Frequently asked questions

Below you find a list for known errors, that may occur and how to work around:

1. HDF5surrogate escape

NameError: global name ‘exc’ is not defined

add:
export LC_ALL=en_AU.utf8
to your .bashrc

2. Theano MKL support

RuntimeError: To use MKL 2018 with Theano you MUST set “MKL_THREADING_LAYER=GNU” in your environement.

add
export MKL_THREADING_LAYER=GNU
to your .bashrc

3. Slow compilation

No error will be thrown, but during “beat sample” the compilation of the forward model function ḿay take a long time. In such a case the default compilation flags of theano may be overwritten. This may result in longer runtime.:

THEANO_FLAGS=optimizer=fast_compile beat sample Projectpath
4. MPI rank always 0

ValueError: Specified more workers that sample in the posterior “8”, than there are total number of workers “0”

There is an inconsistency in the MPI executable that is used for starting the sampler and the library that was used to compile mpi4py.
Please make sure to use the same MPI library. One fix would be to remove all installations of MPI from the machine and install a fresh version.