make a change. I've simply not had the time recently > to dig further, > but I intend to when the field season here settles down. > > It is absolutely related to the changing of windows, but > what exactly is > causing it is unclear to me. It does not happen when in > batch mode. Only > when in interactive mode. > > On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss > <[hidden email] <mailto:[hidden email]>> wrote: > > About a year ago I wrote about Fiji slowing down > during use with Java 8 > and OSX. > > http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html > > As this is still happening, I want to find out if > there is any additional > information about this. > > I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). > I have 16GB RAM. > > Wayne had noted that menu updates are problematic, and > added a parameter > SetMenuBarCount: to follow that. > I note problems when this is over 50, but I cannot say > when it really > becomes unusable and I have to quit and start again. > > One thing that I noticed -- if I allocate 12GB to > Fiji, then the problems > will start much sooner than if I allocate 10GB to Fiji. > So I suspect that some resource that Fiji uses, which > is outside of Fiji, > is using up memory (but I dont know how to check this). > > Do people who are running on high-powered Linux > machines have this > > problem? > > --aryeh > > -- > > > > -- Aryeh Weiss Faculty of Engineering Bar Ilan University Ramat Gan 52900 Israel Ph: 972-3-5317638 FAX: 972-3-7384051 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi fellow ImageJ / OSX users,
I have been experiencing problems too with ImageJ on OSX, showing itsels as slowing down and not reacting to menuclicks. While developing Eclipse I am able to reproduce these effects and obtain stacktraces for which see below. Regards, Koen van Dijken 2016-07-12 12:01:13.854 java[24848:2050853] *** Collection <__NSArrayM: 0x7f94d5bea620> was mutated while being enumerated. 2016-07-12 12:01:13.859 java[24848:2050853] ( 0 CoreFoundation 0x00007fff8ff6064c __exceptionPreprocess + 172 1 libobjc.A.dylib 0x00007fff897166de objc_exception_throw + 43 2 CoreFoundation 0x00007fff8ff5fee5 __NSFastEnumerationMutationHandler + 309 3 AppKit 0x00007fff858e1c24 -[NSView _recursiveSendViewDidChangeAppearance:] + 193 4 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 5 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 6 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 7 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 8 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 9 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 10 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 11 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 12 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 13 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 14 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 15 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 16 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 17 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 18 AppKit 0x00007fff858e1c3b -[NSView _recursiveSendViewDidChangeAppearance:] + 216 19 AppKit 0x00007fff858e1941 -[NSView setAppearance:] + 205 20 AppKit 0x00007fff85ee405c -[NSThemeFrame setAppearance:] + 52 21 AppKit 0x00007fff858603ca -[NSWindow setAppearance:] + 44 22 AppKit 0x00007fff85dc3f93 +[NSSavePanel _crunchyRawUnbonedPanel] + 298 23 libawt_lwawt.dylib 0x000000012535dde9 -[CFileDialog safeSaveOrLoad] + 139 24 Foundation 0x00007fff8482cf4c __NSThreadPerformPerform + 293 25 CoreFoundation 0x00007fff8fe7e661 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 26 CoreFoundation 0x00007fff8fe707ed __CFRunLoopDoSources0 + 269 27 CoreFoundation 0x00007fff8fe6fe1f __CFRunLoopRun + 927 28 CoreFoundation 0x00007fff8fe6f838 CFRunLoopRunSpecific + 296 29 HIToolbox 0x00007fff8d87643f RunCurrentEventLoopInMode + 235 30 HIToolbox 0x00007fff8d8761ba ReceiveNextEventCommon + 431 31 HIToolbox 0x00007fff8d875ffb _BlockUntilNextEventMatchingListInModeWithFilter + 71 32 AppKit 0x00007fff858216d1 _DPSNextEvent + 964 33 AppKit 0x00007fff85820e80 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 194 34 libosxapp.dylib 0x00000001253fe3aa -[NSApplicationAWT nextEventMatchingMask:untilDate:inMode:dequeue:] + 124 35 AppKit 0x00007fff85814e23 -[NSApplication run] + 594 36 libosxapp.dylib 0x00000001253fe14d +[NSApplicationAWT runAWTLoopWithApp:] + 156 37 libawt_lwawt.dylib 0x000000012538b55b -[AWTStarter starter:] + 905 38 Foundation 0x00007fff8482cf4c __NSThreadPerformPerform + 293 39 CoreFoundation 0x00007fff8fe7e661 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17 40 CoreFoundation 0x00007fff8fe707ed __CFRunLoopDoSources0 + 269 41 CoreFoundation 0x00007fff8fe6fe1f __CFRunLoopRun + 927 42 CoreFoundation 0x00007fff8fe6f838 CFRunLoopRunSpecific + 296 43 java 0x000000010c65a463 CreateExecutionEnvironment + 871 44 java 0x000000010c6561ac JLI_Launch + 1952 45 java 0x000000010c65c4c0 main + 101 46 java 0x000000010c655a04 start + 52 47 ??? 