diff options
Diffstat (limited to 'pkgs/applications/science')
11 files changed, 143 insertions, 22 deletions
diff --git a/pkgs/applications/science/biology/cd-hit/default.nix b/pkgs/applications/science/biology/cd-hit/default.nix index ba1d6c27ccb..474c0f292af 100644 --- a/pkgs/applications/science/biology/cd-hit/default.nix +++ b/pkgs/applications/science/biology/cd-hit/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { sha256 = "032nva6iiwmw59gjipm1mv0xlcckhxsf45mc2qbnv19lbis0q22i"; }; - propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick ]; + propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.ImageMagick ]; nativeBuildInputs = [ zlib makeWrapper ]; buildInputs = lib.optional stdenv.cc.isClang openmp; diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix index 4815ddf2f75..715f2ea313b 100644 --- a/pkgs/applications/science/biology/mosdepth/default.nix +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -17,13 +17,13 @@ let in stdenv.mkDerivation rec { pname = "mosdepth"; - version = "0.3.1"; + version = "0.3.2"; src = fetchFromGitHub { owner = "brentp"; repo = "mosdepth"; rev = "v${version}"; - sha256 = "1kcrvamrafz1m0s7mlbhaay8jyg97l1w37p6syl36r2m1plmwxjd"; + sha256 = "sha256-uui4yC7ok+pvbXVKfBVsAarH40fnH4fnP8P4uzOqztQ="; }; nativeBuildInputs = [ nim ]; diff --git a/pkgs/applications/science/chemistry/cp2k/default.nix b/pkgs/applications/science/chemistry/cp2k/default.nix new file mode 100644 index 00000000000..6bb99ce556d --- /dev/null +++ b/pkgs/applications/science/chemistry/cp2k/default.nix @@ -0,0 +1,117 @@ +{ lib, stdenv, fetchFromGitHub, python3, gfortran, blas, lapack +, fftw, libint, libvori, libxc, mpi, gsl, scalapack, openssh, makeWrapper +, libxsmm, spglib, which +} : + +let + cp2kVersion = "psmp"; + arch = "Linux-x86-64-gfortran"; + +in stdenv.mkDerivation rec { + pname = "cp2k"; + version = "8.2.0"; + + src = fetchFromGitHub { + owner = "cp2k"; + repo = "cp2k"; + rev = "v${version}"; + sha256 = "0kykq5p318hxjzd4gzqjwv9gqshbdvbg0gnjbd9bdfjx1r6jkjn3"; + fetchSubmodules = true; + }; + + nativeBuildInputs = [ python3 which openssh makeWrapper ]; + buildInputs = [ + gfortran + fftw + gsl + libint + libvori + libxc + libxsmm + spglib + scalapack + blas + lapack + ]; + + propagatedBuildInputs = [ mpi ]; + propagatedUserEnvPkgs = [ mpi ]; + + makeFlags = [ + "ARCH=${arch}" + "VERSION=${cp2kVersion}" + ]; + + doCheck = true; + + enableParallelBuilding = true; + + postPatch = '' + patchShebangs tools exts/dbcsr/tools/build_utils exts/dbcsr/.cp2k + substituteInPlace exts/dbcsr/.cp2k/Makefile --replace '/usr/bin/env python3' '${python3}/bin/python' + ''; + + configurePhase = '' + cat > arch/${arch}.${cp2kVersion} << EOF + CC = mpicc + CPP = + FC = mpif90 + LD = mpif90 + AR = ar -r + DFLAGS = -D__FFTW3 -D__LIBXC -D__LIBINT -D__parallel -D__SCALAPACK \ + -D__MPI_VERSION=3 -D__F2008 -D__LIBXSMM -D__SPGLIB \ + -D__MAX_CONTR=4 -D__LIBVORI + CFLAGS = -fopenmp + FCFLAGS = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \ + -ftree-vectorize -funroll-loops -msse2 \ + -std=f2008 \ + -fopenmp -ftree-vectorize -funroll-loops \ + -I${libxc}/include -I${libxsmm}/include \ + -I${libint}/include + LIBS = -lfftw3 -lfftw3_threads \ + -lscalapack -lblas -llapack \ + -lxcf03 -lxc -lxsmmf -lxsmm -lsymspg \ + -lint2 -lstdc++ -lvori \ + -lgomp -lpthread -lm \ + -fopenmp + LDFLAGS = \$(FCFLAGS) \$(LIBS) + EOF + ''; + + checkPhase = '' + export OMP_NUM_THREADS=1 + + export HYDRA_IFACE=lo # Fix to make mpich run in a sandbox + export OMPI_MCA_rmaps_base_oversubscribe=1 + export CP2K_DATA_DIR=data + + mpirun -np 2 exe/${arch}/libcp2k_unittest.