Hi Joachim,
On 27/05/16 11:21, Joachim Hein wrote:
Hi everyone,
I have a user request for Gromacs in double precision. The “vanilla”
gromacs configs do not build this, so I have to do some massaging and
would need help with the easy block.
Based on the Gromacs documentation:
http://manual.gromacs.org/documentation/5.1.2/install-guide/index.html#introduction-to-building-gromacs I
need to add a string
-DGMX_DOUBLE=on
to the cmake options. Such things (e.g. OpenMP, MPI support) seem to
be handled in the relevant easyblock and the easyconfig. Hacking into
the easyconfigs I am reasonably competent by now, but it seems the
easyblock is lacking the support for that switch.
Looking how openmp is handled in that easyblock
(EasyBuild/2.8.0/lib/python2.7/site-packages/easybuild_easyblocks-2.8.0-py2.7.egg/easybuild/easyblocks/g/gromacs.py)
It seems one needs to add
# enable double support if desired
if self.toolchain.options.get(‘double', None):
self.cfg.update('configopts', "-DGMX_DOUBLE=ON")
else:
self.cfg.update('configopts', "-DGMX_DOUBLE=OFF”)
after which one could activate double support from the easyconfig
This is only going to work if 'double' is a known toolchain option, but
it's not.
Since this is specific to GROMACS, I would define a 'double_precision'
custom easyconfig parameter for GROMACS instead.
This is done in the easyblock via 'extra_options', see for example
https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/w/wrf.py#L62
(and
https://github.com/hpcugent/easybuild/wiki/Tutorial%3A-building-WRF-after-adding-support-for-it#class-definition-class-constructor-and-defining-extra-easyconfig-options).
However, you should be able to do this straight from the easyconfig,
without any required modifications to the easyblock for GROMACS:
configopts = "-DGMX_DOUBLE=ON"
Be careful you don't hard overwrite possible other 'configopts'
specifications that may be already there...
Now comes the questions (apart from whether there is anything wrong in
the above):
* If I don’t want to mess with the EB supplied easy blocks, where do
I put homegrown ones? I tried with the include-easy*block*s in
the configuration file and copied the gromacs.py into a
gromacsdbl.py in there. From the output of the eb
--list-easyblocks it doesn’t seem to pick this up. How do I do my
own local easy blocks? Is that documented?
--include-easyblocks is the goto way to let EB pick up custom
easyblocks, see also
http://easybuild.readthedocs.io/en/latest/Including_additional_Python_modules.html#including-additional-easyblocks-include-easyblocks
There were some bug fixes related to this in recent EasyBuild versions;
which version are you using?
You should not rename gromacs.py for your custom copy, EasyBuild relies
on the name of the module (and --include-easyblcoks doesn't rename them).
Also, make sure the specify the full path, that may help:
--list-easyblocks $PWD/gromacs.py .
* Is adding the above switch to the gromacs easy block something
that could be done for an upcoming EB release? Perhaps have the
gromacs easyconfig build both (single and double precision). I
used to install both (touching he cmake) before EasyBuild.
That may be an option, yes; enhancements to existing easyblocks are
always welcome.
Note that there's already a pending update, I hope to get to that for
EasyBuild v2.9.0 (planned for end of June-ish).
I'm not sure if building both single & double precision by default is a
good option (I'm not familiar enough with GROMACS to know).
regards,
Kenneth
Any comments?
Thanks
Joachim
