Problems installing preCICE, may be mpi related

Official adapters and tutorials
1

Hi everyone,
I’m new to preCICE and encountered a persistent problem when I tried to install it.

My system description:

At step 4 of the quickstart page, when I execute ./Allwmake, I get this error message:

=== ERROR: Building completed with linking problems: there were undefined symbols. ===
Possible causes:
- Is preCICE discoverable at runtime? Check the content of ADAPTER_PKG_CONFIG_LIBS above.

Here are the created log files:
Allwmake.log (712 Bytes)
ldd.log (9.5 KB)
wmake.log (60 Bytes)

The error seems to be related to the file /usr/lib/x86_64-linux-gnu/libmpi_mpifh.so, so maybe it’s related to mpi.

I’m grateful for your help.

2

Hi @philip,

from the essentially empty wmake.log, I assume that this is not a clean build (you can run ./Allclean first), as no targets were compiled this time. But I also assume that building itself went fine.

Now, from the bottom of your ldd.log, I get the following:

undefined symbol: mpi_conversion_fn_null_	(/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40)
undefined symbol: ompi_fortran_string_f2c	(/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40)
undefined symbol: ompi_fortran_multiple_argvs_f2c	(/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40)
undefined symbol: ompi_fortran_argv_count_f2c	(/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40)
undefined symbol: ompi_fortran_argv_blank_f2c	(/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40)
undefined symbol: ompi_fortran_string_c2f	(/usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40)

and I cherry-pick the following lines from above:

libfftw3_mpi.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3_mpi.so.3 (0x00007fe7e6431000)
libhdf5_openmpi.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103 (0x00007fe7e58a4000)
libmpi_mpifh.so.40 => /usr/lib/x86_64-linux-gnu/libmpi_mpifh.so.40 (0x00007fe7e5634000)
libscalapack-openmpi.so.2.1 => /usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so.2.1 (0x00007fe7e2ee1000)

What I understand is that several dependencies are linking to OpenMPI, while some other dependencies are linking to another MPI version. I wonder, however, where the Fortran-related dependencies come from. Is this just OpenFOAM, or something else?

Unfortunately, linking to MPI is usually a bit messy, since all dependencies need to use the same MPI version (this is not specific to preCICE or the adapter, but a general problem). So, you can try enforcing the same MPI version for OpenFOAM and the rest of the dependencies.

3

Thank you, the conflicting dependencies really seemed to be the problem. I’ve uninstalled my version of OpenMPI and now everything works just fine.

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