[MMTK] MMTK install from source on Mac OSX 10.9.3

Konrad Hinsen research at khinsen.fastmail.net
Thu Jun 26 15:11:24 UTC 2014

Anna Gorska writes:

 > there is also issue with netcdf.h:
 > #warning "Using deprecated NumPy API, disable it by " \

You can ignore this warning. It just means that MMTK will perhaps not
work with future releases of NumPy, which is something I will worry
about if and when it really happens.

 > In file included from Src/MMTK_DCD.c:8:
 > Include/MMTK/trajectory.h:16:11: fatal error: 'netcdf.h' file not found

How did you installScientificPython? I am asking because if you get
ScientificPython installed without any error, then this error
shouldn't occur because ScientificPython has exactly the same
requirements as MMTK. Moreover, if you use a recent version of
ScientificPython (> 2.7.8), then MMTK finds netcdf.h through

 > Command /Users/anna/anaconda/bin/python -c "import setuptools;__file__='/tmp/

This looks like you use Anaconda, so presumably you use netCDF from
Anaconda as well. I have tried this myself in the past, without success,
because Anaconda's binary libraries were not compatible with the gcc
for MacOS 10.9 (they were built for some earlier MacOS version).
I filed a bug report about this in December:

This could have changed in the meantime, of course, but I am not
optimistic since my bug report was never handled. So be prepared for
the possibility that your installation attempt will fail even if you
get around the netcdf.h problem.

 > I tried setting NETCDF variables to proper location it did not help,

MMTK doesn't look at any such variable, since it delegates netCDF
installation issues to ScientificPython.

What *should* work is the following:

 1) export NETCDF_PREFIX=/path/to/anaconda/
 2) Run setup.py from ScientificPython
 3) Run setup.py from MMTK

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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