[Simnibs-discuss] Issues with making Brainstorm compatible with SimNIBS 4.0

[Oula Puonti]

Hi Gülce,

I'm guessing that the brainstorm issue is related to the linking issue
with charm, i.e., that brainstorm complains because the charm command
throws an error.

Can you run a linker on the .so library that is giving problems? You
can do:

cd /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-
packages/simnibs/mesh_tools/cgal/

and then call:

ldd create_mesh_surf.cpython-39-x86_64-linux-gnu.so

For my simnibs installation the output looks like this:

	linux-vdso.so.1 (0x00007ffedc7dc000)
	libmpfr.so.1 => /home/oulap/SimNIBS-
4.0/simnibs_env/lib/python3.9/site-
packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libmpfr.so.
1 (0x00007f4939e00000)
	libgmp.so.3 => /home/oulap/SimNIBS-
4.0/simnibs_env/lib/python3.9/site-
packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libgmp.so.3
(0x00007f4939a00000)
	libz.so.1 => /usr/lib/libz.so.1 (0x00007f493a1d9000)
	libtbb.so.2 => /home/oulap/SimNIBS-
4.0/simnibs_env/lib/python3.9/site-
packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbb.so.2
(0x00007f4939600000)
	libtbbmalloc.so.2 => /home/oulap/SimNIBS-
4.0/simnibs_env/lib/python3.9/site-
packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbbmallo
c.so.2 (0x00007f4939200000)
	libpthread.so.0 => /usr/lib/libpthread.so.0
(0x00007f493a1d2000)
	libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f4938fc8000)
	libm.so.6 => /usr/lib/libm.so.6 (0x00007f493a0ea000)
	libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f493a0ca000)
	libc.so.6 => /usr/lib/libc.so.6 (0x00007f4938de1000)
	/usr/lib64/ld-linux-x86-64.so.2 (0x00007f493a336000)
	libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f493a0c5000)
	librt.so.1 => /usr/lib/librt.so.1 (0x00007f493a0be000)

I'm interested to see if your version links to the correct gmp library.

Thanks,
Oula



On Wed, 2023-03-08 at 13:39 +0100, Gülce Lale wrote:
> Dear SimNIBS Team,
> I have downloaded the newest brainstorm version from March 1st
> (source + binary) and would like to create a FEM Mesh with SimNIBS
> 4.0. However, I receive the following error message: "SimNIBS 4.x is
> not installed or not added to the system path: the command "charm"
> could not be found.".
> Yet SimNIBS is correctly installed on linux and has been added to the
> system variables in the .bashrc file. Additionally, when I check
> system('charm') on the matlab command window it finds the correct
> charm.py file and when I type getenv('PATH') I get the correct system
> variables which include the path to SimNIBS 4.0.0..
> I also get this error when I try to run “system('charm --version’)” :
> ImportError: /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/create_mesh_surf.cpython-39-x86_64-
> linux-gnu.so: undefined symbol: __gmpq_ad
> I already asked this to the Brainstorm team, and they told me that
> the Brainstorm should be working fine, but the problem might be with
> SimNIBS and its installation. I am also able to start and use SimNIBS
> regularly from the terminal and continue to be able to run charm for
> all my subjects.
> Therefore, I wanted to ask you why this problem could emerge?
> Thank you in advance for your time.
> Best,
> Gülce
> 
> 
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