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commit: ab729bfefd782d9a22fb11f00b5de82e5cde502c |
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Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org> |
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AuthorDate: Wed Jul 13 17:07:04 2016 +0000 |
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Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org> |
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CommitDate: Wed Jul 13 17:07:04 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab729bfe |
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|
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sci-chemistry/gromacs: moved to gx86 |
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|
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.../files/gromacs-4.5.7-cmake-cpp-asm.patch | 43 ---- |
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sci-chemistry/gromacs/gromacs-2016.9999.ebuild | 266 ------------------- |
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sci-chemistry/gromacs/gromacs-2016_rc1.ebuild | 266 ------------------- |
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sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 263 ------------------- |
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sci-chemistry/gromacs/gromacs-5.0.9999.ebuild | 284 --------------------- |
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sci-chemistry/gromacs/gromacs-5.1.9999.ebuild | 269 ------------------- |
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sci-chemistry/gromacs/gromacs-9999.ebuild | 266 ------------------- |
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sci-chemistry/gromacs/metadata.xml | 28 -- |
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8 files changed, 1685 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch b/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch |
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deleted file mode 100644 |
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index f39921f..0000000 |
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--- a/sci-chemistry/gromacs/files/gromacs-4.5.7-cmake-cpp-asm.patch |
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+++ /dev/null |
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@@ -1,43 +0,0 @@ |
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-diff -Naur gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake |
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---- gromacs-4.5.7.orig/cmake/CMakeASM-ATTInformation.cmake 1969-12-31 17:00:00.000000000 -0700 |
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-+++ gromacs-4.5.7/cmake/CMakeASM-ATTInformation.cmake 2013-05-03 10:47:52.779868731 -0600 |
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-@@ -0,0 +1,13 @@ |
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-+ |
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-+# This a modified version of CMakeASMInformation.cmake coming with cmake 2.8.6, which |
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-+# supports .S files |
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-+ |
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-+# support for AT&T syntax assemblers, e.g. GNU as |
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-+ |
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-+SET(ASM_DIALECT "-ATT") |
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-+SET(CMAKE_ASM${ASM_DIALECT}_SOURCE_FILE_EXTENSIONS S;s;asm) |
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-+ |
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-+SET(CMAKE_ASM${ASM_DIALECT}_COMPILE_OBJECT "<CMAKE_ASM${ASM_DIALECT}_COMPILER> <FLAGS> -o <OBJECT> <SOURCE>") |
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-+ |
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-+INCLUDE(CMakeASMInformation) |
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-+SET(ASM_DIALECT) |
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-diff -Naur gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt gromacs-4.5.7/src/gmxlib/CMakeLists.txt |
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---- gromacs-4.5.7.orig/src/gmxlib/CMakeLists.txt 2013-05-03 10:46:29.029305075 -0600 |
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-+++ gromacs-4.5.7/src/gmxlib/CMakeLists.txt 2013-05-03 10:50:34.630582295 -0600 |
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-@@ -47,18 +47,18 @@ |
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- if(GMX_IA32_ASM) |
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- file(GLOB GMX_SSEKERNEL_C_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*.c) |
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- if(GMX_ASM_USEASM_NASM) |
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-- file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.s) |
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-+ file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*intel_syntax*.S) |
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- else() |
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-- file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.s) |
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-+ file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_ia32_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_ia32_${SSETYPE}/*asm.S) |
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- endif() |
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- endif(GMX_IA32_ASM) |
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- |
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- if(GMX_X86_64_ASM) |
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- file(GLOB GMX_SSEKERNEL_C_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*.c) |
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- if(GMX_ASM_USEASM_NASM) |
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-- file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.s) |
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-+ file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*intel_syntax*.S) |
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- else() |
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-- file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.s nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.s) |
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-+ file(GLOB GMX_SSEKERNEL_ASM_SRC nonbonded/nb_kernel_x86_64_${SSETYPE}/*${SSETYPE}.S nonbonded/nb_kernel_x86_64_${SSETYPE}/*asm.S) |
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- endif() |
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- endif(GMX_X86_64_ASM) |
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- |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild b/sci-chemistry/gromacs/gromacs-2016.9999.ebuild |
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deleted file mode 100644 |
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index 1ca0343..0000000 |
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--- a/sci-chemistry/gromacs/gromacs-2016.9999.ebuild |
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+++ /dev/null |
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@@ -1,266 +0,0 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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-# Distributed under the terms of the GNU General Public License v2 |
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-# $Id$ |
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- |
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-EAPI=6 |
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- |
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-CMAKE_MAKEFILE_GENERATOR="ninja" |
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- |
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-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
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- |
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-if [[ $PV = *9999* ]]; then |
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- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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- https://gerrit.gromacs.org/gromacs.git |
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- git://github.com/gromacs/gromacs.git |
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- http://repo.or.cz/r/gromacs.git" |
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- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
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- inherit git-r3 |
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- KEYWORDS="" |
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-else |
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- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
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- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
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- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
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-fi |
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- |
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-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
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- |
