On 27/05/16 11:49, Joachim Hein wrote:
Hi Kenneth,
Thanks for the info - that was quick and a fair bit of stuff to
digest. I’ll try the easy thing - having a modified config after
finishing this email.
I want to get back directly on the single double simultaneous build.
In particular to start the required discussion here (I assume you
know the people behind the gromacs stuff, perhaps it is an idea to
prompt them for a comment).
My understanding is that is (was?) standard for Gromacs install. The
double executables get an additional “_d” to avoid name space
conflict. Actually the user requesting said: there is no gmx_mpi_d in
your installation. For info gmx_mpi is the relevant single precision
gromacs call. So the gromacs users who care for double sort of know
that and expect it this way.
In this case, I think also building the double binaries does make sense,
indeed.
So, enhancing the GROMACS easyblock to build the double binaries by
default make sense.
Providing a way to disable that easily may make sense though, for
example by defining a custom easyconfig parameter double_precision and
setting it to True by default.
Once we are at it, the easybuild set up build everything with MPI,
which creates a lot of queries here. (Our?) users only expect mpi
builds of the mdrun but expect the rest of the gromacs suite to be
serial (use gmx instead of gmx_mpi). But using gmx_mpi and an
mpi-joblauncher is is something my users and I can live with, the
double I really need.
We have 'mt' builds of GROMACS too, where MPI is not used (and where you
get 'gmx' instead of 'gmx_mpi'), see for example
https://github.com/hpcugent/easybuild-easyconfigs/pull/3125.
As I said, I like to initiate a discussion here. I appreciate the
work others have put into the existing EB Gromacs support and do not
want to be perceived as complaining.
I think it's clear you're not complaining, suggestions for improvements
are always welcome!
Pull requests for those suggestions are even better... ;-)
regards,
Kenneth
Best wishes
Joachim
On 27 May 2016, at 11:32, Kenneth Hoste <[email protected]
<mailto:[email protected]>> wrote:
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
