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ledigchr / MALPEM

MALPEM whole-brain segmentation framework
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problem with proot #2

Closed volcanofly closed 3 years ago

volcanofly commented 7 years ago

Dear Author, After installing it using the installer, I tried to run: bin/malpem-proot -h

It returns:

WARNING: Didn't find libGL library in /usr/lib/nvid*, offscreen rendering won't work (only relevant for pdf report)

Command in CARE environment: malpem -h proot info: pid 11075: terminated with signal 11

I checked the code in malpem. I think it should print some help info. But it didn't. Also, when I tried to run:

bin/malpem-proot -i atlas/pincram/limages/full/m100.nii.gz -o outputDir -t 8

It also returns:

proot info: pid XXX: terminated with signal 11

I'm not familiar with proot. I was wondering if you could help with this issue. Thank you!

Best, Can

ledigchr commented 7 years ago

Hi Can, I think this is related to a proot issue which was raised in: https://github.com/proot-me/PRoot/issues/106

I can't reproduce the problem at the moment, but perhaps adding export PROOT_NO_SECCOMP=1 to malpem-proot solves the problem. It would be great if you could comment on whether this worked in case you try it.

Cheers, Christian

volcanofly commented 6 years ago

Thank you so much! It works! Sorry for late response. I didn't take a loot at this issue until today. I did it in the same way as you suggested and it worked! Thank you again!

Georgejnr01 commented 5 years ago

I have the same issue...please how did you do it

olivierbarret commented 3 years ago

Hi all,

Here is what I had to do to make MALPEM work under WSL:

1) You have to run WSL2, ie use ext4.vhdx. It does not work with WSL1 and rootfs. 2) I had to remove the –k string option for the kernel from malpem-root. Was giving a sigsecv otherwise. 3) Had to setup PROOT_NO_SECCOMP=1 otherwise sigsegv 4) Or replace proot with proot_5.1.1_x86_64_rc2--no-seccomp. proot_5.1.1_x86_64_rc2 was giving sigsegv if PROOT_NO_SECCOMP not defined.

Hope this helps.

Thanks Olivier

ledigchr commented 3 years ago

Added export PROOT_NO_SECCOMP=1 to malpem-proot in malpem-v1.3.

This should address the problem at least for non-WSL environments. If using WSL see this issue https://github.com/ledigchr/MALPEM/issues/6

Closing this issue.