[gmx-developers] Python package build

Eric Irrgang ericirrgang at gmail.com
Mon Jan 20 13:07:23 CET 2020

On Mon, Jan 20, 2020 at 2:18 PM Benson Muite <benson_muite at emailplus.org>

> Packaging is probably important. In many beginner tutorials, "sudo apt-get
> install gromacs" is commonly used to avoid compilation issues.
That is fine when the version of GROMACS is not so important. For the next
few years, the version of gmxapi will be pretty important. If the Python
package included the necessary GROMACS code, wouldn't "pip install gmxapi"
be just as easy as "sudo apt-get-install gromacs"?

> That being said, it would be helpful if developers could completely turn
> off python and still have a usable installation solely in a relatively low
> level language so that adding new features and testing on new hardware is
> possible.
Agreed. This point should be orthogonal to the present issue.

> Ensuring compatibility between Python packaging and Linux distribution
> packaging can be a pain.
I would say "impossible" as the complexity of a researcher's Python-driven
toolkit grows. I don't see much point in packaging Python-driven scientific
software for Linux distributions.

> One might consider having a Python version on Pypi so that beginners still
> have an easy way to install.
There are gmxapi source distributions on PyPI. My proposal in this email
thread would make it easier to install from PyPI by allowing the GROMACS
dependency to be wrapped into the same package.

> App images (or other similar portable installable linux versions) are
> another possible alternative to avoid beginners needing to compile.
We have Docker and Singularity recipes for gmxapi 0.0.7. I have received
feedback from HPC support staff that they find Spack useful in helping
users to assemble their software tool kits. I am looking into technologies
like Yarn to help provision execution environments. I welcome further
discussion, especially regarding specific use cases.
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