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-DESCRIPTION="The ultimate molecular dynamics simulation package" |
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-HOMEPAGE="http://www.gromacs.org/" |
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- |
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-# see COPYING for details |
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-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
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-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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-SLOT="0/${PV}" |
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-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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- |
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-CDEPEND=" |
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- X? ( |
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- x11-libs/libX11 |
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- x11-libs/libSM |
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- x11-libs/libICE |
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- ) |
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- blas? ( virtual/blas ) |
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- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
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- fftw? ( sci-libs/fftw:3.0 ) |
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- hwloc? ( sys-apps/hwloc ) |
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- lapack? ( virtual/lapack ) |
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- mkl? ( sci-libs/mkl ) |
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- mpi? ( virtual/mpi ) |
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- " |
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-DEPEND="${CDEPEND} |
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- virtual/pkgconfig |
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- doc? ( |
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- app-doc/doxygen |
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- dev-texlive/texlive-latex |
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- dev-texlive/texlive-latexextra |
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- media-gfx/imagemagick |
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- )" |
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-RDEPEND="${CDEPEND}" |
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- |
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-REQUIRED_USE=" |
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- || ( single-precision double-precision ) |
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- cuda? ( single-precision ) |
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- mkl? ( !blas !fftw !lapack )" |
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- |
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-DOCS=( AUTHORS README ) |
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- |
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-if [[ ${PV} != *9999 ]]; then |
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- S="${WORKDIR}/${PN}-${PV/_/-}" |
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-fi |
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- |
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-pkg_pretend() { |
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- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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- use openmp && ! tc-has-openmp && \ |
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- die "Please switch to an openmp compatible compiler" |
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-} |
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- |
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-src_unpack() { |
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- if [[ ${PV} != *9999 ]]; then |
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- default |
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- else |
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- git-r3_src_unpack |
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- if use test; then |
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- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
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- EGIT_BRANCH="${EGIT_BRANCH}" \ |
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- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
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- git-r3_src_unpack |
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- fi |
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- fi |
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-} |
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- |
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-src_prepare() { |
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- #notes/todos |
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- # -on apple: there is framework support |
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- |
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- cmake-utils_src_prepare |
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- |
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- use cuda && cuda_src_prepare |
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- |
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- GMX_DIRS="" |
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- use single-precision && GMX_DIRS+=" float" |
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- use double-precision && GMX_DIRS+=" double" |
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- |
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- if use test; then |
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- for x in ${GMX_DIRS}; do |
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- mkdir -p "${WORKDIR}/${P}_${x}" || die |
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- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
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- done |
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- fi |
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- |
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- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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-} |
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- |
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-src_configure() { |
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- local mycmakeargs_pre=( ) extra fft_opts=( ) |
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- |
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- #go from slowest to fastest acceleration |
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- local acce="None" |
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- use cpu_flags_x86_sse2 && acce="SSE2" |
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- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
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- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
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- use cpu_flags_x86_avx && acce="AVX_256" |
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- use cpu_flags_x86_avx2 && acce="AVX2_256" |
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- |
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- #to create man pages, build tree binaries are executed (bug #398437) |
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- [[ ${CHOST} = *-darwin* ]] && \ |
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- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
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- |
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- if use fftw; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
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- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
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- ) |
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- elif use mkl; then |
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- local bits=$(get_libdir) |
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- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
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- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
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- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
216 |
- ) |
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- else |
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- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
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- fi |
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- |
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- mycmakeargs_pre+=( |
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- "${fft_opts[@]}" |
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- -DGMX_X11=$(usex X) |
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- -DGMX_EXTERNAL_BLAS=$(usex blas) |
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- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
