<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><span style="font-size: 14px;" class="">Hi Oula,</span><div class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div class=""><span style="font-size: 14px;" class="">Thank you for your reply.</span></div><div class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div class=""><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">I repeated the steps below. This was my outcome:</span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><p style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""></p><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">ldd create_mesh_surf.cpython-39-x86_64-linux-gnu.so<br class=""> linux-vdso.so.1 (0x00007ffe67fb8000)<br class=""> 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)<br class=""> 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)<br class=""> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f8ece586000)<br class=""> 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)<br class=""> 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)<br class=""> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f8ece0a0000)<br class=""> libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f8ecded3000)<br class=""> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8ecdd8f000)<br class=""> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f8ecdd75000)<br class=""> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8ecdba0000)<br class=""> /lib64/ld-linux-x86-64.so.2 (0x00007f8eceb7b000)<br class=""> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f8ecdb9a000)<br class=""> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f8ecdb8e000)</span></div><p style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""></p><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">From what I can tell it is linking to the correct gmp library. I am very confused.</span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">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.) <br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">I ran the same command in the other folder named /sw/SImNIBS/4.0.0_daniela/ and got this:</span></div><div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><p style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Helvetica, sans-serif;" class=""></p><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">/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<br class=""> linux-vdso.so.1 (0x00007ffc4e505000)<br class=""> 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)<br class=""> 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)<br class=""> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f92b05f8000)<br class=""> 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)<br class=""> 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)<br class=""> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f92b0112000)<br class=""> libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f92aff45000)<br class=""> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f92afe01000)<br class=""> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f92afde7000)<br class=""> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f92afc12000)<br class=""> /lib64/ld-linux-x86-64.so.2 (0x00007f92b0bed000)<br class=""> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f92afc0c000)<br class=""> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f92afc00000)<br class=""><br class="">From what I gather the new 4.0.0_daniela option made no difference. (I may be wrong).</span></div><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class=""><br class=""></span></div><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">Looking forward to your response.</span></div><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">Thank you for your time and answers in advance.</span></div><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">Best wishes,</span></div><div style="font-family: Calibri, Helvetica, sans-serif;" class=""><span style="font-size: 14px;" class="">Gülce</span></div>
<div><br class=""><blockquote type="cite" class=""><div class="">On 10 Mar 2023, at 17:17, Oula Puonti <<a href="mailto:oulap@drcmr.dk" class="">oulap@drcmr.dk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Gülce,<br class=""><br class="">I'm guessing that the brainstorm issue is related to the linking issue<br class="">with charm, i.e., that brainstorm complains because the charm command<br class="">throws an error.<br class=""><br class="">Can you run a linker on the .so library that is giving problems? You<br class="">can do:<br class=""><br class="">cd /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-<br class="">packages/simnibs/mesh_tools/cgal/<br class=""><br class="">and then call:<br class=""><br class="">ldd create_mesh_surf.cpython-39-x86_64-linux-gnu.so<br class=""><br class="">For my simnibs installation the output looks like this:<br class=""><br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>linux-vdso.so.1 (0x00007ffedc7dc000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libmpfr.so.1 => /home/oulap/SimNIBS-<br class="">4.0/simnibs_env/lib/python3.9/site-<br class="">packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libmpfr.so.<br class="">1 (0x00007f4939e00000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libgmp.so.3 => /home/oulap/SimNIBS-<br class="">4.0/simnibs_env/lib/python3.9/site-<br class="">packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libgmp.so.3<br class="">(0x00007f4939a00000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libz.so.1 => /usr/lib/libz.so.1 (0x00007f493a1d9000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libtbb.so.2 => /home/oulap/SimNIBS-<br class="">4.0/simnibs_env/lib/python3.9/site-<br class="">packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbb.so.2<br class="">(0x00007f4939600000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libtbbmalloc.so.2 => /home/oulap/SimNIBS-<br class="">4.0/simnibs_env/lib/python3.9/site-<br class="">packages/simnibs/mesh_tools/cgal/./../../external/lib/linux/libtbbmallo<br class="">c.so.2 (0x00007f4939200000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libpthread.so.0 => /usr/lib/libpthread.so.0<br class="">(0x00007f493a1d2000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f4938fc8000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libm.so.6 => /usr/lib/libm.so.6 (0x00007f493a0ea000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f493a0ca000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libc.so.6 => /usr/lib/libc.so.6 (0x00007f4938de1000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>/usr/lib64/ld-linux-x86-64.so.2 (0x00007f493a336000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>libdl.so.2 => /usr/lib/libdl.so.2 (0x00007f493a0c5000)<br class=""><span class="Apple-tab-span" style="white-space:pre"> </span>librt.so.1 => /usr/lib/librt.so.1 (0x00007f493a0be000)<br class=""><br class="">I'm interested to see if your version links to the correct gmp library.<br class=""><br class="">Thanks,<br class="">Oula<br class=""><br class=""><br class=""><br class="">On Wed, 2023-03-08 at 13:39 +0100, Gülce Lale wrote:<br class=""><blockquote type="cite" class="">Dear SimNIBS Team,<br class="">I have downloaded the newest brainstorm version from March 1st<br class="">(source + binary) and would like to create a FEM Mesh with SimNIBS<br class="">4.0. However, I receive the following error message: "SimNIBS 4.x is<br class="">not installed or not added to the system path: the command "charm"<br class="">could not be found.".<br class="">Yet SimNIBS is correctly installed on linux and has been added to the<br class="">system variables in the .bashrc file. Additionally, when I check<br class="">system('charm') on the matlab command window it finds the correct<br class="">charm.py file and when I type getenv('PATH') I get the correct system<br class="">variables which include the path to SimNIBS 4.0.0..<br class="">I also get this error when I try to run “system('charm --version’)” :<br class="">ImportError: /sw/SimNIBS/4.0.0/simnibs_env/lib/python3.9/site-<br class="">packages/simnibs/mesh_tools/cgal/create_mesh_surf.cpython-39-x86_64-<br class="">linux-gnu.so: undefined symbol: __gmpq_ad<br class="">I already asked this to the Brainstorm team, and they told me that<br class="">the Brainstorm should be working fine, but the problem might be with<br class="">SimNIBS and its installation. I am also able to start and use SimNIBS<br class="">regularly from the terminal and continue to be able to run charm for<br class="">all my subjects.<br class="">Therefore, I wanted to ask you why this problem could emerge?<br class="">Thank you in advance for your time.<br class="">Best,<br class="">Gülce<br class=""><br class=""><br class="">_______________________________________________<br class="">Simnibs-discuss mailing list<br class=""><a href="mailto:Simnibs-discuss@drcmr.dk" class="">Simnibs-discuss@drcmr.dk</a><br class="">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss<br class=""></blockquote><br class=""></div></div></blockquote></div><br class=""></div></body></html>