Installation from source on a CentOS

[Riccardo Munafò]

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 packages (gcc, boost, cmake, eigen ...) on that env. I've followed all the instructions reported here https://fenics.readthedocs.io/en/latest/installation.html#from-source 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.

[David Nolte]

Hi,

not a direct answer to your question, but I compiled dolfin 2019 on CentOS 8.1 with these scripts: https://github.com/dajuno/fenics-centos-build
A number of dependencies (openmpi, boost, etc) were installed by the administrator as system packages, though.
Maybe this can be useful if you can't get the conda build to work.

David

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[David Nolte]

Sorry, I don't know and haven't tried. You might be able to adapt the scripts to your needs for your system, depending on the available packages.

On 9/22/21 09:17, Riccardo Munafò wrote:

Hi,

thanks for your reply. I'm actually working on a CentOS 7. Do you know if a similar solution exists for this version?

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