DUNEURO error libdl.so.2

Discussions
1

Hi everyone, I was trying to use DUNEURO for the FEM forward model but I have the following error:

DUNEURO> Installation path: /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64
DUNEURO> Writing temporary files to: /home/duma/.brainstorm/tmp
DUNEURO> System call: "/home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64" "/home/duma/.brainstorm/tmp/duneuro_minifile.mini"
DUNEURO> Error log:
/home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64: error while loading shared libraries: libldl.so.2: cannot open shared object file: No such file or directory

I checked and the libdl.so.2 is correctly installed.
What do you think I should do?
I'm using Debian, and I'm not a great expert, may be this is a trivial question.
Thanks

2

Libdl and libldl are different things.
Confusing, right? :slight_smile:

sudo apt install libldl2

Maybe you'll need some additional things. The other libraries needed to compile bst-duneuro are listed there: https://github.com/brainstorm-tools/bst-duneuro

sudo apt-get install git pkg-config cmake mingw-w64 g++-mingw-w64 libc6-dev-i386 python3-pip libeigen3-dev

@tmedani @juangpc
Maybe this would be worth adding to the tutorial on the Brainstorm website?
(unless it is already there, sorry I haven't checked)

1 Like
3

Hi @gianmarcoduma,

Let us know if you're able to solve the issue following Francois' instructions.

The library is actually not part of Duneuro project, but do let us know, I'll be happy to help.

1 Like
4

It seems that we did some improvements, but now I have another error

/home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64: error while loading shared libraries: libspqr.so.2: cannot open shared object file: No such file or directory

I check on internet and this is a library to handle with sparse matrices, but I'm having some troubles in downloading it and install it correctly.

Do you have suggestions?
Thanks

5

Which OS are you using?

This package is available in the recent Ubuntu (and probably other debian-based distrib):
sudo apt install libspqr2

https://packages.ubuntu.com/bionic/all/libspqr2/filelist

@juangpc?

6

Sorry @gianmarcoduma I don't, I don't have any suggestions.

I originally did all the testing in ubuntu lts version. I'm not sure in other linux distros, even if ubuntu is based on debian, there will be differences in the packaged libraries. If you go with debian, we can be certain that it is possible to make the application run, but you'll have to navigate through the particular adaptation.

Take care,

7

I have downloaded two libspqr2, then I had another error from DUNEURO which ask me the libumfpack5, I downloaded it, and now I have this error

home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64: /home/duma/R2017b/sys/os/glnxa64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64) /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64: /home/duma/R2017b/sys/os/glnxa64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64)

I have already checked and I have the latest version of the libstdc++, so I think that it is something specific you are using in DUNEURO. Any suggestion?
Thanks

8

@gianmarcoduma Which distribution of Linux are you using?

@juangpc Any option to compile duneuro with some more static libraries?

9

Hi, three suggestions. Please consider that the DUNEURO-Brainstorm integration is still under development.

  • Try to use ubuntu, where all those libraries seem to be installed out of the box.
  • Wait a while until we have a final stable version running and I can dive deeper and perhaps build a static version with all the dependencies compiled together.
  • Go to Duneuro project's web and try to reach help there. (www.duneuro.org)

I'll ask myself on our next meeting with Duneuro people but right now I think this is what I can say.

Take care,

2 Likes
10

Hi again @gianmarcoduma. Probably you've moved on. :slight_smile: and rightfully so. But allow me to me put this answer here so that others can find it, if it ever happens again.

If you encounter this issue try installing the following packages: libdune-grid-dev libdune-istl-dev. If you have a debian-based distribution (like ubuntu), try the following command.

sudo apt-get install libdune-grid-dev libdune-istl-dev

Hope this helps.

Juan.

11

Hi @juangpc, first of all thank you so much for this precious information. Unfortunately I tried with your solution, but it keeps generating this error message

DUNEURO> System call: "/home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64.app" "/home/duma/.brainstorm/tmp/duneuro_minifile.mini"
DUNEURO> Error log:
/home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64.app: /home/duma/R2017b/sys/os/glnxa64/libstdc++.so.6: version GLIBCXX_3.4.21' not found (required by /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64.app) /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64.app: /home/duma/R2017b/sys/os/glnxa64/libstdc++.so.6: version CXXABI_1.3.9' not found (required by /home/duma/.brainstorm/bst_duneuro/bin/bst_duneuro_meeg_linux64.app)

I think that matlab is picking the wrong file, but I have no idea how to force it to pick the right one, because I checked and I have both GLICXX and CXXABI correct versions

12

Have you tried with different versions of Matlab?

13

Hi, I think that problem is related to this answer. Could you please try the fixes proposed in the following link?

In any case, I'm going to try to replicate your error to see what's going on.