Merge pull request #46667 from costrouc/costrouc/lammps-update

lammps: update, hoomd-blue, dl_poly: init
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markuskowa 2018-11-13 21:00:02 +01:00 committed by GitHub
commit 2823b5e698
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5 changed files with 145 additions and 41 deletions

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@ -0,0 +1,37 @@
{ stdenv, fetchurl
, gfortran, mpi
}:
stdenv.mkDerivation rec {
version = "1.10";
name = "DL_POLY_Classic-${version}";
src = fetchurl {
url = "https://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/574/8924/dl_class_1.10.tar.gz";
sha256 = "1r76zvln3bwycxlmqday0sqzv5j260y7mdh66as2aqny6jzd5ld7";
};
buildInputs = [ mpi gfortran ];
configurePhase = ''
cd source
cp -v ../build/MakePAR Makefile
'';
buildPhase = ''
make dlpoly
'';
installPhase = ''
mkdir -p $out/bin
cp -v ../execute/DLPOLY.X $out/bin
'';
meta = with stdenv.lib; {
homepage = https://www.ccp5.ac.uk/DL_POLY_C;
description = "DL_POLY Classic is a general purpose molecular dynamics simulation package";
license = licenses.bsdOriginal;
platforms = [ "x86_64-linux" ];
maintainers = [ maintainers.costrouc ];
};
}

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@ -1,63 +1,56 @@
{ lib
, bash
, stdenv
, writeText
, fetchFromGitHub
, libpng
, gzip
, fftw
, openblas
, mpiSupport ? false, mpi ? null
{ stdenv, fetchFromGitHub
, libpng, gzip, fftw, openblas
, mpi ? null
}:
assert mpiSupport -> mpi != null;
let packages = [
"asphere" "body" "class2" "colloid" "compress" "coreshell"
"dipole" "granular" "kspace" "manybody" "mc" "misc" "molecule"
"opt" "peri" "qeq" "replica" "rigid" "shock" "snap" "srd" "user-reaxc"
];
lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
withMPI = (mpi != null);
in
stdenv.mkDerivation rec {
# LAMMPS has weird versioning converted to ISO 8601 format
version = "patch_2Aug2018";
version = "stable_22Aug2018";
name = "lammps-${version}";
lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
src = fetchFromGitHub {
owner = "lammps";
repo = "lammps";
rev = "${version}";
sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
sha256 = "1dlifm9wm1jcw2zwal3fnzzl41ng08c7v48w6hx2mz84zljg1nsj";
};
passthru = {
inherit mpi;
inherit packages;
};
buildInputs = [ fftw libpng openblas gzip bash ]
++ (stdenv.lib.optionals mpiSupport [ mpi ]);
buildInputs = [ fftw libpng openblas gzip ]
++ (stdenv.lib.optionals withMPI [ mpi ]);
configurePhase = ''
cd src
for pack in ${stdenv.lib.concatStringsSep " " packages}; do make "yes-$pack" SHELL=$SHELL; done
'';
# Must do manual build due to LAMMPS requiring a seperate build for
# the libraries and executable
builder = writeText "builder.sh" ''
source $stdenv/setup
# the libraries and executable. Also non-typical make script
buildPhase = ''
make mode=exe ${if withMPI then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
make mode=shlib ${if withMPI then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
'';
mkdir lammps
cp -r $src/lib $src/src lammps
chmod -R 755 lammps/src/
cd lammps/src
for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
installPhase = ''
mkdir -p $out/bin $out/include $out/lib
mkdir -p $out/bin
cp -v lmp_* $out/bin/
mkdir -p $out/include
cp -v *.h $out/include/
mkdir -p $out/lib
cp -v liblammps* $out/lib/
'';
meta = {
meta = with stdenv.lib; {
description = "Classical Molecular Dynamics simulation code";
longDescription = ''
LAMMPS is a classical molecular dynamics simulation code designed to
@ -67,8 +60,8 @@ stdenv.mkDerivation rec {
under the terms of the GNU Public License (GPL).
'';
homepage = http://lammps.sandia.gov;
license = stdenv.lib.licenses.gpl2;
platforms = stdenv.lib.platforms.linux;
maintainers = with lib.maintainers; [ costrouc ];
license = licenses.gpl2;
platforms = platforms.linux;
maintainers = [ maintainers.costrouc ];
};
}

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@ -0,0 +1,67 @@
{ stdenv, buildPythonPackage, fetchgit
, cmake, pkgconfig
, python
, mpi ? null
}:
let components = {
cgcmm = true;
depreciated = true;
hpmc = true;
md = true;
metal = true;
testing = false;
};
onOffBool = b: if b then "ON" else "OFF";
withMPI = (mpi != null);
in
stdenv.mkDerivation rec {
version = "2.3.4";
name = "hoomd-blue-${version}";
src = fetchgit {
url = "https://bitbucket.org/glotzer/hoomd-blue";
rev = "v${version}";
sha256 = "0in49f1dvah33nl5n2qqbssfynb31pw1ds07j8ziryk9w252j1al";
};
passthru = {
inherit components mpi;
};
nativeBuildInputs = [ cmake pkgconfig ];
buildInputs = stdenv.lib.optionals withMPI [ mpi ];
propagatedBuildInputs = [ python.pkgs.numpy ]
++ stdenv.lib.optionals withMPI [ python.pkgs.mpi4py ];
enableParallelBuilding = true;
dontAddPrefix = true;
cmakeFlags = [
"-DENABLE_MPI=${onOffBool withMPI}"
"-DBUILD_CGCMM=${onOffBool components.cgcmm}"
"-DBUILD_DEPRECIATED=${onOffBool components.depreciated}"
"-DBUILD_HPMC=${onOffBool components.hpmc}"
"-DBUILD_MD=${onOffBool components.md}"
"-DBUILD_METAL=${onOffBool components.metal}"
"-DBUILD_TESTING=${onOffBool components.testing}"
];
preConfigure = ''
# Since we can't expand $out in `cmakeFlags`
cmakeFlags="$cmakeFlags -DCMAKE_INSTALL_PREFIX=$out/${python.sitePackages}"
'';
# tests fail but have tested that package runs properly
doCheck = false;
checkTarget = "test";
meta = with stdenv.lib; {
homepage = http://glotzerlab.engin.umich.edu/hoomd-blue/;
description = "HOOMD-blue is a general-purpose particle simulation toolkit";
license = licenses.bsdOriginal;
platforms = [ "x86_64-linux" ];
maintainers = [ maintainers.costrouc ];
};
}

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@ -21378,12 +21378,15 @@ with pkgs;
### SCIENCE/MOLECULAR-DYNAMICS
dl-poly-classic-mpi = callPackage ../applications/science/molecular-dynamics/dl-poly-classic {
mpi = openmpi;
};
lammps = callPackage ../applications/science/molecular-dynamics/lammps {
fftw = fftw;
};
lammps-mpi = appendToName "mpi" (lammps.override {
mpiSupport = true;
lammps-mpi = lowPrio (lammps.override {
mpi = openmpi;
});

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@ -392,6 +392,10 @@ in {
hdmedians = callPackage ../development/python-modules/hdmedians { };
hoomd-blue = toPythonModule (callPackage ../development/python-modules/hoomd-blue {
inherit python;
});
httpsig = callPackage ../development/python-modules/httpsig { };
i3ipc = callPackage ../development/python-modules/i3ipc { };