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- -DGMX_OPENMP=$(usex openmp) |
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- -DGMX_COOL_QUOTES=$(usex offensive) |
228 |
- -DGMX_USE_TNG=$(usex tng) |
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- -DGMX_BUILD_MANUAL=$(usex doc) |
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- -DGMX_HWLOC=$(usex hwloc) |
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- -DGMX_DEFAULT_SUFFIX=off |
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- -DGMX_SIMD="$acce" |
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- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
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- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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- -DBUILD_TESTING=OFF |
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- -DGMX_BUILD_UNITTESTS=OFF |
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- ${extra} |
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- ) |
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- |
240 |
- for x in ${GMX_DIRS}; do |
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- einfo "Configuring for ${x} precision" |
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- local suffix="" |
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- #if we build single and double - double is suffixed |
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- use double-precision && use single-precision && \ |
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- [[ ${x} = "double" ]] && suffix="_d" |
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- local p |
247 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
248 |
- local cuda=( "-DGMX_GPU=OFF" ) |
249 |
- [[ ${x} = "float" ]] && use cuda && \ |
250 |
- cuda=( -DGMX_GPU=ON ) |
251 |
- mycmakeargs=( |
252 |
- ${mycmakeargs_pre[@]} ${p} |
253 |
- -DGMX_MPI=OFF |
254 |
- -DGMX_THREAD_MPI=$(usex threads) |
255 |
- "${cuda[@]}" |
256 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
257 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
258 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
259 |
- ) |
260 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
261 |
- [[ ${CHOST} != *-darwin* ]] || \ |
262 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
263 |
- use mpi || continue |
264 |
- einfo "Configuring for ${x} precision with mpi" |
265 |
- mycmakeargs=( |
266 |
- ${mycmakeargs_pre[@]} ${p} |
267 |
- -DGMX_THREAD_MPI=OFF |
268 |
- -DGMX_MPI=ON ${cuda} |
269 |
- -DGMX_OPENMM=OFF |
270 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
271 |
- -DBUILD_SHARED_LIBS=OFF |
272 |
- -DGMX_BUILD_MANUAL=OFF |
273 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
274 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
275 |
- ) |
276 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
277 |
- [[ ${CHOST} != *-darwin* ]] || \ |
278 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
279 |
- done |
280 |
-} |
281 |
- |
282 |
-src_compile() { |
283 |
- for x in ${GMX_DIRS}; do |
284 |
- einfo "Compiling for ${x} precision" |
285 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
286 |
- cmake-utils_src_compile |
287 |
- # not 100% necessary for rel ebuilds as available from website |
288 |
- if use doc; then |
289 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
290 |
- cmake-utils_src_compile manual |
291 |
- fi |
292 |
- use mpi || continue |
293 |
- einfo "Compiling for ${x} precision with mpi" |
294 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
295 |
- cmake-utils_src_compile |
296 |
- done |
297 |
-} |
298 |
- |
299 |
-src_test() { |
300 |
- for x in ${GMX_DIRS}; do |
301 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
302 |
- cmake-utils_src_make check |
303 |
- done |
304 |
-} |
305 |
- |
306 |
-src_install() { |
307 |
- for x in ${GMX_DIRS}; do |
308 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
309 |
- cmake-utils_src_install |
310 |
- if use doc; then |
311 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
312 |
- fi |
313 |
- use mpi || continue |
314 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
315 |
- cmake-utils_src_install |
316 |
- done |
317 |
- |
318 |
- if use tng; then |
319 |
- insinto /usr/include/tng |
320 |
- doins src/external/tng_io/include/tng/*h |
321 |
- fi |
322 |
- # drop unneeded stuff |
323 |
- rm "${ED}"usr/bin/GMXRC* || die |
324 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
325 |
- local n=${x##*/gmx-completion-} |
326 |
- n="${n%.bash}" |
327 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
328 |
- newbashcomp "${T}"/"${n}" "${n}" |
329 |
- done |
330 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
331 |
- readme.gentoo_create_doc |
332 |
-} |
333 |
- |
334 |
-pkg_postinst() { |
335 |
- einfo |
336 |
- einfo "Please read and cite:" |
337 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
338 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
339 |
- einfo |
340 |
- readme.gentoo_print_elog |
341 |
-} |
342 |
|
343 |
diff --git a/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild |
344 |
deleted file mode 100644 |
345 |
index 1ca0343..0000000 |
346 |
--- a/sci-chemistry/gromacs/gromacs-2016_rc1.ebuild |
347 |
+++ /dev/null |
348 |
@@ -1,266 +0,0 @@ |
349 |
-# Copyright 1999-2016 Gentoo Foundation |
350 |
-# Distributed under the terms of the GNU General Public License v2 |
351 |
-# $Id$ |
352 |
- |
353 |
-EAPI=6 |
354 |
- |
355 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
356 |
- |
357 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
358 |
- |
359 |
-if [[ $PV = *9999* ]]; then |
360 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
361 |
- https://gerrit.gromacs.org/gromacs.git |
362 |
- git://github.com/gromacs/gromacs.git |
363 |
- http://repo.or.cz/r/gromacs.git" |
364 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
365 |
- inherit git-r3 |
366 |
- KEYWORDS="" |
367 |
-else |
368 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
369 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
370 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
371 |
-fi |
372 |
- |
373 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
374 |
- |
375 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
376 |
-HOMEPAGE="http://www.gromacs.org/" |
377 |
- |
378 |
-# see COPYING for details |
379 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
380 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
381 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
382 |
-SLOT="0/${PV}" |
383 |
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
384 |
- |
385 |
-CDEPEND=" |
386 |
- X? ( |
387 |
- x11-libs/libX11 |
388 |
- x11-libs/libSM |
389 |
- x11-libs/libICE |
390 |
- ) |
391 |
- blas? ( virtual/blas ) |
392 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
393 |
- fftw? ( sci-libs/fftw:3.0 ) |
394 |
- hwloc? ( sys-apps/hwloc ) |
395 |
- lapack? ( virtual/lapack ) |
396 |
- mkl? ( sci-libs/mkl ) |
397 |
- mpi? ( virtual/mpi ) |
398 |
- " |
399 |
-DEPEND="${CDEPEND} |
400 |
- virtual/pkgconfig |
401 |
- doc? ( |
402 |
- app-doc/doxygen |
403 |
- dev-texlive/texlive-latex |
404 |
- dev-texlive/texlive-latexextra |
405 |
- media-gfx/imagemagick |
406 |
- )" |
407 |
-RDEPEND="${CDEPEND}" |
408 |
- |
409 |
-REQUIRED_USE=" |
410 |
- || ( single-precision double-precision ) |
411 |
- cuda? ( single-precision ) |
412 |
- mkl? ( !blas !fftw !lapack )" |
413 |
- |
414 |
-DOCS=( AUTHORS README ) |
415 |
- |
416 |
-if [[ ${PV} != *9999 ]]; then |
417 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
418 |
-fi |
419 |
- |
420 |
-pkg_pretend() { |
421 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
422 |
- use openmp && ! tc-has-openmp && \ |
423 |
- die "Please switch to an openmp compatible compiler" |
424 |
-} |
425 |
- |
426 |
-src_unpack() { |
427 |
- if [[ ${PV} != *9999 ]]; then |
428 |
- default |
429 |
- else |
430 |
- git-r3_src_unpack |
431 |
- if use test; then |
432 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
433 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
434 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
435 |
- git-r3_src_unpack |
436 |
- fi |
437 |
- fi |
438 |
-} |
439 |
- |
440 |
-src_prepare() { |
441 |
- #notes/todos |
442 |
- # -on apple: there is framework support |
443 |
- |
444 |
- cmake-utils_src_prepare |
445 |
- |
446 |
- use cuda && cuda_src_prepare |
447 |
- |
448 |
- GMX_DIRS="" |
449 |
- use single-precision && GMX_DIRS+=" float" |
450 |
- use double-precision && GMX_DIRS+=" double" |
451 |
- |
452 |
- if use test; then |
453 |
- for x in ${GMX_DIRS}; do |
454 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
455 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
456 |
- done |
457 |
- fi |
458 |
- |
459 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
460 |
-} |
461 |
- |
462 |
-src_configure() { |
463 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
464 |
- |
465 |
- #go from slowest to fastest acceleration |
466 |
- local acce="None" |
467 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
468 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
469 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
470 |
- use cpu_flags_x86_avx && acce="AVX_256" |
471 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
472 |
- |
473 |
- #to create man pages, build tree binaries are executed (bug #398437) |
474 |
- [[ ${CHOST} = *-darwin* ]] && \ |
