From 7717a2b844967ab1f53b7b89de7a35596fa9616d Mon Sep 17 00:00:00 2001 From: Chris Ostrouchov Date: Fri, 14 Sep 2018 02:08:48 -0400 Subject: [PATCH 1/3] dl-poly-classic: init 1.10 only mpi version provided --- .../dl-poly-classic/default.nix | 37 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 ++ 2 files changed, 41 insertions(+) create mode 100644 pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix diff --git a/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix new file mode 100644 index 000000000000..1986f3b75ec1 --- /dev/null +++ b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix @@ -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 ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index aaa8da74333d..661bf5086c02 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -21138,6 +21138,10 @@ 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; }; From 397e15f89e849d255db2384b38c5594357cc8daa Mon Sep 17 00:00:00 2001 From: Chris Ostrouchov Date: Fri, 14 Sep 2018 02:09:39 -0400 Subject: [PATCH 2/3] lammps: patch_2Aug2018 -> stable_22Aug2018 nix derivation was cleaned significantly to follow nixpkgs better --- .../molecular-dynamics/lammps/default.nix | 71 +++++++++---------- pkgs/top-level/all-packages.nix | 3 +- 2 files changed, 33 insertions(+), 41 deletions(-) diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index 03e37ad9d935..f4491053e4c8 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -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* $out/lib/ ''; - meta = { + meta = with stdenv.lib; { description = "Classical Molecular Dynamics simulation code"; longDescription = '' LAMMPS is a classical molecular dynamics simulation code designed to @@ -67,8 +60,8 @@ stdenv.mkDerivation rec { under the terms of the GNU Public License (GPL). ''; homepage = http://lammps.sandia.gov; - license = stdenv.lib.licenses.gpl2; - platforms = stdenv.lib.platforms.linux; - maintainers = with lib.maintainers; [ costrouc ]; + license = licenses.gpl2; + platforms = platforms.linux; + maintainers = [ maintainers.costrouc ]; }; } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 661bf5086c02..ec37c90851d2 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -21146,8 +21146,7 @@ with pkgs; fftw = fftw; }; - lammps-mpi = appendToName "mpi" (lammps.override { - mpiSupport = true; + lammps-mpi = lowPrio (lammps.override { mpi = openmpi; }); From ae66a9244b28e14320a24b97bc1c8a29f2e7c87d Mon Sep 17 00:00:00 2001 From: Chris Ostrouchov Date: Fri, 14 Sep 2018 02:10:49 -0400 Subject: [PATCH 3/3] hoomd-blue: init at 2.3.4 --- .../python-modules/hoomd-blue/default.nix | 67 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 4 ++ 2 files changed, 71 insertions(+) create mode 100644 pkgs/development/python-modules/hoomd-blue/default.nix diff --git a/pkgs/development/python-modules/hoomd-blue/default.nix b/pkgs/development/python-modules/hoomd-blue/default.nix new file mode 100644 index 000000000000..3463f471c5eb --- /dev/null +++ b/pkgs/development/python-modules/hoomd-blue/default.nix @@ -0,0 +1,67 @@ +{ stdenv, buildPythonPackage, fetchgit +, cmake, pkgconfig +, python +, mpi ? null +}: + +let components = { + cgcmm = true; + depreciated = true; + hpmc = true; + md = true; + metal = true; + testing = false; + }; + onOffBool = b: if b then "ON" else "OFF"; + withMPI = (mpi != null); +in +stdenv.mkDerivation rec { + version = "2.3.4"; + name = "hoomd-blue-${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 ]; + }; + +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 116226428239..a73b269d1801 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -366,6 +366,10 @@ 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 { };