Segmentation violation detected about mcx

[fangq]

@Eidantz, sorry for the delay, only saw it today.

I noticed the same when I upgraded my desktop from 14.04 to 16.04 yesterday. I am not yet sure what cause the crash, but it seems matlab 2016 does not seem to like the mex compiled on Ubuntu 16.04.

I, however, found that matlab 2017a and 2018a work fine with mcxlab. Do you have those versions? if yes, do you see the same?

[Eidantz]

I am using MATLAB R2017a (9.2.0.556344) 64-bit (glnxa64). I contact MATLAB company but they haven't responded yet.
If it helps the mcxlab stop at this point:

normalizing raw data ...        normalization factor alpha=33.333332
simulated 30000000 photons (30000000) with 57344 threads (repeat x1)
MCX simulation speed: 9511.73 photon/ms
total simulated energy: 30000000.00     absorbed: 28.61906%
(loss due to initial specular reflection is excluded in the total)

[fangq]

the above log is the end of mcxlab's kernel command line messages - so it looks like the kernel was completed correctly.

can you checkout the current dev branch "etherdome" and recompile on your system (git clone first, and then git checkout etherdome inside mcx folder), and see if this issue remains.

If this does not help, to really figure out what happened, you should install valgrind on your system, and run the below command

matlab -nojvm -r "scriptname_caused_crash" -D"valgrind --error-limit=no --tool=memcheck -v --log-file=valgrind.log" ”

then, the valgrind.log will contain the debug info for the crashes, if you can post it, I would be able to find out which line of the code failed in your simulation.

[fangq]

let me know if you have tested the above command with the valgrind debug log. happy to look into the log file and find any clue.

[Eidantz]

I tried the Etherdome version, but the mcx.mex I took from the old version and the problem is from the mcx.mex file, doesn't it?
Did you update the mcx.mex file?
I will try tomorrow the Valgrind and I will update you.

[fangq]

I assume you meant the mcx.mexa64 file? it is a binary recompiled in the nightly build. you can download the latest binary from http://mcx.space/nightly/linux64/

[Eidantz]

I used this version

http://mcx.space/nightly/linux64/mcxlab-linux-x86_64-v2018.12.zip

and it works perfectly!

[fangq]

thanks, I will close this issue for now.