0x0000000000000007 0x0 + 7 ) On Wed, Jul 13, 2016 at 8:15 PM, Aryeh Weiss <[hidden email]> wrote: > On 13/07/2016 8:04 PM, Manu Tiwari wrote: > >> Hello Pioneers and Users, >> >> Is there any progress in resolving this issue? >> What has been posted are workarounds, but what is needed is a solution. >> I am experiencing the exact same problem: Mac + ImageJ (1.50b) + Java8 >> (latest update)—> very long loading times…the Menus appear very late >> especially with z-stacks. >> Any help is appreciated. >> > > There is no solution yet. My situation improved a lot when I ran my macros > in batch mode, so I recommend you do that when possible. > > The other action that appears to help is leaving zs much memory available > to the OS 9outside of ImageJ, as you can . Since my images are often more > than a GB, that can be a problem , but I manage with 10GB in ImageJ out of > 16GB. > > These steps significantly lengthened the intervals between quitting and > restarting. > > Curtiss wrote that he may be able to work on this in the Fall, so there is > hope. > > If you are braver than I, Albert Cardona posted a link (see below) with > instructions on how to run Linux on your mac. > > Best regards > --aryeh > > > Best >> Manu >> >> >> >> >> ******************************** >> Manu Tiwari >> Molekulare Zellbiologie >> Institut I für Anatomie >> Universität zu Köln >> Kerpener Str. 62, Geb.37 >> D-50937 Köln Germany >> Tel. +49 - 221 - 478 32655 >> >> >> >> >> >> >> On 11 Jul 2016, at 19:58, Albert Cardona <[hidden email]<mailto: >> [hidden email]>> wrote: >> >> Hi Aryeh, >> >> I have used linux in macbook pros since 2005. Works better than MacOSX >> itself, and by better I mean better wifi, same battery life, same programs >> run faster, no swapping. >> >> The main motivation was the same issue you are experiencing now: Java >> never >> worked as well in macosx as it did in other operating systems. >> >> The best guide for installing Ubuntu in a MacBook Pro, better than my own >> guides, is this one: >> >> http://heeris.id.au/2014/ubuntu-plus-mac-pure-efi-boot/ >> >> Make sure to read the whole thing before you start. You can also dual-boot >> easily. >> >> Best, >> >> Albert >> >> 2016-07-11 3:39 GMT-04:00 Aryeh Weiss <[hidden email]>: >> >> On 11/07/2016 10:29 AM, Curtis Rueden wrote: >> >> Hi Aryeh, >> >> Is there anything that I can do in either my Fiji configuration or my >> Java configuration to improve performance? >> >> The only workarounds I know of right now: >> >> - On OS X, use Apple Java 6 >> >> I am using some plugins that require Java 7 or higher, so that is no >> longer an option. >> >> - Use Linux instead of OS X >> >> I am seriously considering that, but it will require new laptop because >> switching to Linux on a macbook pro is not for the faint of heart. For >> those who wish to try, this is relevant: >> http://www.makeuseof.com/tag/install-linux-macbook-pro/ >> >> - Do not open and close many windows >> >> I will try to use batch mode as much as possible, and it buys some time. >> >> -- Of course, if you are doing exploratory viz and processing, you can't >> avoid it >> - Restart ImageJ after opening and closing many windows >> >> yes -- I have been doing a lot of that. >> I will add the one other thing that I found -- reducing ImageJ's memory >> appears to buy some time. >> >> >> Regards, >> Curtis >> >> -- >> Curtis Rueden >> LOCI software architect - http://loci.wisc.edu/software >> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden >> Did you know ImageJ has a forum? http://forum.imagej.net/ >> >> Best regards >> >> -- >> Aryeh Weiss >> Faculty of Engineering >> Bar Ilan University >> Ramat Gan 52900 Israel >> >> Ph: 972-3-5317638 >> FAX: 972-3-7384051 >> >> >> >> >> >> On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email] >> <mailto:[hidden email]>> wrote: >> >> Hi Curtis >> >> Thank you for your reply. It is good to know that there is hope... >> >> Is there anything that I can do in either my Fiji configuration or >> my Java configuration to improve performance? >> >> Best regards >> --aryeh >> >> >> >> On 11/07/2016 1:25 AM, Curtis Rueden wrote: >> >> Hi Brandon & Aryeh, >> >> I am fairly confident that the cause is attaching AWT menus >> bars, as I >> outline here: >> http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden >> >> Someone with a technical background needs to investigate the >> potential >> solutions to the issue that I mention in that post. >> >> In particular, using the Apple-specific >> "Application.setDefaultMenuBar" >> method is highly likely to fix the issue. However, as I >> outline here: >> http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden >> >> It would be a bit of work to add code to ImageJ2 to >> hot-translate the >> ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is >> that doing >> this would have multiple advantages: >> >> * The "grinding to a halt" performance problem would likely >> disappear. >> * We would have a richer menu bar with icons for ImageJ2 >> commands that >> provide them. ;-) >> * The menu bar flashing when you switch windows would no >> longer happen. >> >> The downside is that it is more complex internally, since we >> would need to >> keep the JMenuBar internally synchronized with the menu bar >> that IJ1 >> believes is its menu bar (but in actuality is now never >> actually attached >> to any windows). >> >> There might also be unforeseen technical obstacles with my >> proposed >> solution here. All in all, it would probably cost me several >> days to >> explore and implement this fix, and I currently have other >> more urgent >> priorities. But I will try to make time to do this work early >> this fall. >> >> Regards, >> Curtis >> >> >> -- >> Curtis Rueden >> LOCI software architect - http://loci.wisc.edu/software >> ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden >> Did you know ImageJ has a forum? http://forum.imagej.net/ >> >> >> On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr >> <[hidden email] <mailto:[hidden email]>> >> wrote: >> >> We've been going back and forth on it a bit on the forums too: >> http://forum.imagej.net/t/mac-java-speed-issues/304 >> >> I think we really need to help pin this down for Chris and >> Wayne so they >> can make a change. I've simply not had the time recently >> to dig further, >> but I intend to when the field season here settles down. >> >> It is absolutely related to the changing of windows, but >> what exactly is >> causing it is unclear to me. It does not happen when in >> batch mode. Only >> when in interactive mode. >> >> On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss >> <[hidden email] <mailto:[hidden email]>> wrote: >> >> About a year ago I wrote about Fiji slowing down >> during use with Java 8 >> and OSX. >> >> http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html >> >> As this is still happening, I want to find out if >> there is any additional >> information about this. >> >> I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). >> I have 16GB RAM. >> >> Wayne had noted that menu updates are problematic, and >> added a parameter >> SetMenuBarCount: to follow that. >> I note problems when this is over 50, but I cannot say >> when it really >> becomes unusable and I have to quit and start again. >> >> One thing that I noticed -- if I allocate 12GB to >> Fiji, then the problems >> will start much sooner than if I allocate 10GB to Fiji. >> So I suspect that some resource that Fiji uses, which >> is outside of Fiji, >> is using up memory (but I dont know how to check this). >> >> Do people who are running on high-powered Linux >> machines have this >> >> problem? >> >> --aryeh >> >> -- >> >> >> >> >> > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: java 8 and OSX
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In reply to this post by Manu Tiwari
> On Jul 13, 2016, at 1:04 PM, Manu Tiwari <[hidden email]> wrote:
> > Hello Pioneers and Users, > > Is there any progress in resolving this issue? > What has been posted are workarounds, but what is needed is a solution. > I am experiencing the exact same problem: Mac + ImageJ (1.50b) + Java8 (latest update)—> very long loading times…the Menus appear very late especially with z-stacks. > Any help is appreciated. There is a bug the setMenuBar() method in Java 8 on OS X that causes it to become slower after repeated calls. The latest ImageJ daily build (1.51e31) tries to work around this bug by not setting the menu bar when an image is activated if setMenuBar() is going to take more than one second. This prevents ImageJ from becoming unresponsive but you may need to recover the menu bar by clicking on the "ImageJ" window or by pressing return, the shortcut for the Window>Main Window command. Enable “Debug mode" in the Edit>Options>Misc dialog and ImageJ will display the execution time of setMenuBar() calls. -wayne > On 11 Jul 2016, at 19:58, Albert Cardona <[hidden email]<mailto:[hidden email]>> wrote: > > Hi Aryeh, > > I have used linux in macbook pros since 2005. Works better than MacOSX > itself, and by better I mean better wifi, same battery life, same programs > run faster, no swapping. > > The main motivation was the same issue you are experiencing now: Java never > worked as well in macosx as it did in other operating systems. > > The best guide for installing Ubuntu in a MacBook Pro, better than my own > guides, is this one: > > http://heeris.id.au/2014/ubuntu-plus-mac-pure-efi-boot/ > > Make sure to read the whole thing before you start. You can also dual-boot > easily. > > Best, > > Albert > > 2016-07-11 3:39 GMT-04:00 Aryeh Weiss <[hidden email]>: > > On 11/07/2016 10:29 AM, Curtis Rueden wrote: > > Hi Aryeh, > > Is there anything that I can do in either my Fiji configuration or my > Java configuration to improve performance? > > The only workarounds