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Doc clarifications.
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jeromekelleher committed Sep 2, 2019
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2 changes: 1 addition & 1 deletion docs/inference.rst
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Expand Up @@ -168,7 +168,7 @@ point in the sequence: from a genealogical perspective, we know its
parent node. This information is encoded precisely as an `edge
<https://tskit.readthedocs.io/en/latest/data-model.html#edge-table>`_ in a
`tree sequence
<https://tskit.readthedocs.io/en/latest/python-api.html#trees-and-tree-sequences>`_.
<https://tskit.readthedocs.io/en/latest/data-model.html>`_.
Thus, we refer to the output of this step as the "ancestors tree sequence",
which is conventionally stored in a file ending with ``.ancestors.trees``.

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26 changes: 10 additions & 16 deletions docs/installation.rst
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Expand Up @@ -35,22 +35,16 @@ first using `venv <https://docs.python.org/3/library/venv.html>`_::

.. _sec_installation_installation_problems:

+++++++++++++++++++++
Installation problems
+++++++++++++++++++++


There are situations (usually where the GSL libraries are not in the
default locations) where ``tskit`` installation can fail. The same issue can
occur when installing ``msprime``, so you can consult the
`msprime installation documentation <https://msprime.readthedocs.io/en/stable/installation.html>`_
for details on the various ways to address this problem.

Note that one of the dependencies of ``tsinfer``, ``numcodecs``, can be compiled to
use AVX2 instructions if those are available on your hardware. This has led to
issues when installing on hardware with AVX2, then trying to use ``tsinfer``
from a cluster compute node without AVX2. To resolve this, ``numcodecs`` has a
****************
Potential issues
****************

One of the dependencies of ``tsinfer``,
`numcodecs <https://numcodecs.readthedocs.io/>`_, is compiled to
use AVX2 instructions (where available) when installed using pip. This can lead to
issues when ``numcodecs`` is compiled on a machine that supports AVX2
and subsequently run on older machines that do not. To resolve this, ``numcodecs`` has a
``DISABLE_NUMCODECS_AVX2`` variable which can be turned on before calling
``pip install``, see
``pip install``, see
`these instructions <https://numcodecs.readthedocs.io/en/stable/#installation>`_
for details.

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