475 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
476 |
- |
477 |
- if use fftw; then |
478 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
479 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
480 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
481 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
482 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
483 |
- ) |
484 |
- elif use mkl; then |
485 |
- local bits=$(get_libdir) |
486 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
487 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
488 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
489 |
- ) |
490 |
- else |
491 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
492 |
- fi |
493 |
- |
494 |
- mycmakeargs_pre+=( |
495 |
- "${fft_opts[@]}" |
496 |
- -DGMX_X11=$(usex X) |
497 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
498 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
499 |
- -DGMX_OPENMP=$(usex openmp) |
500 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
501 |
- -DGMX_USE_TNG=$(usex tng) |
502 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
503 |
- -DGMX_HWLOC=$(usex hwloc) |
504 |
- -DGMX_DEFAULT_SUFFIX=off |
505 |
- -DGMX_SIMD="$acce" |
506 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
507 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
508 |
- -DBUILD_TESTING=OFF |
509 |
- -DGMX_BUILD_UNITTESTS=OFF |
510 |
- ${extra} |
511 |
- ) |
512 |
- |
513 |
- for x in ${GMX_DIRS}; do |
514 |
- einfo "Configuring for ${x} precision" |
515 |
- local suffix="" |
516 |
- #if we build single and double - double is suffixed |
517 |
- use double-precision && use single-precision && \ |
518 |
- [[ ${x} = "double" ]] && suffix="_d" |
519 |
- local p |
520 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
521 |
- local cuda=( "-DGMX_GPU=OFF" ) |
522 |
- [[ ${x} = "float" ]] && use cuda && \ |
523 |
- cuda=( -DGMX_GPU=ON ) |
524 |
- mycmakeargs=( |
525 |
- ${mycmakeargs_pre[@]} ${p} |
526 |
- -DGMX_MPI=OFF |
527 |
- -DGMX_THREAD_MPI=$(usex threads) |
528 |
- "${cuda[@]}" |
529 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
530 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
531 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
532 |
- ) |
533 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
534 |
- [[ ${CHOST} != *-darwin* ]] || \ |
535 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
536 |
- use mpi || continue |
537 |
- einfo "Configuring for ${x} precision with mpi" |
538 |
- mycmakeargs=( |
539 |
- ${mycmakeargs_pre[@]} ${p} |
540 |
- -DGMX_THREAD_MPI=OFF |
541 |
- -DGMX_MPI=ON ${cuda} |
542 |
- -DGMX_OPENMM=OFF |
543 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
544 |
- -DBUILD_SHARED_LIBS=OFF |
545 |
- -DGMX_BUILD_MANUAL=OFF |
546 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
547 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
548 |
- ) |
549 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
550 |
- [[ ${CHOST} != *-darwin* ]] || \ |
551 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
552 |
- done |
553 |
-} |
554 |
- |
555 |
-src_compile() { |
556 |
- for x in ${GMX_DIRS}; do |
557 |
- einfo "Compiling for ${x} precision" |
558 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
559 |
- cmake-utils_src_compile |
560 |
- # not 100% necessary for rel ebuilds as available from website |
561 |
- if use doc; then |
562 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
563 |
- cmake-utils_src_compile manual |
564 |
- fi |
565 |
- use mpi || continue |
566 |
- einfo "Compiling for ${x} precision with mpi" |
567 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
568 |
- cmake-utils_src_compile |
569 |
- done |
570 |
-} |
571 |
- |
572 |
-src_test() { |
573 |
- for x in ${GMX_DIRS}; do |
574 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
575 |
- cmake-utils_src_make check |
576 |
- done |
577 |
-} |
578 |
- |
579 |
-src_install() { |
580 |
- for x in ${GMX_DIRS}; do |
581 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
582 |
- cmake-utils_src_install |
583 |
- if use doc; then |
584 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
585 |
- fi |
586 |
- use mpi || continue |
587 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
588 |
- cmake-utils_src_install |
589 |
- done |
590 |
- |
591 |
- if use tng; then |
592 |
- insinto /usr/include/tng |
593 |
- doins src/external/tng_io/include/tng/*h |
594 |
- fi |
595 |
- # drop unneeded stuff |
596 |
- rm "${ED}"usr/bin/GMXRC* || die |
597 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
598 |
- local n=${x##*/gmx-completion-} |
599 |
- n="${n%.bash}" |
600 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
601 |
- newbashcomp "${T}"/"${n}" "${n}" |
602 |
- done |
603 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
604 |
- readme.gentoo_create_doc |
605 |
-} |
606 |
- |
607 |
-pkg_postinst() { |
608 |
- einfo |
609 |
- einfo "Please read and cite:" |
610 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
611 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
612 |
- einfo |
613 |
- readme.gentoo_print_elog |
614 |
-} |
615 |
|
616 |
diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |
617 |
deleted file mode 100644 |
618 |
index e00c4f9..0000000 |
619 |
--- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild |
620 |
+++ /dev/null |
621 |
@@ -1,263 +0,0 @@ |
622 |
-# Copyright 1999-2016 Gentoo Foundation |
623 |
-# Distributed under the terms of the GNU General Public License v2 |
624 |
-# $Id$ |
625 |
- |
626 |
-EAPI=6 |
627 |
- |
628 |
-TEST_PV="4.6.6" |
629 |
-MANUAL_PV="4.6.6" |
630 |
- |
631 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
632 |
- |
633 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
634 |
- |
635 |
-if [[ $PV = *9999* ]]; then |
636 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
637 |
- https://gerrit.gromacs.org/gromacs.git |
638 |
- git://github.com/gromacs/gromacs.git |
639 |
- http://repo.or.cz/r/gromacs.git" |
640 |
- EGIT_BRANCH="release-4-6" |
641 |
- inherit git-r3 |
642 |
- LIVE_DEPEND="doc? ( |
643 |
- app-doc/doxygen |
644 |
- dev-texlive/texlive-latex |
645 |
- dev-texlive/texlive-latexextra |
646 |
- media-gfx/imagemagick |
647 |
- sys-apps/coreutils |
648 |
- )" |
649 |
- KEYWORDS="" |
650 |
-else |
651 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz |
652 |
- doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf ) |
653 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )" |
654 |
- LIVE_DEPEND="" |
655 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" |
656 |
-fi |
657 |
- |
658 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx" |
659 |
- |
660 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
661 |
-HOMEPAGE="http://www.gromacs.org/" |
662 |
- |
663 |
-# see COPYING for details |
664 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
665 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
666 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
667 |
-SLOT="0/${PV}" |
668 |
-IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" |
669 |
- |
670 |
-CDEPEND=" |
671 |
- X? ( |
672 |
- x11-libs/libX11 |
673 |
- x11-libs/libSM |
674 |
- x11-libs/libICE |
675 |
- ) |
676 |
- blas? ( virtual/blas ) |
677 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
678 |
- fftw? ( sci-libs/fftw:3.0 ) |
679 |
- gsl? ( sci-libs/gsl ) |
680 |
- lapack? ( virtual/lapack ) |
681 |
- mkl? ( sci-libs/mkl ) |
682 |
- mpi? ( virtual/mpi )" |
683 |
-DEPEND="${CDEPEND} |
684 |
- virtual/pkgconfig |
685 |
- ${LIVE_DEPEND} |
686 |
- doc? ( app-doc/doxygen )" |
687 |
-RDEPEND="${CDEPEND}" |
688 |
- |
689 |
-REQUIRED_USE=" |
690 |
- || ( single-precision double-precision ) |
691 |
- cuda? ( single-precision ) |
692 |
- mkl? ( !blas !fftw !lapack )" |
693 |
- |
694 |
-DOCS=( AUTHORS README ) |
695 |
-HTML_DOCS=( "${ED}"/usr/share/gromacs/html/ ) |
696 |
- |
697 |
-pkg_pretend() { |
698 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
699 |
- use openmp && ! tc-has-openmp && \ |
700 |
- die "Please switch to an openmp compatible compiler" |
701 |
-} |
702 |
- |
703 |
-src_unpack() { |
704 |
- if [[ ${PV} != *9999 ]]; then |
705 |
- default |
706 |
- else |
707 |
- git-r3_src_unpack |
708 |
- if use doc; then |
709 |
- EGIT_REPO_URI="git://git.gromacs.org/manual.git" \ |
710 |
- EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \ |
711 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/manual"\ |
712 |
- git-r3_src_unpack |
713 |
- fi |
714 |
- if use test; then |
715 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
716 |
- EGIT_BRANCH="release-4-6" EGIT_COMMIT="release-4-6" \ |
717 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
718 |
- git-r3_src_unpack |
719 |
- fi |
720 |
- fi |
721 |
-} |
722 |
- |
723 |
-src_prepare() { |
724 |
- #notes/todos |
725 |
- # -on apple: there is framework support |
726 |
- |
727 |
- cmake-utils_src_prepare |
728 |
- |
729 |
- use cuda && cuda_src_prepare |
730 |
- |
731 |
- GMX_DIRS="" |
732 |
- use single-precision && GMX_DIRS+=" float" |
733 |
- use double-precision && GMX_DIRS+=" double" |
734 |
- |
735 |
- if use test; then |
736 |
- for x in ${GMX_DIRS}; do |
737 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
738 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
739 |
- done |
740 |
- fi |
741 |
- |
742 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
743 |
-} |
744 |
- |
745 |
-src_configure() { |
746 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
