Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
{
mpi = super.mpich;
}
All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
* make CPU acceleration selectable.
* update cmake flag for acceleration CPU_ACCELERATION -> SIMD
GMX_CPU_ACCELERATION is outdated and has been ignored.
* add hwloc to inputs
* always build with OpenMP
* change name -> pname
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.
treewide: cleanup from blas/lapack changes
A few issues in the original treewide:
- can’t assume blas64 is a bool
- unused commented code
Major changes and update to lammps build
- using fetchFromGitHub to get source instead of lammps mirror
- configurable lammps packages included and includes for compilation
- cleaner build script
- preserving the executable, shared library names, and include headers
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/gromacs/versions.
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC had a zero exit code or showed the expected version
- /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC.bash passed the binary check.
- /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC.zsh passed the binary check.
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC.csh had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/demux.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/xplor2gmx.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/gmx-completion.bash had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/gmx-completion-gmx.bash had a zero exit code or showed the expected version
- /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/gmx passed the binary check.
- 3 of 9 passed binary check by having a zero exit code.
- 0 of 9 passed binary check by having the new version present in output.
- found 2018.2 with grep in /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2
- directory tree listing: https://gist.github.com/1679f0362dfcc7299a6d5b8d9e76c14e
- du listing: https://gist.github.com/2f848bb0fe181676c17b61a9d5a94953
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.
This update was made based on information from https://repology.org/metapackage/gromacs/versions.
These checks were done:
- built on NixOS
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC had a zero exit code or showed the expected version
- /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC.bash passed the binary check.
- /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC.zsh passed the binary check.
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC.csh had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/demux.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/xplor2gmx.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/gmx-completion.bash had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/gmx-completion-gmx.bash had a zero exit code or showed the expected version
- /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/gmx passed the binary check.
- 3 of 9 passed binary check by having a zero exit code.
- 0 of 9 passed binary check by having the new version present in output.
- found 2018.1 with grep in /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1
- directory tree listing: https://gist.github.com/4d089bde03168c17ad10db514f47d339
- du listing: https://gist.github.com/5dd10f02ed60d442ec148efcf18c7661
Semi-automatic update. These checks were done:
- built on NixOS
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/GMXRC.bash -h` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/GMXRC.bash --help` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/GMXRC.bash help` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/GMXRC.zsh -h` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/GMXRC.zsh --help` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/GMXRC.zsh help` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/gmx -h` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/gmx help` got 0 exit code
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/gmx --version` and found version 2018
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/gmx -h` and found version 2018
- ran `/nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018/bin/gmx help` and found version 2018
- found 2018 with grep in /nix/store/i2ls9z094j6a3vqvq6gz4hyhl86dh31d-gromacs-2018
* pkgs: refactor needless quoting of homepage meta attribute
A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.
* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit
* Fixed some instances
Many (less easily automatically converted) old-style strings
remain.
Where there was any possible ambiguity about the exact version or
variant intended, nothing was changed. IANAL, nor a search robot.
Use `with stdenv.lib` wherever it makes sense.
(My OCD kicked in today...)
Remove repeated package names, capitalize first word, remove trailing
periods and move overlong descriptions to longDescription.
I also simplified some descriptions as well, when they were particularly
long or technical, often based on Arch Linux' package descriptions.
I've tried to stay away from generated expressions (and I think I
succeeded).
Some specifics worth mentioning:
* cron, has "Vixie Cron" in its description. The "Vixie" part is not
mentioned anywhere else. I kept it in a parenthesis at the end of the
description.
* ctags description started with "Exuberant Ctags ...", and the
"exuberant" part is not mentioned elsewhere. Kept it in a parenthesis
at the end of description.
* nix has the description "The Nix Deployment System". Since that
doesn't really say much what it is/does (especially after removing
the package name!), I changed that to "Powerful package manager that
makes package management reliable and reproducible" (borrowed from
nixos.org).
* Tons of "GNU Foo, Foo is a [the important bits]" descriptions
is changed to just [the important bits]. If the package name doesn't
contain GNU I don't think it's needed to say it in the description
either.
