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. 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. 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. 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> 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-easyblocks 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