747 |
- |
748 |
- #go from slowest to fastest acceleration |
749 |
- local acce="None" |
750 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
751 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
752 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
753 |
- use cpu_flags_x86_avx && acce="AVX_256" |
754 |
- |
755 |
- #to create man pages, build tree binaries are executed (bug #398437) |
756 |
- [[ ${CHOST} = *-darwin* ]] && \ |
757 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
758 |
- |
759 |
- if use fftw; then |
760 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
761 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
762 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
763 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
764 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
765 |
- ) |
766 |
- elif use mkl; then |
767 |
- local bits=$(get_libdir) |
768 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
769 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
770 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
771 |
- ) |
772 |
- else |
773 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
774 |
- fi |
775 |
- |
776 |
- mycmakeargs_pre+=( |
777 |
- "${fft_opts[@]}" |
778 |
- -DGMX_X11=$(usex X) |
779 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
780 |
- -DGMX_GSL=$(usex gsl) |
781 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
782 |
- -DGMX_OPENMP=$(usex openmp) |
783 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
784 |
- -DGMX_DEFAULT_SUFFIX=off |
785 |
- -DGMX_ACCELERATION="$acce" |
786 |
- -DGMXLIB="$(get_libdir)" |
787 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
788 |
- -DGMX_PREFIX_LIBMD=ON |
789 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
790 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
791 |
- ${extra} |
792 |
- ) |
793 |
- |
794 |
- for x in ${GMX_DIRS}; do |
795 |
- einfo "Configuring for ${x} precision" |
796 |
- local suffix="" |
797 |
- #if we build single and double - double is suffixed |
798 |
- use double-precision && use single-precision && \ |
799 |
- [[ ${x} = "double" ]] && suffix="_d" |
800 |
- local p |
801 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
802 |
- local cuda=( "-DGMX_GPU=OFF" ) |
803 |
- [[ ${x} = "float" ]] && use cuda && \ |
804 |
- cuda=( -DGMX_GPU=ON ) |
805 |
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF |
806 |
- -DGMX_THREAD_MPI=$(usex threads) "${cuda[@]}" -DGMX_OPENMM=OFF |
807 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
808 |
- -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) |
809 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
810 |
- use mpi || continue |
811 |
- einfo "Configuring for ${x} precision with mpi" |
812 |
- mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF |
813 |
- -DGMX_MPI=ON ${cuda} -DGMX_OPENMM=OFF |
814 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) |
815 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
816 |
- done |
817 |
-} |
818 |
- |
819 |
-src_compile() { |
820 |
- for x in ${GMX_DIRS}; do |
821 |
- einfo "Compiling for ${x} precision" |
822 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
823 |
- cmake-utils_src_compile |
824 |
- use mpi || continue |
825 |
- einfo "Compiling for ${x} precision with mpi" |
826 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
827 |
- cmake-utils_src_compile mdrun |
828 |
- done |
829 |
-} |
830 |
- |
831 |
-src_test() { |
832 |
- for x in ${GMX_DIRS}; do |
833 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
834 |
- cmake-utils_src_make check |
835 |
- done |
836 |
-} |
837 |
- |
838 |
-src_install() { |
839 |
- for x in ${GMX_DIRS}; do |
840 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
841 |
- cmake-utils_src_install |
842 |
- #manual can only be build after gromacs was installed once in image |
843 |
- if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then |
844 |
- mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" ) |
845 |
- BUILD_DIR="${WORKDIR}"/manual_build \ |
846 |
- CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure |
847 |
- [[ ${CHOST} = *-darwin* ]] && \ |
848 |
- export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)" |
849 |
- BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make |
850 |
- [[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)" |
851 |
- newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf" |
852 |
- fi |
853 |
- use mpi || continue |
854 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
855 |
- DESTDIR="${D}" cmake-utils_src_make install-mdrun |
856 |
- done |
857 |
- |
858 |
- use doc && [[ $PV != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf" |
859 |
- newbashcomp "${ED}"/usr/bin/completion.bash ${PN} |
860 |
- if use zsh-completion ; then |
861 |
- insinto /usr/share/zsh/site-functions |
862 |
- newins "${ED}"/usr/bin/completion.zsh _${PN} |
863 |
- fi |
864 |
- rm -f "${ED}"usr/bin/completion.* |
865 |
- rm -rf "${ED}"usr/share/gromacs/html |
866 |
- rm -f "${ED}"usr/bin/g_options* |
867 |
- rm -f "${ED}"usr/bin/GMXRC* |
868 |
- |
869 |
- readme.gentoo_create_doc |
870 |
-} |
871 |
- |
872 |
-pkg_postinst() { |
873 |
- einfo |
874 |
- einfo "Please read and cite:" |
875 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
876 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
877 |
- if use offensive; then |
878 |
- einfo |
879 |
- einfo $(g_luck) |
880 |
- einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" |
881 |
- fi |
882 |
- einfo |
883 |
- readme.gentoo_print_elog |
884 |
-} |
885 |
|
886 |
diff --git a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild |
887 |
deleted file mode 100644 |
888 |
index 5d1717e..0000000 |
889 |
--- a/sci-chemistry/gromacs/gromacs-5.0.9999.ebuild |
890 |
+++ /dev/null |
891 |
@@ -1,284 +0,0 @@ |
892 |
-# Copyright 1999-2016 Gentoo Foundation |
893 |
-# Distributed under the terms of the GNU General Public License v2 |
894 |
-# $Id$ |
895 |
- |
896 |
-EAPI=6 |
897 |
- |
898 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
899 |
- |
900 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
901 |
- |
902 |
-if [[ $PV = *9999* ]]; then |
903 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
904 |
- https://gerrit.gromacs.org/gromacs.git |
905 |
- git://github.com/gromacs/gromacs.git |
906 |
- http://repo.or.cz/r/gromacs.git" |
907 |
- EGIT_BRANCH="release-5-0" |
908 |
- inherit git-r3 |
909 |
- KEYWORDS="" |
910 |
-else |
911 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
912 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
913 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
914 |
-fi |
915 |
- |
916 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
917 |
- |
918 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
919 |
-HOMEPAGE="http://www.gromacs.org/" |
920 |
- |
921 |
-# see COPYING for details |
922 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
923 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
924 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
925 |
-SLOT="0/${PV}" |
926 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
927 |
- |
928 |
-CDEPEND=" |
929 |
- X? ( |
930 |
- x11-libs/libX11 |
931 |
- x11-libs/libSM |
932 |
- x11-libs/libICE |
933 |
- ) |
934 |
- blas? ( virtual/blas ) |
935 |
- boost? ( >=dev-libs/boost-1.55 ) |
936 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
937 |
- fftw? ( sci-libs/fftw:3.0 ) |
938 |
- lapack? ( virtual/lapack ) |
939 |
- mkl? ( sci-libs/mkl ) |
940 |
- mpi? ( virtual/mpi ) |
941 |
- " |
942 |
-DEPEND="${CDEPEND} |
943 |
- virtual/pkgconfig |
944 |
- doc? ( |
945 |
- app-doc/doxygen |
946 |
- dev-texlive/texlive-latex |
947 |
- dev-texlive/texlive-latexextra |
948 |
- media-gfx/imagemagick |
949 |
- )" |
950 |
-RDEPEND="${CDEPEND}" |
951 |
- |
952 |
-REQUIRED_USE=" |
953 |
- || ( single-precision double-precision ) |
954 |
- cuda? ( single-precision ) |
955 |
- mkl? ( !blas !fftw !lapack )" |
956 |
- |
957 |
-DOCS=( AUTHORS README ) |
958 |
- |
959 |
-if [[ ${PV} != *9999 ]]; then |
960 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
961 |
-fi |
962 |
- |
963 |
-pkg_pretend() { |
964 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
965 |
- use openmp && ! tc-has-openmp && \ |
966 |
- die "Please switch to an openmp compatible compiler" |
967 |
-} |
968 |
- |
969 |
-src_unpack() { |
970 |
- if [[ ${PV} != *9999 ]]; then |
971 |
- default |
972 |
- else |
973 |
- git-r3_src_unpack |
974 |
- if use test; then |
975 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
976 |
- EGIT_BRANCH="master" EGIT_COMMIT="master" \ |
977 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
978 |
- git-r3_src_unpack |
979 |
- fi |
980 |
- fi |
981 |
-} |
982 |
- |
983 |
-src_prepare() { |
984 |
- #notes/todos |
985 |
- # -on apple: there is framework support |
986 |
- |
987 |
- cmake-utils_src_prepare |
988 |
- |
989 |
- use cuda && cuda_src_prepare |
990 |
- |
991 |
- GMX_DIRS="" |
992 |
- use single-precision && GMX_DIRS+=" float" |
993 |
- use double-precision && GMX_DIRS+=" double" |
994 |
- |
995 |
- if use test; then |
996 |
- for x in ${GMX_DIRS}; do |
997 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
998 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
999 |
- done |
1000 |
- fi |
1001 |
- |
1002 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
1003 |
-} |
1004 |
- |
1005 |
-src_configure() { |
1006 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
