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problem with proot #2

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volcanofly opened this issue May 19, 2017 · 5 comments
Closed

problem with proot #2

volcanofly opened this issue May 19, 2017 · 5 comments

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@volcanofly
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volcanofly commented May 19, 2017 •
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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
@volcanofly volcanofly changed the title problem with proof problem with proot May 19, 2017
@ledigchr
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Hi Can, I think this is related to a proot issue which was raised in:
proot-me/proot#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
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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!

@ledigchr ledigchr mentioned this issue May 23, 2018
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@ledigchr ledigchr reopened this May 24, 2018
@Georgejnr01
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I have the same issue...please how did you do it

@olivierbarret
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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 pushed a commit that referenced this issue May 28, 2021
FIX: issue #2 proot info: pid XXX: terminated with signal 11
5159d3e
ledigchr added a commit that referenced this issue May 30, 2021
@ledigchr
Merge pull request #11 from ledigchr/malpem_v1.3
6f69ab6 
Updates for MALPEM v1.3 release.

Functional:
* Updated initial N4 bias correction from potentially using OTSU mask to always use complete image domain as foreground
* Perform consistently two N4 bias correction (1st: N4 on full image domain, 2nd: N4 w/ mask) regardless of whether user specified a mask
* Updated installer script to allow user to select among various version

Reproducibility:
* Fix issue #8 : Fixed itk threads to 8 to make N4 bias correction deterministic (depends on number of threads)

Robustness/Compatibility:
* Fix issue #9 : Ensure input image and mask have numerically same header information to avoid N4 failing, don't fail silently in case of another unexpected problem.
* Fix issue #2 : Added 'export PROOT_NO_SECCOMP=1' to avoid Error 'root info: pid XXX: terminated with signal 11' 
* ingore_errors = True when attempting to delete temporary files when 'cleanup' flag is used

Minor:
* removed unused imports, cosmetics
@ledigchr
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ledigchr commented May 31, 2021 •
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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 #6

Closing this issue.

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4 participants
@ledigchr @volcanofly @Georgejnr01 @olivierbarret