Hi all,
I’m trying to install from source dolfin library on a CentOS machine. I don’t have access as super user so I’ve created a conda env on my home and I’ve installed all the needed dependencies (gcc, boost, cmake, eigen …) on that env. I’ve followed all the instructions reported here Installation — FEniCS Project documentation and everything seems to work fine. Howevere, when I try to import dolfin with python3 -c “import dolfin” I get this error:
ImportError: /home/bioeng/rmunafo/fdir/lib64/libdolfin.so.2019.1: undefined symbol: _ZNK5boost15program_options22error_with_option_name23substitute_placeholdersERKSs
Then, by running this command ldd /home/bioeng/rmunafo/fdir/lib64/libdolfin.so.2019.1, I get this output:
linux-vdso.so.1 => (0x00007ffc11749000)
libboost_timer.so.1.76.0 => /home/bioeng/rmunafo/fenv/lib/libboost_timer.so.1.76.0 (0x00007f935b652000)
libboost_filesystem.so.1.76.0 => /home/bioeng/rmunafo/fenv/lib/libboost_filesystem.so.1.76.0 (0x00007f935b630000)
libboost_program_options.so.1.76.0 => /home/bioeng/rmunafo/fenv/lib/libboost_program_options.so.1.76.0 (0x00007f935b5c7000)
libboost_iostreams.so.1.76.0 => /home/bioeng/rmunafo/fenv/lib/libboost_iostreams.so.1.76.0 (0x00007f935b5ae000)
libhdf5.so.103 => /software/energia/anaconda3/lib/libhdf5.so.103 (0x00007f935a921000)
librt.so.1 => /lib64/librt.so.1 (0x00007f935a719000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f935a4fd000)
libz.so.1 => /home/bioeng/rmunafo/fenv/lib/libz.so.1 (0x00007f935b57f000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f935a2f9000)
libm.so.6 => /lib64/libm.so.6 (0x00007f9359ff7000)
libmpi.so.40 => /home/bioeng/rmunafo/fenv/lib/libmpi.so.40 (0x00007f9359ed3000)
libboost_chrono.so.1.76.0 => /home/bioeng/rmunafo/fenv/lib/libboost_chrono.so.1.76.0 (0x00007f935b573000)
libboost_regex.so.1.76.0 => /home/bioeng/rmunafo/fenv/lib/libboost_regex.so.1.76.0 (0x00007f935b529000)
libstdc++.so.6 => /home/bioeng/rmunafo/fenv/lib/libstdc++.so.6 (0x00007f9359d28000)
libgcc_s.so.1 => /home/bioeng/rmunafo/fenv/lib/libgcc_s.so.1 (0x00007f935b513000)
libc.so.6 => /lib64/libc.so.6 (0x00007f935995b000)
libbz2.so.1.0 => /home/bioeng/rmunafo/fenv/lib/./libbz2.so.1.0 (0x00007f935b4fe000)
liblzma.so.5 => /home/bioeng/rmunafo/fenv/lib/./liblzma.so.5 (0x00007f935b4d5000)
libzstd.so.1 => /home/bioeng/rmunafo/fenv/lib/./libzstd.so.1 (0x00007f935986d000)
/lib64/ld-linux-x86-64.so.2 (0x00007f935b43d000)
libopen-rte.so.40 => /home/bioeng/rmunafo/fenv/lib/./libopen-rte.so.40 (0x00007f93597b1000)
libopen-orted-mpir.so => /home/bioeng/rmunafo/fenv/lib/./libopen-orted-mpir.so (0x00007f935b4ce000)
libopen-pal.so.40 => /home/bioeng/rmunafo/fenv/lib/./libopen-pal.so.40 (0x00007f93596aa000)
libicudata.so.68 => /home/bioeng/rmunafo/fenv/lib/./libicudata.so.68 (0x00007f9357b69000)
libicui18n.so.68 => /home/bioeng/rmunafo/fenv/lib/./libicui18n.so.68 (0x00007f9357865000)
libicuuc.so.68 => /home/bioeng/rmunafo/fenv/lib/./libicuuc.so.68 (0x00007f935767b000)
libutil.so.1 => /lib64/libutil.so.1 (0x00007f9357478000)
Does anyone know how I can fix this problem??
Thanks in advance,
Riccardo.