${cp2kVersion} + ''; + + installPhase = '' + mkdir -p $out/bin $out/share/cp2k + + cp exe/${arch}/* $out/bin + + for i in cp2k cp2k_shell graph; do + wrapProgram $out/bin/$i.${cp2kVersion} \ + --set-default CP2K_DATA_DIR $out/share/cp2k + done + + wrapProgram $out/bin/cp2k.popt \ + --set-default CP2K_DATA_DIR $out/share/cp2k \ + --set OMP_NUM_THREADS 1 + + cp -r data/* $out/share/cp2k + ''; + + passthru = { inherit mpi; }; + + meta = with lib; { + description = "Quantum chemistry and solid state physics program"; + homepage = "https://www.cp2k.org"; + license = licenses.gpl2Plus; + maintainers = [ maintainers.sheepforce ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/pkgs/applications/science/logic/poly/default.nix b/pkgs/applications/science/logic/poly/default.nix index 75ad91bc54d..c80b9bf1f0c 100644 --- a/pkgs/applications/science/logic/poly/default.nix +++ b/pkgs/applications/science/logic/poly/default.nix @@ -2,14 +2,14 @@ stdenv.mkDerivation rec { pname = "libpoly"; - version = "0.1.9"; + version = "0.1.10"; src = fetchFromGitHub { owner = "SRI-CSL"; repo = "libpoly"; # they've pushed to the release branch, use explicit tag rev = "refs/tags/v${version}"; - sha256 = "sha256-E2lHo8Bt4ujoGQ623fjkQbqRnDYJYilXdRt4lnF4wJk="; + sha256 = "sha256-22Y4L5NFnCzKwZt0A/ChMuGPU4Dk1Qyke6mdvfN063w="; }; # https://github.com/SRI-CSL/libpoly/pull/52 diff --git a/pkgs/applications/science/logic/verifast/default.nix b/pkgs/applications/science/logic/verifast/default.nix index e426f7b8098..a33c4941ac4 100644 --- a/pkgs/applications/science/logic/verifast/default.nix +++ b/pkgs/applications/science/logic/verifast/default.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { meta = { description = "Verification for C and Java programs via separation logic"; - homepage = "http://people.cs.kuleuven.be/~bart.jacobs/verifast/"; + homepage = "https://people.cs.kuleuven.be/~bart.jacobs/verifast/"; license = lib.licenses.mit; platforms = [ "x86_64-linux" ]; maintainers = [ lib.maintainers.thoughtpolice ]; diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix index 01f086c92c7..7edbeaee085 100644 --- a/pkgs/applications/science/math/maxima/default.nix +++ b/pkgs/applications/science/math/maxima/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, autoreconfHook +{ lib, stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python3, makeWrapper, autoreconfHook , rlwrap ? null, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false }: @@ -6,9 +6,11 @@ let name = "maxima"; version = "5.44.0"; + lisp-compiler = if ecl-fasl then ecl else sbcl; + searchPath = lib.makeBinPath - (lib.filter (x: x != null) [ sbcl ecl rlwrap tk gnuplot ]); + (lib.filter (x: x != null) [ lisp-compiler rlwrap tk gnuplot ]); in stdenv.mkDerivation ({ inherit version; @@ -19,11 +21,18 @@ stdenv.mkDerivation ({ sha256 = "1v6jr5s6hhj6r18gfk6hgxk2qd6z1dxkrjq9ss2z1y6sqi45wgyr"; }; - nativeBuildInputs = [ autoreconfHook ]; + nativeBuildInputs = [ + autoreconfHook + lisp-compiler + makeWrapper + python3 + texinfo + ]; + + strictDeps = true; - buildInputs = lib.filter (x: x != null) [ - sbcl ecl texinfo perl python makeWrapper - gnuplot # required in the test suite + checkInputs = [ + gnuplot ]; postPatch = '' diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index a941a633450..c435c63ab2e 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -6,7 +6,7 @@ stdenv.mkDerivation rec { pname = "nauty"; version = "27r1"; src = fetchurl { - url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz"; + url = "https://pallini.di.uniroma1.it/nauty${version}.tar.gz"; sha256 = "0xsfqfcknbd6g6wzpa5l7crmmk3bf3zjh37rhylq6b20dqcmvjkn"; }; outputs = [ "out" "dev" ]; @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { # I'm not sure if the filename will remain the same for future changelog or # if it will track changes to minor releases. Lets see. Better than nothing # in any case. - changelog = "http://pallini.di.uniroma1.it/changes24-27.txt"; - homepage = "http://pallini.di.uniroma1.it/"; + changelog = "https://pallini.di.uniroma1.it/changes24-27.txt"; + homepage = "https://pallini.di.uniroma1.it/"; }; } diff --git a/pkgs/applications/science/physics/xflr5/default.nix b/pkgs/applications/science/physics/xflr5/default.nix index 5ae56528f96..85e20f38b66 100644 --- a/pkgs/applications/science/physics/xflr5/default.nix +++ b/pkgs/applications/science/physics/xflr5/default.nix @@ -9,8 +9,6 @@ mkDerivation rec { sha256 = "02x3r9iv3ndwxa65mxn9m5dlhcrnjiq7cffi6rmb456gs3v3dnav"; }; - enableParallelBuilding = true; - nativeBuildInputs = [ qmake ]; meta = with lib; { diff --git a/pkgs/applications/science/robotics/apmplanner2/default.nix b/pkgs/applications/science/robotics/apmplanner2/default.nix index 0f5e7e6daa8..b65c2352139 100644 --- a/pkgs/applications/science/robotics/apmplanner2/default.nix +++ b/pkgs/applications/science/robotics/apmplanner2/default.nix @@ -30,8 +30,6 @@ mkDerivation rec { --replace /usr $out ''; - enableParallelBuilding = true; - meta = { description = "Ground station software for autonomous vehicles"; longDescription = '' diff --git a/pkgs/applications/science/robotics/mavproxy/default.nix b/pkgs/applications/science/robotics/mavproxy/default.nix index ba0c2530849..4f83f957dbf 100644 --- a/pkgs/applications/science/robotics/mavproxy/default.nix +++ b/pkgs/applications/science/robotics/mavproxy/default.nix @@ -3,11 +3,11 @@ buildPythonApplication rec { pname = "MAVProxy"; - version = "1.8.39"; + version = "1.8.40"; src = fetchPypi { inherit pname version; - sha256 = "sha256-1RXuAiz9i5ZnLtDGQ+o3DNgWJ2FDJGIoelmlDmEzrts="; + sha256 = "cad317e2e879f1f7cb59af078788aaf0d09cd761ecd91ad091adf7ac6cc1bcdb"; }; postPatch = '' diff --git a/pkgs/applications/science/robotics/qgroundcontrol/default.nix b/pkgs/applications/science/robotics/qgroundcontrol/default.nix index 1b9304d49e7..2759723841c 100644 --- a/pkgs/applications/science/robotics/qgroundcontrol/default.nix +++ b/pkgs/applications/science/robotics/qgroundcontrol/default.nix @@ -17,7 +17,6 @@ mkDerivation rec { gstreamer gst-plugins-base gst-plugins-good gst-plugins-bad wayland ]; - enableParallelBuilding = true; buildInputs = [ SDL2 ] ++ gstInputs ++ qtInputs; nativeBuildInputs = [ pkg-config qmake qttools ]; |