Re: [caret-users] Using caret_stats for TFCE
>From what I remember of the issue, some JREs were holding onto memory that should have been deallocated, which eventually fills the memory pool and crashes, while the good JREs kept their memory usage fairly constant. The issue was solved in Sun's java before the default java debian/ubuntu install, but I think it got solved in that one also in more recent versions. If all else fails, you could try updating to the latest available JRE. Note that you may have multiple versions of java installed, and may need to configure which one is used by default, for instance http://java.dzone.com/articles/choosing-java-version-ubuntu . Tim On Thu, Jan 23, 2014 at 9:04 AM, Donna Dierker wrote: > This sounds very much like a problem I had before switching JRE's. This > version has been known to work with Ubuntu 10.10, Ubuntu 10.10, Linux it > 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 > GNU/Linux: > > java version "1.6.0_21" > Java(TM) SE Runtime Environment (build 1.6.0_21-b06) > Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode) > > Tim Coalson believed the problem was somehow related to a cache size. > Once it reached that cache size, then java performance plummeted, as you > saw. Switching JRE's fixed the problem, and I don't have a non-java TFCE > version I can send you. > > > On Jan 22, 2014, at 4:27 PM, Eshita Shah wrote: > > > Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems > to get really slow after 1000, but continues on to about 2600 until it > crashes. > > > > > > On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker > wrote: > > How many iterations did you specify? Have you tried it with 1000 > iterations? > > > > > > On Jan 22, 2014, at 3:09 PM, Eshita Shah wrote: > > > > > Hi Donna, > > > > > > I have been trying to allocate more memory to caret_stats so it can > run java properly without crashing. However, this has not worked. I just > downloaded the JRE you provided, and it is actually the same one that I am > using. > > > > > > Do you think there is another source of this problem? > > > > > > Thank you, > > > Eshita > > > > > > > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker < > donna.dier...@sbcglobal.net> wrote: > > > At the end of the TFCE processing, you should get a text file named > something like *report.txt, along with a *ignif*metric. If you don't, then > it's not finishing normally. > > > > > > How many iterations are you using? If it doesn't finish overnight > with 5k iterations, then it might be your java runtime engine. Before I > started using this one, my java runtime engine just hung or grinded to a > near halt after a few thousand iterations: > > > > > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > > > login pub > > > password download > > > > > > You can use others; just be aware that the JRE can be an obstacle. > > > > > > > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > > > > > Hi Donna, > > > > > > > > I am running a script you sent me a while ago, which uses > caret_stats to run ANOVA and then TFCE for significant cluster analysis. I > am noticing that the output files generated after running the script do not > match up to the expected outputs. I am seeing files such as > ".metric.data1", ".metric.data2", etc. I'm not sure where they are coming > from - my hunch is that the script is being aborted at some point (because > I am not getting any of the TFCE outputs), but I'm not exactly sure why > these files would be generated or what they are. > > > > > > > > Please let me know if you have any ideas. > > > > > > > > Thank you, > > > > Eshita > > > > > > > > -- > > > > Eshita Shah > > > > University of California, Los Angeles | 2014 > > > > B.S. Neuroscience > > > > eshs...@ucla.edu > > > > > > > > > > > > ___ > > > > caret-users mailing list > > > > caret-users@brainvis.wustl.edu > > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > > ___ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > -- > > Eshita Shah > > University of California, Los Angeles | 2014 > > B.S. Neuroscience > > eshs...@ucla.edu > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/
Re: [caret-users] Using caret_stats for TFCE
This sounds very much like a problem I had before switching JRE's. This version has been known to work with Ubuntu 10.10, Ubuntu 10.10, Linux it 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux: java version "1.6.0_21" Java(TM) SE Runtime Environment (build 1.6.0_21-b06) Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode) Tim Coalson believed the problem was somehow related to a cache size. Once it reached that cache size, then java performance plummeted, as you saw. Switching JRE's fixed the problem, and I don't have a non-java TFCE version I can send you. On Jan 22, 2014, at 4:27 PM, Eshita Shah wrote: > Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems to > get really slow after 1000, but continues on to about 2600 until it crashes. > > > On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker > wrote: > How many iterations did you specify? Have you tried it with 1000 iterations? > > > On Jan 22, 2014, at 3:09 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I have been trying to allocate more memory to caret_stats so it can run > > java properly without crashing. However, this has not worked. I just > > downloaded the JRE you provided, and