1007 |
- |
1008 |
- #go from slowest to fastest acceleration |
1009 |
- local acce="None" |
1010 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
1011 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
1012 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
1013 |
- use cpu_flags_x86_avx && acce="AVX_256" |
1014 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
1015 |
- |
1016 |
- #to create man pages, build tree binaries are executed (bug #398437) |
1017 |
- [[ ${CHOST} = *-darwin* ]] && \ |
1018 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
1019 |
- |
1020 |
- if use fftw; then |
1021 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
1022 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
1023 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1024 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
1025 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
1026 |
- ) |
1027 |
- elif use mkl; then |
1028 |
- local bits=$(get_libdir) |
1029 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1030 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
1031 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
1032 |
- ) |
1033 |
- else |
1034 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
1035 |
- fi |
1036 |
- |
1037 |
- mycmakeargs_pre+=( |
1038 |
- "${fft_opts[@]}" |
1039 |
- -DGMX_X11=$(usex X) |
1040 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
1041 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
1042 |
- -DGMX_OPENMP=$(usex openmp) |
1043 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
1044 |
- -DGMX_EXTERNAL_BOOST=$(usex boost) |
1045 |
- -DGMX_USE_TNG=$(usex tng) |
1046 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
1047 |
- -DGMX_SYMLINK_OLD_BINARY_NAMES=$(usex make-symlinks) |
1048 |
- -DGMX_DEFAULT_SUFFIX=off |
1049 |
- -DGMX_SIMD="$acce" |
1050 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
1051 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1052 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
1053 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
1054 |
- -DBUILD_TESTING=OFF |
1055 |
- -DGMX_BUILD_UNITTESTS=OFF |
1056 |
- ${extra} |
1057 |
- ) |
1058 |
- |
1059 |
- for x in ${GMX_DIRS}; do |
1060 |
- einfo "Configuring for ${x} precision" |
1061 |
- local suffix="" |
1062 |
- #if we build single and double - double is suffixed |
1063 |
- use double-precision && use single-precision && \ |
1064 |
- [[ ${x} = "double" ]] && suffix="_d" |
1065 |
- local p |
1066 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1067 |
- local cuda=( "-DGMX_GPU=OFF" ) |
1068 |
- [[ ${x} = "float" ]] && use cuda && \ |
1069 |
- cuda=( -DGMX_GPU=ON ) |
1070 |
- mycmakeargs=( |
1071 |
- ${mycmakeargs_pre[@]} ${p} |
1072 |
- -DGMX_MPI=OFF |
1073 |
- -DGMX_THREAD_MPI=$(usex threads) |
1074 |
- "${cuda[@]}" |
1075 |
- -DGMX_OPENMM=OFF |
1076 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1077 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1078 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1079 |
- ) |
1080 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
1081 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1082 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1083 |
- use mpi || continue |
1084 |
- einfo "Configuring for ${x} precision with mpi" |
1085 |
- mycmakeargs=( |
1086 |
- ${mycmakeargs_pre[@]} ${p} |
1087 |
- -DGMX_THREAD_MPI=OFF |
1088 |
- -DGMX_MPI=ON ${cuda} |
1089 |
- -DGMX_OPENMM=OFF |
1090 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1091 |
- -DBUILD_SHARED_LIBS=OFF |
1092 |
- -DGMX_BUILD_MANUAL=OFF |
1093 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1094 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1095 |
- ) |
1096 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
1097 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1098 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1099 |
- done |
1100 |
-} |
1101 |
- |
1102 |
-src_compile() { |
1103 |
- for x in ${GMX_DIRS}; do |
1104 |
- einfo "Compiling for ${x} precision" |
1105 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1106 |
- cmake-utils_src_compile |
1107 |
- # generate bash completion, not 100% necessary for |
1108 |
- # rel ebuilds as bundled |
1109 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1110 |
- cmake-utils_src_compile completion |
1111 |
- # not 100% necessary for rel ebuilds as available from website |
1112 |
- if use doc; then |
1113 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1114 |
- cmake-utils_src_compile manual |
1115 |
- fi |
1116 |
- use mpi || continue |
1117 |
- einfo "Compiling for ${x} precision with mpi" |
1118 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1119 |
- cmake-utils_src_compile |
1120 |
- done |
1121 |
-} |
1122 |
- |
1123 |
-src_test() { |
1124 |
- for x in ${GMX_DIRS}; do |
1125 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1126 |
- cmake-utils_src_make check |
1127 |
- done |
1128 |
-} |
1129 |
- |
1130 |
-src_install() { |
1131 |
- for x in ${GMX_DIRS}; do |
1132 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1133 |
- cmake-utils_src_install |
1134 |
- if use doc; then |
1135 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1136 |
- fi |
1137 |
- #release ebuild does this automatically |
1138 |
- if [[ $PV = *9999* ]]; then |
1139 |
- cp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash "${ED}/usr/bin" || die |
1140 |
- echo "complete -o nospace -F _gmx_compl gmx" > "${ED}/usr/bin/gmx-completion-gmx.bash" || die |
1141 |
- fi |
1142 |
- use mpi || continue |
1143 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1144 |
- cmake-utils_src_install |
1145 |
- done |
1146 |
- |
1147 |
- if use tng; then |
1148 |
- insinto /usr/include/tng |
1149 |
- doins src/external/tng_io/include/tng/*h |
1150 |
- fi |
1151 |
- # drop unneeded stuff |
1152 |
- rm "${ED}"usr/bin/GMXRC* || die |
1153 |
- #concatenate all gmx-completion*, starting with gmx-completion.bash (fct defs) |
1154 |
- #little hacckery as some gmx-completion* newlines ,so cat won't work |
1155 |
- for x in "${ED}"usr/bin/gmx-completion{,?*}.bash ; do |
1156 |
- echo $(<${x}) |
1157 |
- done > "${T}"/gmx-bashcomp || die |
1158 |
- newbashcomp "${T}"/gmx-bashcomp gmx |
1159 |
- bashcomp_alias gmx mdrun |
1160 |
- rm "${ED}"usr/bin/gmx-completion{,?*}.bash || die |
1161 |
- if use double-precision && use single-precision; then |
1162 |
- bashcomp_alias gmx gmx_d |
1163 |
- bashcomp_alias gmx mdrun_d |
1164 |
- fi |
1165 |
- readme.gentoo_create_doc |
1166 |
-} |
1167 |
- |
1168 |
-pkg_postinst() { |
1169 |
- einfo |
1170 |
- einfo "Please read and cite:" |
1171 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1172 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
1173 |
- einfo |
1174 |
- readme.gentoo_print_elog |
1175 |
-} |
1176 |
|
1177 |
diff --git a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild b/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild |
1178 |
deleted file mode 100644 |
1179 |
index 9711c22..0000000 |
1180 |
--- a/sci-chemistry/gromacs/gromacs-5.1.9999.ebuild |
1181 |
+++ /dev/null |
1182 |
@@ -1,269 +0,0 @@ |
1183 |
-# Copyright 1999-2016 Gentoo Foundation |
1184 |
-# Distributed under the terms of the GNU General Public License v2 |
1185 |
-# $Id$ |
1186 |
- |
1187 |
-EAPI=6 |
1188 |
- |
1189 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
1190 |
- |
1191 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
1192 |
- |
1193 |
-if [[ $PV = *9999* ]]; then |
1194 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
1195 |
- https://gerrit.gromacs.org/gromacs.git |
1196 |
- git://github.com/gromacs/gromacs.git |
1197 |
- http://repo.or.cz/r/gromacs.git" |
1198 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
1199 |
- inherit git-r3 |
1200 |
- KEYWORDS="" |
1201 |
-else |
1202 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
1203 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" |
1204 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
1205 |
-fi |
1206 |
- |
1207 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
1208 |
- |
1209 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
1210 |
-HOMEPAGE="http://www.gromacs.org/" |
1211 |
- |
1212 |
-# see COPYING for details |
1213 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
1214 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
1215 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
1216 |
-SLOT="0/${PV}" |
1217 |
-IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
1218 |
- |
1219 |
-CDEPEND=" |
1220 |
- X? ( |
1221 |
- x11-libs/libX11 |
1222 |
- x11-libs/libSM |
1223 |
- x11-libs/libICE |
1224 |
- ) |
1225 |
- blas? ( virtual/blas ) |
1226 |
- boost? ( >=dev-libs/boost-1.55 ) |
1227 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
1228 |
- fftw? ( sci-libs/fftw:3.0 ) |
1229 |
- lapack? ( virtual/lapack ) |
1230 |
- mkl? ( sci-libs/mkl ) |
1231 |
- mpi? ( virtual/mpi ) |
1232 |
- " |
1233 |
-DEPEND="${CDEPEND} |
1234 |
- virtual/pkgconfig |
1235 |
- doc? ( |
1236 |
- app-doc/doxygen |
1237 |
- dev-texlive/texlive-latex |
1238 |
- dev-texlive/texlive-latexextra |
1239 |
- media-gfx/imagemagick |
1240 |
- )" |
1241 |
-RDEPEND="${CDEPEND}" |
1242 |
- |
1243 |
-REQUIRED_USE=" |
1244 |
- || ( single-precision double-precision ) |
1245 |
- cuda? ( single-precision ) |
1246 |
- mkl? ( !blas !fftw !lapack )" |
1247 |
- |
1248 |
-DOCS=( AUTHORS README ) |
1249 |
- |
1250 |
