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

Oula Puonti oulap at drcmr.dk
Wed Mar 15 17:10:25 CET 2023 

Hi Gülce,

Can you send the details of the linux setup you're running?

One option would be to build simnibs for source, which would hopefully
then work on your computer as it would be build specifically for that
setup. It's not that difficult but you need to have gcc8 devtools
available, see here for some instructions:

https://stackoverflow.com/questions/53310625/how-to-install-gcc8-using-devtoolset-8-gcc

Other than that you would need to have anaconda or miniconda available
for creating the virtual python environment.

If the linux you're running is not a very exotic one, I can also try to
build an installer for it andd send it to you. We can try if that works
first before you trying to build simnibs from source.

Best,
Oula



On Tue, 2023-03-14 at 14:27 +0100, Gülce Lale wrote:
> Hi Oula,
> 
> Thank you for your reply.
> 
> I repeated the steps below. This was my outcome:
> 
> ldd create_mesh_surf.cpython-39-x86_64-linux-gnu.so
>     linux-vdso.so.1 (0x00007ffe67fb8000)
>     libmpfr.so.1 => /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libmpfr.s
> o.1 (0x00007f8ece819000)
>     libgmp.so.3 => /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libgmp.so
> .3 (0x00007f8ece5be000)
>     libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f8ece586000)
>     libtbb.so.2 => /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbb.so
> .2 (0x00007f8ece31f000)
>     libtbbmalloc.so.2 =>
> /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbbmal
> loc.so.2 (0x00007f8ece0c4000)
>     libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f8ece0a0000)
>     libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007f8ecded3000)
>     libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8ecdd8f000)
>     libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007f8ecdd75000)
>     libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8ecdba0000)
>     /lib64/ld-linux-x86-64.so.2 (0x00007f8eceb7b000)
>     libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
> (0x00007f8ecdb9a000)
>     librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1
> (0x00007f8ecdb8e000)
> 
> From what I can tell it is linking to the correct gmp library. I am
> very confused.
> 
> Then, I created another version of the 4.0.0 where I installed a gmp
> package, which had not been present originally. (I am unsure whether
> this made a difference.) 
> 
> I ran the same command in the other folder named
> /sw/SImNIBS/4.0.0_daniela/ and got this:
> 
> /sw/SimNIBS/4.0.0_daniela/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal$ ldd create_mesh_surf.cpython-39-
> x86_64-linux-gnu.so
>     linux-vdso.so.1 (0x00007ffc4e505000)
>     libmpfr.so.1 =>
> /sw/SimNIBS/4.0.0_daniela/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libmpfr.s
> o.1 (0x00007f92b088b000)
>     libgmp.so.3 =>
> /sw/SimNIBS/4.0.0_daniela/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libgmp.so
> .3 (0x00007f92b0630000)
>     libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f92b05f8000)
>     libtbb.so.2 =>
> /sw/SimNIBS/4.0.0_daniela/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbb.so
> .2 (0x00007f92b0391000)
>     libtbbmalloc.so.2 =>
> /sw/SimNIBS/4.0.0_daniela/simnibs_env/lib/python3.9/site-
> packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbbmal
> loc.so.2 (0x00007f92b0136000)
>     libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
> (0x00007f92b0112000)
>     libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6
> (0x00007f92aff45000)
>     libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f92afe01000)
>     libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
> (0x00007f92afde7000)
>     libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f92afc12000)
>     /lib64/ld-linux-x86-64.so.2 (0x00007f92b0bed000)
>     libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
> (0x00007f92afc0c000)
>     librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1
> (0x00007f92afc00000)
> 
> From what I gather the new 4.0.0_daniela option made no difference.
> (I may be wrong).
> 
> Looking forward to your response.
> Thank you for your time and answers in advance.
> Best wishes,
> Gülce
> 
> > On 10 Mar 2023, at 17:17, Oula Puonti <oulap at drcmr.dk> wrote:
> > 
> > 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/libtbbm
> > allo
> > 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
> > > 
> > > 
> > > _______________________________________________
> > > Simnibs-discuss mailing list
> > > Simnibs-discuss at drcmr.dk
> > > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
> > 
>

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