| Message ID | 5ff814d6-e0da-f5c9-8ae1-29cf40f87702@gmail.com |
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Hi Vincent, Vincent Legoll <vincent.legoll@gmail.com> skribis: > here is my latest work on adding gromacs to guix. > > - rebased on latest guix master > - gromacs had a new version > - unbundling 3rdparties > - packaged some 3rdparties to have our own > > I unbundled googletest by extracting our tarball in > place of the bundled copy. > > Zlib got unbundled via packaging tng and unbundling > it from there. > > Unbundled lmfit by packaging it separately and using that. > I put it with gromacs, but its legitimate place may be > elsewhere, like in maths.scm. > > Unbundled tinyxml2 to use our version, which is newer and > broke code compatibility, so I added a patch to fix the > fallout. I am trying to get those fixes upstream, but that > may not be always practical, they may want to keep their > well tested version. I'll follow up updating the patch in > case parts of it get applied / released upstream. Woow, quite an achievement! Thanks for taking the time to go down this rabbit hole, I think it’s worth it. > The remaining bundled 3rdparties are vmd_molfile & thread_mpi. > > Vmd_molfile source is behind a registration-only web form, I'm > not going there. Sounds reasonable: the headers say it’s part of Gromacs, and it’s definitely free software, so it’s OK to keep it here. > Thread_mpi looks like it is made to be bundled like that, and > is part of the parallelizing of gromacs which is above my > level of understanding (I'm only trying to package it, I'm not > a user). More info here: > http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI Sounds good. Perhaps a comment in the code to state that would be welcome, for our future selves. > Latest license change for tng say "revised bsd", I don't know > which one to choose, I put bsd-3. > > https://github.com/gromacs/tng/commit/65443992d81a8845ba3597620d84e8652e83a254 > > Lmfit is freebsd license, I choose bsd-2. > > https://jugit.fz-juelich.de/mlz/lmfit/-/blob/master/COPYING > > Gromacs itself is lgpl2.1+ and its copying file has bundled > 3parties license explanations. > > https://github.com/gromacs/gromacs/blob/master/COPYING > > Please advise how to proceed further, this is already quite an > adventure for me. I’ll look at the individual patches but it looks like we’re close to the end line! Ludo’.
Hello Ludo, I removed the leftover scm code that was duplicating what is now in the patch, and added a patch header explaining what's going on. >> Vmd_molfile source is behind a registration-only web form, I'm >> not going there. > > Sounds reasonable: the headers say it’s part of Gromacs, and it’s > definitely free software, so it’s OK to keep it here. Added comment. >> Thread_mpi looks like it is made to be bundled like that, and >> is part of the parallelizing of gromacs which is above my >> level of understanding (I'm only trying to package it, I'm not >> a user). More info here: > > Sounds good. Perhaps a comment in the code to state that would be > welcome, for our future selves. Added comment. Put tng & gromacs in chemistry.scm, in fact gromacs sci domain is chemistry, even if also used in bioinfo. Added more comments for patch & still bundled 3rdparties. Moved lmfit to algebra.scm, shortened synopsis. I think I fixed all review comments. Thanks, patches follow.