-if [[ ${PV} != *9999 ]]; then |
1251 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
1252 |
-fi |
1253 |
- |
1254 |
-pkg_pretend() { |
1255 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
1256 |
- use openmp && ! tc-has-openmp && \ |
1257 |
- die "Please switch to an openmp compatible compiler" |
1258 |
-} |
1259 |
- |
1260 |
-src_unpack() { |
1261 |
- if [[ ${PV} != *9999 ]]; then |
1262 |
- default |
1263 |
- else |
1264 |
- git-r3_src_unpack |
1265 |
- if use test; then |
1266 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
1267 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
1268 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
1269 |
- git-r3_src_unpack |
1270 |
- fi |
1271 |
- fi |
1272 |
-} |
1273 |
- |
1274 |
-src_prepare() { |
1275 |
- #notes/todos |
1276 |
- # -on apple: there is framework support |
1277 |
- |
1278 |
- cmake-utils_src_prepare |
1279 |
- |
1280 |
- use cuda && cuda_src_prepare |
1281 |
- |
1282 |
- GMX_DIRS="" |
1283 |
- use single-precision && GMX_DIRS+=" float" |
1284 |
- use double-precision && GMX_DIRS+=" double" |
1285 |
- |
1286 |
- if use test; then |
1287 |
- for x in ${GMX_DIRS}; do |
1288 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
1289 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
1290 |
- done |
1291 |
- fi |
1292 |
- |
1293 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
1294 |
-} |
1295 |
- |
1296 |
-src_configure() { |
1297 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
1298 |
- |
1299 |
- #go from slowest to fastest acceleration |
1300 |
- local acce="None" |
1301 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
1302 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
1303 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
1304 |
- use cpu_flags_x86_avx && acce="AVX_256" |
1305 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
1306 |
- |
1307 |
- #to create man pages, build tree binaries are executed (bug #398437) |
1308 |
- [[ ${CHOST} = *-darwin* ]] && \ |
1309 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
1310 |
- |
1311 |
- if use fftw; then |
1312 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
1313 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
1314 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1315 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
1316 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
1317 |
- ) |
1318 |
- elif use mkl; then |
1319 |
- local bits=$(get_libdir) |
1320 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1321 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
1322 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
1323 |
- ) |
1324 |
- else |
1325 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
1326 |
- fi |
1327 |
- |
1328 |
- mycmakeargs_pre+=( |
1329 |
- "${fft_opts[@]}" |
1330 |
- -DGMX_X11=$(usex X) |
1331 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
1332 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
1333 |
- -DGMX_OPENMP=$(usex openmp) |
1334 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
1335 |
- -DGMX_EXTERNAL_BOOST=$(usex boost) |
1336 |
- -DGMX_USE_TNG=$(usex tng) |
1337 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
1338 |
- -DGMX_DEFAULT_SUFFIX=off |
1339 |
- -DGMX_SIMD="$acce" |
1340 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
1341 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1342 |
- -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF |
1343 |
- -DGMX_USE_GCC44_BUG_WORKAROUND=OFF |
1344 |
- -DBUILD_TESTING=OFF |
1345 |
- -DGMX_BUILD_UNITTESTS=OFF |
1346 |
- ${extra} |
1347 |
- ) |
1348 |
- |
1349 |
- for x in ${GMX_DIRS}; do |
1350 |
- einfo "Configuring for ${x} precision" |
1351 |
- local suffix="" |
1352 |
- #if we build single and double - double is suffixed |
1353 |
- use double-precision && use single-precision && \ |
1354 |
- [[ ${x} = "double" ]] && suffix="_d" |
1355 |
- local p |
1356 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1357 |
- local cuda=( "-DGMX_GPU=OFF" ) |
1358 |
- [[ ${x} = "float" ]] && use cuda && \ |
1359 |
- cuda=( -DGMX_GPU=ON ) |
1360 |
- mycmakeargs=( |
1361 |
- ${mycmakeargs_pre[@]} ${p} |
1362 |
- -DGMX_MPI=OFF |
1363 |
- -DGMX_THREAD_MPI=$(usex threads) |
1364 |
- "${cuda[@]}" |
1365 |
- -DGMX_OPENMM=OFF |
1366 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1367 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1368 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1369 |
- ) |
1370 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
1371 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1372 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1373 |
- use mpi || continue |
1374 |
- einfo "Configuring for ${x} precision with mpi" |
1375 |
- mycmakeargs=( |
1376 |
- ${mycmakeargs_pre[@]} ${p} |
1377 |
- -DGMX_THREAD_MPI=OFF |
1378 |
- -DGMX_MPI=ON ${cuda} |
1379 |
- -DGMX_OPENMM=OFF |
1380 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1381 |
- -DBUILD_SHARED_LIBS=OFF |
1382 |
- -DGMX_BUILD_MANUAL=OFF |
1383 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1384 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1385 |
- ) |
1386 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
1387 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1388 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1389 |
- done |
1390 |
-} |
1391 |
- |
1392 |
-src_compile() { |
1393 |
- for x in ${GMX_DIRS}; do |
1394 |
- einfo "Compiling for ${x} precision" |
1395 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1396 |
- cmake-utils_src_compile |
1397 |
- # not 100% necessary for rel ebuilds as available from website |
1398 |
- if use doc; then |
1399 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1400 |
- cmake-utils_src_compile manual |
1401 |
- fi |
1402 |
- use mpi || continue |
1403 |
- einfo "Compiling for ${x} precision with mpi" |
1404 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1405 |
- cmake-utils_src_compile |
1406 |
- done |
1407 |
-} |
1408 |
- |
1409 |
-src_test() { |
1410 |
- for x in ${GMX_DIRS}; do |
1411 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1412 |
- cmake-utils_src_make check |
1413 |
- done |
1414 |
-} |
1415 |
- |
1416 |
-src_install() { |
1417 |
- for x in ${GMX_DIRS}; do |
1418 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1419 |
- cmake-utils_src_install |
1420 |
- if use doc; then |
1421 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1422 |
- fi |
1423 |
- use mpi || continue |
1424 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1425 |
- cmake-utils_src_install |
1426 |
- done |
1427 |
- |
1428 |
- if use tng; then |
1429 |
- insinto /usr/include/tng |
1430 |
- doins src/external/tng_io/include/tng/*h |
1431 |
- fi |
1432 |
- # drop unneeded stuff |
1433 |
- rm "${ED}"usr/bin/GMXRC* || die |
1434 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
1435 |
- local n=${x##*/gmx-completion-} |
1436 |
- n="${n%.bash}" |
1437 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
1438 |
- newbashcomp "${T}"/"${n}" "${n}" |
1439 |
- done |
1440 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
1441 |
- readme.gentoo_create_doc |
1442 |
-} |
1443 |
- |
1444 |
-pkg_postinst() { |
1445 |
- einfo |
1446 |
- einfo "Please read and cite:" |
1447 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1448 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
1449 |
- einfo |
1450 |
- readme.gentoo_print_elog |
1451 |
-} |
1452 |
|
1453 |
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild |
1454 |
deleted file mode 100644 |
1455 |
index 1ca0343..0000000 |
1456 |
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild |
1457 |
+++ /dev/null |
1458 |
@@ -1,266 +0,0 @@ |
1459 |
-# Copyright 1999-2016 Gentoo Foundation |
1460 |
-# Distributed under the terms of the GNU General Public License v2 |
1461 |
-# $Id$ |
1462 |
- |
1463 |
-EAPI=6 |
1464 |
- |
1465 |
-CMAKE_MAKEFILE_GENERATOR="ninja" |
1466 |
- |
1467 |
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs |
1468 |
- |
1469 |
-if [[ $PV = *9999* ]]; then |
1470 |
- EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
1471 |
- https://gerrit.gromacs.org/gromacs.git |
1472 |
- git://github.com/gromacs/gromacs.git |
1473 |
- http://repo.or.cz/r/gromacs.git" |
1474 |
- [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" |
1475 |
- inherit git-r3 |
1476 |
- KEYWORDS="" |
1477 |
-else |
1478 |
- SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz |
1479 |
- test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )" |
1480 |
- KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" |
1481 |
-fi |
1482 |
- |
1483 |
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" |
1484 |
- |
1485 |
-DESCRIPTION="The ultimate molecular dynamics simulation package" |
1486 |
-HOMEPAGE="http://www.gromacs.org/" |
1487 |
- |
1488 |
-# see COPYING for details |
1489 |
-# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING |
1490 |
-# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
1491 |
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
1492 |
-SLOT="0/${PV}" |
1493 |
-IUSE="X blas cuda +doc -double-precision +fftw +hwloc lapack mkl mpi +offensive openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
1494 |
- |
1495 |
-CDEPEND=" |
1496 |
- X? ( |
1497 |
- x11-libs/libX11 |
1498 |
- x11-libs/libSM |
1499 |
- x11-libs/libICE |
1500 |
- ) |
1501 |
- blas? ( virtual/blas ) |
1502 |
- cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) |
1503 |