I know of right now: > > - On OS X, use Apple Java 6 > > I am using some plugins that require Java 7 or higher, so that is no > longer an option. > > - Use Linux instead of OS X > > I am seriously considering that, but it will require new laptop because > switching to Linux on a macbook pro is not for the faint of heart. For > those who wish to try, this is relevant: > http://www.makeuseof.com/tag/install-linux-macbook-pro/ > > - Do not open and close many windows > > I will try to use batch mode as much as possible, and it buys some time. > > -- Of course, if you are doing exploratory viz and processing, you can't > avoid it > - Restart ImageJ after opening and closing many windows > > yes -- I have been doing a lot of that. > I will add the one other thing that I found -- reducing ImageJ's memory > appears to buy some time. > > > Regards, > Curtis > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > Best regards > > -- > Aryeh Weiss > Faculty of Engineering > Bar Ilan University > Ramat Gan 52900 Israel > > Ph: 972-3-5317638 > FAX: 972-3-7384051 > > > > > > On Mon, Jul 11, 2016 at 2:03 AM, Aryeh Weiss <[hidden email] > <mailto:[hidden email]>> wrote: > > Hi Curtis > > Thank you for your reply. It is good to know that there is hope... > > Is there anything that I can do in either my Fiji configuration or > my Java configuration to improve performance? > > Best regards > --aryeh > > > > On 11/07/2016 1:25 AM, Curtis Rueden wrote: > > Hi Brandon & Aryeh, > > I am fairly confident that the cause is attaching AWT menus > bars, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/4?u=ctrueden > > Someone with a technical background needs to investigate the > potential > solutions to the issue that I mention in that post. > > In particular, using the Apple-specific > "Application.setDefaultMenuBar" > method is highly likely to fix the issue. However, as I > outline here: > http://forum.imagej.net/t/mac-java-speed-issues/304/8?u=ctrueden > > It would be a bit of work to add code to ImageJ2 to > hot-translate the > ImageJ 1.x AWT menu bar to a Swing JMenuBar. The good news is > that doing > this would have multiple advantages: > > * The "grinding to a halt" performance problem would likely > disappear. > * We would have a richer menu bar with icons for ImageJ2 > commands that > provide them. ;-) > * The menu bar flashing when you switch windows would no > longer happen. > > The downside is that it is more complex internally, since we > would need to > keep the JMenuBar internally synchronized with the menu bar > that IJ1 > believes is its menu bar (but in actuality is now never > actually attached > to any windows). > > There might also be unforeseen technical obstacles with my > proposed > solution here. All in all, it would probably cost me several > days to > explore and implement this fix, and I currently have other > more urgent > priorities. But I will try to make time to do this work early > this fall. > > Regards, > Curtis > > > -- > Curtis Rueden > LOCI software architect - http://loci.wisc.edu/software > ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden > Did you know ImageJ has a forum? http://forum.imagej.net/ > > > On Sun, Jul 10, 2016 at 5:15 PM, Brandon Hurr > <[hidden email] <mailto:[hidden email]>> > wrote: > > We've been going back and forth on it a bit on the forums too: > http://forum.imagej.net/t/mac-java-speed-issues/304 > > I think we really need to help pin this down for Chris and > Wayne so they > can make a change. I've simply not had the time recently > to dig further, > but I intend to when the field season here settles down. > > It is absolutely related to the changing of windows, but > what exactly is > causing it is unclear to me. It does not happen when in > batch mode. Only > when in interactive mode. > > On Sun, Jul 10, 2016 at 4:23 AM, Aryeh Weiss > <[hidden email] <mailto:[hidden email]>> wrote: > > About a year ago I wrote about Fiji slowing down > during use with Java 8 > and OSX. > > http://imagej.1557.x6.nabble.com/java-8-and-OSX-td5013642.html > > As this is still happening, I want to find out if > there is any additional > information about this. > > I am now using OSX 10.11.5 with Java 1.8.0_92 (64-bit). > I have 16GB RAM. > > Wayne had noted that menu updates are problematic, and > added a parameter > SetMenuBarCount: to follow that. > I note problems when this is over 50, but I cannot say > when it really > becomes unusable and I have to quit and start again. > > One thing that I noticed -- if I allocate 12GB to > Fiji, then the problems > will start much sooner than if I allocate 10GB to Fiji. > So I suspect that some resource that Fiji uses, which > is outside of Fiji, > is using up memory (but I dont know how to check this). > > Do people who are running on high-powered Linux > machines have this > > problem? > > --aryeh > > -- -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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