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<p><font face="VictorMono Nerd Font">Hi Gulce</font></p>
<p><font face="VictorMono Nerd Font">Allow me to weigh in. Someone
from our department had the same issue you describe today;
getting a linking error when calling charm from within MATLAB.
It turns out that MATLAB includes some libraries itself (among
these are gmp, tbb etc.) and when you execute programs from
within MATLAB, these are prepended (or rather their paths) to
LD_LIBRARY_PATH and hence are used by the program. You can
verify if this is the case by comparing the output of running
ldd on the .so file in the terminal (what I believe you showed
in your previous email) and running ldd on the .so *from within
MATLAB*, e.g., using `system` or `unix`.</font></p>
<p><font face="VictorMono Nerd Font">One solution is to *prepend*
the path to the libraries included in SimNIBS to LD_LIBRARY_PATH
like so</font></p>
<p><font face="VictorMono Nerd Font"> setenv(‘LD_LIBRARY_PATH’,
sprintf(‘/path/to/simnibs/external/lib/linux:%s’,
getenv(‘LD_LIBRARY_PATH’)))<br>
</font></p>
<p><font face="VictorMono Nerd Font">Put this in your .m file before
you call charm from MATLAB.</font></p>
<p><font face="VictorMono Nerd Font">Best,</font></p>
<p><font face="VictorMono Nerd Font">Jesper</font></p>
<div class="moz-cite-prefix">On 3/15/23 17:10, Oula Puonti wrote:<br>
</div>
<blockquote type="cite"
cite="mid:7ae7d1915493ff4b5430e76795c2aa277e95b797.camel@drcmr.dk">
<pre class="moz-quote-pre" wrap="">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:
<a class="moz-txt-link-freetext" href="https://stackoverflow.com/questions/53310625/how-to-install-gcc8-using-devtoolset-8-gcc">https://stackoverflow.com/questions/53310625/how-to-install-gcc8-using-devtoolset-8-gcc</a>
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:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">On 10 Mar 2023, at 17:17, Oula Puonti <a class="moz-txt-link-rfc2396E" href="mailto:oulap@drcmr.dk"><oulap@drcmr.dk></a> 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:
</pre>
<blockquote type="cite">
<pre class="moz-quote-pre" wrap="">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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</pre>
</blockquote>
<pre class="moz-quote-pre" wrap="">
</pre>
</blockquote>
<pre class="moz-quote-pre" wrap="">
</pre>
</blockquote>
<pre class="moz-quote-pre" wrap="">
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