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dorianps / LINDA

Lesion Identification with Neighborhood Data Analysis
Apache License 2.0
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Memory not mapped error on Ubuntu #17

Closed fgfmds closed 5 years ago

fgfmds commented 5 years ago

Getting a memory not mapped error as soon as I try to load the T1 file. Tried two different cases from two different collections. Any insight will be greatly appreciated. Thank you!

Attached is the error message I am getting.

linda-error

dorianps commented 5 years ago

How much RAM do you have? Is this straight ubuntu or WSL. Check the memory with:

dp@CFIWKLMP04Y690A:/mnt/c/Users/test$ free -m
              total        used        free      shared  buff/cache   available
Mem:           8117        5343        2542          17         230        2636
Swap:         24576         365       24210

Also, please get the latest version 0.2.7, there was a bug in 0.2.6.

fgfmds commented 5 years ago

Dear Dorian,

Thank you so much for your quick reply. This is WSL. Do you think that might be an issue?

The physical machine has 24 GB of RAM. Here is what I get when I run the command in WSL:

linda-ram

I will also be sure to download the latest version! Thanks again.

dorianps commented 5 years ago

That was my first guess but you have plenty of memory. Not sure what else is going on. Give it another try with 0.2.7 and see if the problem presents again.

fgfmds commented 5 years ago

Will try 0.2.7 on WSL and let you know what happens. Thanks a lot.

dorianps commented 5 years ago

Also, please report the output of sessionInfo() if the error persists. And, if you remember, when did you install ANTsR?

fgfmds commented 5 years ago

I will send you the output if I get the error again. Thanks for the tip.

I installed ANTsR about two or three weeks ago. Should I get an updated version? or I should be good?

dorianps commented 5 years ago

If you can, please get the latest. There is several changes in ANTsR and ANTsRCore in the last few weeks. You need to also get ITKR, because the whole tools have now switched from ITKv4 to ITKv5.

Thanks.

fgfmds commented 5 years ago

I will do that. Quick question though.. on this page: http://dorianps.github.io/LINDA/, it says not to download the software from GitHub because it does not include the pre-trained models, etc.. In fact, I noticed that the full download is more than 500 MB, but the GitHub repo is about 200 MB. Should I just overwrite the files with the same name in my original download?

fgfmds commented 5 years ago

The directory structure is not the same in the 0.2.6 and 0.2.7 downloads. Do you have a suggestion how I should "upgrade" my installation?

dorianps commented 5 years ago

Here is some code (may contain typos).

First remove packages.

remove.packages(c('ITKR','ANTsRCore','ANTsR'))

If you have devtools installed then go:

devtools::install_github('ANTsX/ANTsR')

If you don't have devtools, follow Method 2 from here (which I use myself): https://github.com/ANTsX/ANTsR

If you get the LINDA release 0.2.7 from the link, the structure will be the same. What you currently see on Github is the new LINDA R package we are working on for the last few days. It kind of works ok, and you can try it you like (same git clone -> R CMD installation), but we are still working on it and it may have bugs. As a new user you should stick with the 0.2.7 release which doesn't have known bugs.

fgfmds commented 5 years ago

Got it. Now I see what did wrong. Thank you for the instructions. Let me get things straightened out and will report back. Thanks a lot!

fgfmds commented 5 years ago

So 0.2.7 failed with the same error message. Will try updating the packages next as you suggested. In the meantime, here is the sessionInfo() output:

sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.4.4

dorianps commented 5 years ago

If things don't work, please report also: 

installed.packages()[,'Version']
fgfmds commented 5 years ago

Here is the output for the last command while I work on the issues. r.packages.txt

fgfmds commented 5 years ago

Please feel free to close this ticket. My issues were eventually resolved by running LINDA in a native UBUNTU environment. It does not seem to work in WSL. Thank you for your help.