Troubleshoot
************

Here is a list of some common errors at the different steps and their
possible solutions.

Configuration issues
====================

**Q:** configure: error: No Fortran compiler found

**A:** The configure script will try to find a fortran compiler in your
PATH. So you need to either update it, or specify directly the directory
with :

::

    $  ./configure MPI_DIRECTORY=/usr/local/openmpi143/bin/

**Q:** configure: error: Fortran compiler cannot create executables

**A:** You need to add the correct path for the MPI static library
issue. The configure script will give you what is has found. Example :

::

    searching MPI compiler PGF .../usr/local/openmpi143/bin/mpif90

You can use ``LD_LIBRARY_PATH`` for that. On Bash :

::

    $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/openmpi143/lib 

This is a temporary fix. Here are the normal ways to do that on Linux :

-  Create a symlink to a directory listed in
   /etc/ld.so.conf
-  Copy the library to a directory listed in this file
-  Edit this file to add the directory containing the library

If everything else fails, you can specify the compiler with the FC
flags:

::

    $ $ ./configure FC=/mypath/mycompiler

**Q:** configure: WARNING: HDF5 is not parallel

**A:** This probably means you did not enable the parallel version in
your HDF5 installation. See ?. Otherwise, it means the script fails to
detect the parallel features. Here is how it works: it searchs for
``define HAVE_PARALLEL 1`` in the header files. It is most likely the
include path is not correct then. You can add more include path with:

::

     $  ./configure HDF5_FLAGS=" -I/yourincludepath"

**Q:** configure: error: Could not compile and link with HDF5

**A:** HDF5 is the default and must be installed. Please check ?.

**Q:** configure: error: Could not compile and link with parallel HDF5

**A:** You have HDF5 installed but a conflict between the fortran module
files and the install.

Compilation issues
==================

**Q:** undefined reference to 'mpi\_get\_address\_'

**A:** Try a ``make clean``. Otherwise, check your MPI implementation.

**Q:** Fatal Error: Can't open module file 'configuration\_class.mod'

**A:** Fortran module dependencies are not well integrated with Automake
and managed by our code. For the moment, try a ``make clean`` and
recompile.

**Q:** undefined reference to 'mpi\_get\_address\_'

**A:** Try a ``make clean``. Otherwise, check your MPI implementation.

**Q:** partitioning\_class.F90: undefined reference to
h5pset\_fapl\_mpio\_f\_

**A:** This happens when you try to use a parallel HDF5 version but the
linker fails to find the propery librairy. In practice, it may mean you
are using the wrong ``hdf5.mod``.

Look at the compilation flags to find the include directory, and search
for ``hdf5.mod`` in them. Then check it really contains
``h5pset_fapl_mpio_``. Then you can set ``HDF5_DIR`` and ``HDF5_FLAGS``
as explained in ?.

Run issues
==========

**Q:** Can't exec "/usr/lib64/openmpi/bin/mpirun": No such file or
directory

**A:** You probably did not do a ``make install``.

**Q:** error while loading shared libraries: libmpichf90.so.1.2: cannot
open shared object file: No such file or directory

**A:** The executable was linked with the wrong library. Try a ``make
              clean && make``.

**Q:** I compiled Pangolin but my modifications are not taken into
account !

**A:** By default, the executable is in ``src/``, so you have to do a
``make install`` to put the new version in ``bin/``.

Other issues
============

Data generation issues
----------------------

**Q:** SyntaxError in generate/pangolingrid.py

**A:** If you have a message similar to :

::

    File "/home/alex/phd/pangolin/generate/pangolingrid.py", line 819
    print "No winds for random"
    ^
    SyntaxError: invalid syntax

then you are using Python 3. This version of Pangolin is only compatible
with Python 2.7+ at the moment.

Documentation issues
--------------------

**Q:** xsl:import : unable to load
/usr/share/xml/docbook/stylesheet/docbook-xsl/html/chunk.xsl

**A:** The location of the stylesheet for docbook is not correct. First,
locate the folder for the stylesheet file ``html/chunk.xsl`` with:

::

    $ locate html/chunk.xsl
    /usr/share/xml/docbook/stylesheet/docbook-xsl/html/chunk.xsl

Then modify the folling line in ``doc/docbook/Makefile`` to the location
you found:

::

    LOC_HTML=/usr/share/xml/docbook/stylesheet/docbook-xsl/html/chunk.xsl 

Testing issues
--------------

**Q:** Bailout called. Further testing stopped: Backtrace for this
error:

**A:** If you have something like :

::

    Running tests from 1 to 12
    ok 1 - Checking west to east advection (1 partition(s))
    Bailout called.  Further testing stopped:  Backtrace for this error:
    Bail out!  Backtrace for this error:
    # Child (Nb partitions = 1) exited without calling finalize()

    #   Failed test 'Nb partitions = 1'
    #   at /space/praga/perl/lib/perl5/Test/Builder.pm line
    #   1212.
    # Tests were run but no plan was declared and
    # done_testing() was not seen.
                    FAILED--Further testing stopped: Backtrace for this error:
                  

send a bug report to the maintainer.