[Simnibs-discuss] Issues with making Brainstorm compatible with SimNIBS 4.0
Gülce Lale
G.Lale at campus.lmu.de
Tue Mar 14 14:27:44 CET 2023
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.so.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/libtbbmalloc.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.so.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/libtbbmalloc.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/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
>>
>>
>> _______________________________________________
>> Simnibs-discuss mailing list
>> Simnibs-discuss at drcmr.dk
>> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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