it is actually the same one that I am > > using. > > > > Do you think there is another source of this problem? > > > > Thank you, > > Eshita > > > > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker > > wrote: > > At the end of the TFCE processing, you should get a text file named > > something like *report.txt, along with a *ignif*metric. If you don't, then > > it's not finishing normally. > > > > How many iterations are you using? If it doesn't finish overnight with 5k > > iterations, then it might be your java runtime engine. Before I started > > using this one, my java runtime engine just hung or grinded to a near halt > > after a few thousand iterations: > > > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > > login pub > > password download > > > > You can use others; just be aware that the JRE can be an obstacle. > > > > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > > > Hi Donna, > > > > > > I am running a script you sent me a while ago, which uses caret_stats to > > > run ANOVA and then TFCE for significant cluster analysis. I am noticing > > > that the output files generated after running the script do not match up > > > to the expected outputs. I am seeing files such as ".metric.data1", > > > ".metric.data2", etc. I'm not sure where they are coming from - my hunch > > > is that the script is being aborted at some point (because I am not > > > getting any of the TFCE outputs), but I'm not exactly sure why these > > > files would be generated or what they are. > > > > > > Please let me know if you have any ideas. > > > > > > Thank you, > > > Eshita > > > > > > -- > > > Eshita Shah > > > University of California, Los Angeles | 2014 > > > B.S. Neuroscience > > > eshs...@ucla.edu > > > > > > > > > ___ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > -- > Eshita Shah > University of California, Los Angeles | 2014 > B.S. Neuroscience > eshs...@ucla.edu > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Using caret_stats for TFCE
Yes, it works fine at 1000 iterations. I am trying to run 5000. It seems to get really slow after 1000, but continues on to about 2600 until it crashes. On Wed, Jan 22, 2014 at 2:13 PM, Donna Dierker wrote: > How many iterations did you specify? Have you tried it with 1000 > iterations? > > > On Jan 22, 2014, at 3:09 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I have been trying to allocate more memory to caret_stats so it can run > java properly without crashing. However, this has not worked. I just > downloaded the JRE you provided, and it is actually the same one that I am > using. > > > > Do you think there is another source of this problem? > > > > Thank you, > > Eshita > > > > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker < > donna.dier...@sbcglobal.net> wrote: > > At the end of the TFCE processing, you should get a text file named > something like *report.txt, along with a *ignif*metric. If you don't, then > it's not finishing normally. > > > > How many iterations are you using? If it doesn't finish overnight with > 5k iterations, then it might be your java runtime engine. Before I started > using this one, my java runtime engine just hung or grinded to a near halt > after a few thousand iterations: > > > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > > login pub > > password download > > > > You can use others; just be aware that the JRE can be an obstacle. > > > > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > > > Hi Donna, > > > > > > I am running a script you sent me a while ago, which uses caret_stats > to run ANOVA and then TFCE for significant cluster analysis. I am noticing > that the output files generated after running the script do not match up to > the expected outputs. I am seeing files such as ".metric.data1", > ".metric.data2", etc. I'm not sure where they are coming from - my hunch is > that the script is being aborted at some point (because I am not getting > any of the TFCE outputs), but I'm not exactly sure why these files would be > generated or what they are. > > > > > > Please let me know if you have any ideas. > > > > > > Thank you, > > > Eshita > > > > > > -- > > > Eshita Shah > > > University of California, Los Angeles | 2014 > > > B.S. Neuroscience > > > eshs...@ucla.edu > > > > > > > > > ___ > > > caret-users mailing list > > > caret-users@brainvis.wustl.edu > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > -- Eshita Shah University of California, Los Angeles | 2014 B.S. Neuroscience eshs...@ucla.edu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Using caret_stats for TFCE
