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.