- fftw? ( sci-libs/fftw:3.0 ) |
1504 |
- hwloc? ( sys-apps/hwloc ) |
1505 |
- lapack? ( virtual/lapack ) |
1506 |
- mkl? ( sci-libs/mkl ) |
1507 |
- mpi? ( virtual/mpi ) |
1508 |
- " |
1509 |
-DEPEND="${CDEPEND} |
1510 |
- virtual/pkgconfig |
1511 |
- doc? ( |
1512 |
- app-doc/doxygen |
1513 |
- dev-texlive/texlive-latex |
1514 |
- dev-texlive/texlive-latexextra |
1515 |
- media-gfx/imagemagick |
1516 |
- )" |
1517 |
-RDEPEND="${CDEPEND}" |
1518 |
- |
1519 |
-REQUIRED_USE=" |
1520 |
- || ( single-precision double-precision ) |
1521 |
- cuda? ( single-precision ) |
1522 |
- mkl? ( !blas !fftw !lapack )" |
1523 |
- |
1524 |
-DOCS=( AUTHORS README ) |
1525 |
- |
1526 |
-if [[ ${PV} != *9999 ]]; then |
1527 |
- S="${WORKDIR}/${PN}-${PV/_/-}" |
1528 |
-fi |
1529 |
- |
1530 |
-pkg_pretend() { |
1531 |
- [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
1532 |
- use openmp && ! tc-has-openmp && \ |
1533 |
- die "Please switch to an openmp compatible compiler" |
1534 |
-} |
1535 |
- |
1536 |
-src_unpack() { |
1537 |
- if [[ ${PV} != *9999 ]]; then |
1538 |
- default |
1539 |
- else |
1540 |
- git-r3_src_unpack |
1541 |
- if use test; then |
1542 |
- EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ |
1543 |
- EGIT_BRANCH="${EGIT_BRANCH}" \ |
1544 |
- EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ |
1545 |
- git-r3_src_unpack |
1546 |
- fi |
1547 |
- fi |
1548 |
-} |
1549 |
- |
1550 |
-src_prepare() { |
1551 |
- #notes/todos |
1552 |
- # -on apple: there is framework support |
1553 |
- |
1554 |
- cmake-utils_src_prepare |
1555 |
- |
1556 |
- use cuda && cuda_src_prepare |
1557 |
- |
1558 |
- GMX_DIRS="" |
1559 |
- use single-precision && GMX_DIRS+=" float" |
1560 |
- use double-precision && GMX_DIRS+=" double" |
1561 |
- |
1562 |
- if use test; then |
1563 |
- for x in ${GMX_DIRS}; do |
1564 |
- mkdir -p "${WORKDIR}/${P}_${x}" || die |
1565 |
- cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die |
1566 |
- done |
1567 |
- fi |
1568 |
- |
1569 |
- DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
1570 |
-} |
1571 |
- |
1572 |
-src_configure() { |
1573 |
- local mycmakeargs_pre=( ) extra fft_opts=( ) |
1574 |
- |
1575 |
- #go from slowest to fastest acceleration |
1576 |
- local acce="None" |
1577 |
- use cpu_flags_x86_sse2 && acce="SSE2" |
1578 |
- use cpu_flags_x86_sse4_1 && acce="SSE4.1" |
1579 |
- use cpu_flags_x86_fma4 && acce="AVX_128_FMA" |
1580 |
- use cpu_flags_x86_avx && acce="AVX_256" |
1581 |
- use cpu_flags_x86_avx2 && acce="AVX2_256" |
1582 |
- |
1583 |
- #to create man pages, build tree binaries are executed (bug #398437) |
1584 |
- [[ ${CHOST} = *-darwin* ]] && \ |
1585 |
- extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" |
1586 |
- |
1587 |
- if use fftw; then |
1588 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) |
1589 |
- elif use mkl && has_version "=sci-libs/mkl-10*"; then |
1590 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1591 |
- -DMKL_INCLUDE_DIR="${MKLROOT}/include" |
1592 |
- -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)" |
1593 |
- ) |
1594 |
- elif use mkl; then |
1595 |
- local bits=$(get_libdir) |
1596 |
- fft_opts=( -DGMX_FFT_LIBRARY=mkl |
1597 |
- -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" |
1598 |
- -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" |
1599 |
- ) |
1600 |
- else |
1601 |
- fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) |
1602 |
- fi |
1603 |
- |
1604 |
- mycmakeargs_pre+=( |
1605 |
- "${fft_opts[@]}" |
1606 |
- -DGMX_X11=$(usex X) |
1607 |
- -DGMX_EXTERNAL_BLAS=$(usex blas) |
1608 |
- -DGMX_EXTERNAL_LAPACK=$(usex lapack) |
1609 |
- -DGMX_OPENMP=$(usex openmp) |
1610 |
- -DGMX_COOL_QUOTES=$(usex offensive) |
1611 |
- -DGMX_USE_TNG=$(usex tng) |
1612 |
- -DGMX_BUILD_MANUAL=$(usex doc) |
1613 |
- -DGMX_HWLOC=$(usex hwloc) |
1614 |
- -DGMX_DEFAULT_SUFFIX=off |
1615 |
- -DGMX_SIMD="$acce" |
1616 |
- -DGMX_LIB_INSTALL_DIR="$(get_libdir)" |
1617 |
- -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
1618 |
- -DBUILD_TESTING=OFF |
1619 |
- -DGMX_BUILD_UNITTESTS=OFF |
1620 |
- ${extra} |
1621 |
- ) |
1622 |
- |
1623 |
- for x in ${GMX_DIRS}; do |
1624 |
- einfo "Configuring for ${x} precision" |
1625 |
- local suffix="" |
1626 |
- #if we build single and double - double is suffixed |
1627 |
- use double-precision && use single-precision && \ |
1628 |
- [[ ${x} = "double" ]] && suffix="_d" |
1629 |
- local p |
1630 |
- [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" |
1631 |
- local cuda=( "-DGMX_GPU=OFF" ) |
1632 |
- [[ ${x} = "float" ]] && use cuda && \ |
1633 |
- cuda=( -DGMX_GPU=ON ) |
1634 |
- mycmakeargs=( |
1635 |
- ${mycmakeargs_pre[@]} ${p} |
1636 |
- -DGMX_MPI=OFF |
1637 |
- -DGMX_THREAD_MPI=$(usex threads) |
1638 |
- "${cuda[@]}" |
1639 |
- "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
1640 |
- -DGMX_BINARY_SUFFIX="${suffix}" |
1641 |
- -DGMX_LIBS_SUFFIX="${suffix}" |
1642 |
- ) |
1643 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
1644 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1645 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die |
1646 |
- use mpi || continue |
1647 |
- einfo "Configuring for ${x} precision with mpi" |
1648 |
- mycmakeargs=( |
1649 |
- ${mycmakeargs_pre[@]} ${p} |
1650 |
- -DGMX_THREAD_MPI=OFF |
1651 |
- -DGMX_MPI=ON ${cuda} |
1652 |
- -DGMX_OPENMM=OFF |
1653 |
- -DGMX_BUILD_MDRUN_ONLY=ON |
1654 |
- -DBUILD_SHARED_LIBS=OFF |
1655 |
- -DGMX_BUILD_MANUAL=OFF |
1656 |
- -DGMX_BINARY_SUFFIX="_mpi${suffix}" |
1657 |
- -DGMX_LIBS_SUFFIX="_mpi${suffix}" |
1658 |
- ) |
1659 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure |
1660 |
- [[ ${CHOST} != *-darwin* ]] || \ |
1661 |
- sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die |
1662 |
- done |
1663 |
-} |
1664 |
- |
1665 |
-src_compile() { |
1666 |
- for x in ${GMX_DIRS}; do |
1667 |
- einfo "Compiling for ${x} precision" |
1668 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1669 |
- cmake-utils_src_compile |
1670 |
- # not 100% necessary for rel ebuilds as available from website |
1671 |
- if use doc; then |
1672 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1673 |
- cmake-utils_src_compile manual |
1674 |
- fi |
1675 |
- use mpi || continue |
1676 |
- einfo "Compiling for ${x} precision with mpi" |
1677 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ |
1678 |
- cmake-utils_src_compile |
1679 |
- done |
1680 |
-} |
1681 |
- |
1682 |
-src_test() { |
1683 |
- for x in ${GMX_DIRS}; do |
1684 |
- BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
1685 |
- cmake-utils_src_make check |
1686 |
- done |
1687 |
-} |
1688 |
- |
1689 |
-src_install() { |
1690 |
- for x in ${GMX_DIRS}; do |
1691 |
- BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
1692 |
- cmake-utils_src_install |
1693 |
- if use doc; then |
1694 |
- newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
1695 |
- fi |
1696 |
- use mpi || continue |
1697 |
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ |
1698 |
- cmake-utils_src_install |
1699 |
- done |
1700 |
- |
1701 |
- if use tng; then |
1702 |
- insinto /usr/include/tng |
1703 |
- doins src/external/tng_io/include/tng/*h |
1704 |
- fi |
1705 |
- # drop unneeded stuff |
1706 |
- rm "${ED}"usr/bin/GMXRC* || die |
1707 |
- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
1708 |
- local n=${x##*/gmx-completion-} |
1709 |
- n="${n%.bash}" |
1710 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
1711 |
- newbashcomp "${T}"/"${n}" "${n}" |
1712 |
- done |
1713 |
- rm "${ED}"usr/bin/gmx-completion*.bash || die |
1714 |
- readme.gentoo_create_doc |
1715 |
-} |
1716 |
- |
1717 |
-pkg_postinst() { |
1718 |
- einfo |
1719 |
- einfo "Please read and cite:" |
1720 |
- einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " |
1721 |
- einfo "http://dx.doi.org/10.1021/ct700301q" |
1722 |
- einfo |
1723 |
- readme.gentoo_print_elog |
1724 |
-} |
1725 |
|
1726 |
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml |
1727 |
deleted file mode 100644 |
1728 |
index e98cd51..0000000 |
1729 |
--- a/sci-chemistry/gromacs/metadata.xml |
1730 |
+++ /dev/null |
1731 |
@@ -1,28 +0,0 @@ |
1732 |
-<?xml version="1.0" encoding="UTF-8"?> |
1733 |
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
1734 |
-<pkgmetadata> |
1735 |
- <maintainer type="person"> |
1736 |
- <email>ottxor@g.o</email> |
1737 |
- <name>Christoph Junghans</name> |
1738 |
- </maintainer> |
1739 |
- <maintainer type="person"> |
1740 |
- <email>alexxy@g.o</email> |
1741 |
- <name>Alexey Shvetsov</name> |
1742 |
- </maintainer> |
1743 |
- <maintainer type="project"> |
1744 |
- <email>sci-chemistry@g.o</email> |
1745 |
- <name>Gentoo Chemistry Project</name> |
1746 |
- </maintainer> |
1747 |
- <use> |
1748 |
- <flag name="cuda">Enable cuda non-bonded kernels</flag> |
1749 |
- <flag name="double-precision">More precise calculations at the expense of speed</flag> |
1750 |
- <flag name="single-precision">Single precision version of gromacs (default)</flag> |
1751 |
- <flag name="boost">Enable external boost library</flag> |
1752 |
- <flag name="hwloc">Enable HWLoc lib support</flag> |
1753 |
- <flag name="tng">Enable new trajectory format - tng</flag> |
1754 |
- <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> |
1755 |
- <!-- acceleration optimization flags --> |
1756 |
- <flag name="offensive">Enable gromacs partly offensive quotes</flag> |
1757 |
- <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag> |
1758 |
- </use> |
1759 |
-</pkgmetadata> |