How many iterations did you specify? Have you tried it with 1000 iterations? On Jan 22, 2014, at 3:09 PM, Eshita Shah wrote: > Hi Donna, > > I have been trying to allocate more memory to caret_stats so it can run java > properly without crashing. However, this has not worked. I just downloaded > the JRE you provided, and it is actually the same one that I am using. > > Do you think there is another source of this problem? > > Thank you, > Eshita > > > On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker > wrote: > At the end of the TFCE processing, you should get a text file named something > like *report.txt, along with a *ignif*metric. If you don't, then it's not > finishing normally. > > How many iterations are you using? If it doesn't finish overnight with 5k > iterations, then it might be your java runtime engine. Before I started > using this one, my java runtime engine just hung or grinded to a near halt > after a few thousand iterations: > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > login pub > password download > > You can use others; just be aware that the JRE can be an obstacle. > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I am running a script you sent me a while ago, which uses caret_stats to > > run ANOVA and then TFCE for significant cluster analysis. I am noticing > > that the output files generated after running the script do not match up to > > the expected outputs. I am seeing files such as ".metric.data1", > > ".metric.data2", etc. I'm not sure where they are coming from - my hunch is > > that the script is being aborted at some point (because I am not getting > > any of the TFCE outputs), but I'm not exactly sure why these files would be > > generated or what they are. > > > > Please let me know if you have any ideas. > > > > Thank you, > > Eshita > > > > -- > > Eshita Shah > > University of California, Los Angeles | 2014 > > B.S. Neuroscience > > eshs...@ucla.edu > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Using caret_stats for TFCE
Hi Donna, I have been trying to allocate more memory to caret_stats so it can run java properly without crashing. However, this has not worked. I just downloaded the JRE you provided, and it is actually the same one that I am using. Do you think there is another source of this problem? Thank you, Eshita On Wed, Jan 15, 2014 at 7:23 PM, Donna Dierker wrote: > At the end of the TFCE processing, you should get a text file named > something like *report.txt, along with a *ignif*metric. If you don't, then > it's not finishing normally. > > How many iterations are you using? If it doesn't finish overnight with 5k > iterations, then it might be your java runtime engine. Before I started > using this one, my java runtime engine just hung or grinded to a near halt > after a few thousand iterations: > > http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip > login pub > password download > > You can use others; just be aware that the JRE can be an obstacle. > > > On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > > > Hi Donna, > > > > I am running a script you sent me a while ago, which uses caret_stats to > run ANOVA and then TFCE for significant cluster analysis. I am noticing > that the output files generated after running the script do not match up to > the expected outputs. I am seeing files such as ".metric.data1", > ".metric.data2", etc. I'm not sure where they are coming from - my hunch is > that the script is being aborted at some point (because I am not getting > any of the TFCE outputs), but I'm not exactly sure why these files would be > generated or what they are. > > > > Please let me know if you have any ideas. > > > > Thank you, > > Eshita > > > > -- > > Eshita Shah > > University of California, Los Angeles | 2014 > > B.S. Neuroscience > > eshs...@ucla.edu > > > > > > ___ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
Re: [caret-users] Using caret_stats for TFCE
At the end of the TFCE processing, you should get a text file named something like *report.txt, along with a *ignif*metric. If you don't, then it's not finishing normally. How many iterations are you using? If it doesn't finish overnight with 5k iterations, then it might be your java runtime engine. Before I started using this one, my java runtime engine just hung or grinded to a near halt after a few thousand iterations: http://brainmap.wustl.edu/pub/donna/US/WVU/linux_java.zip login pub password download You can use others; just be aware that the JRE can be an obstacle. On Jan 15, 2014, at 3:32 PM, Eshita Shah wrote: > Hi Donna, > > I am running a script you sent me a while ago, which uses caret_stats to run > ANOVA and then TFCE for significant cluster analysis. I am noticing that the > output files generated after running the script do not match up to the > expected outputs. I am seeing files such as ".metric.data1", ".metric.data2", > etc. I'm not sure where they are coming from - my hunch is that the script is > being aborted at some point (because I am not getting any of the TFCE > outputs), but I'm not exactly sure why these files would be generated or what > they are. > > Please let me know if you have any ideas. > > Thank you, > Eshita > > -- > Eshita Shah > University of California, Los Angeles | 2014 > B.S. Neuroscience > eshs...@ucla.edu > > > ___ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
[caret-users] Using caret_stats for TFCE
Hi Donna, I am running a script you sent me a while ago, which uses caret_stats to run ANOVA and then TFCE for significant cluster analysis. I am noticing that the output files generated after running the script do not match up to the expected outputs. I am seeing files such as ".metric.data1", ".metric.data2", etc. I'm not sure where they are coming from - my hunch is that the script is being aborted at some point (because I am not getting any of the TFCE outputs), but I'm not exactly sure why these files would be generated or what they are. Please let me know if you have any ideas. Thank you, Eshita -- Eshita Shah University of California, Los Angeles | 2014 B.S. Neuroscience eshs...@ucla.edu ___ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
