From 3e2a2a3baebbc26bdcd1ee23a765bf04ebed7ee3 Mon Sep 17 00:00:00 2001 From: Pacho Ramos Date: Thu, 30 May 2019 13:14:56 +0200 Subject: sci-chemistry/vmd: Multiple fixes and update ebuild - Longer explanation to download sources files (#640440) - Fix tachyon support (#644122) - Install netcdf plugin (#661636) Bug: https://bugs.gentoo.org/640440 Closes: https://bugs.gentoo.org/644122 Closes: https://bugs.gentoo.org/661636 Package-Manager: Portage-2.3.66, Repoman-2.3.12 Signed-off-by: Pacho Ramos --- .../vmd/files/vmd-1.9.1-cuda-device_ptr.patch | 8 +- .../vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 + sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 262 +++++++++++++++++++++ 3 files changed, 279 insertions(+), 4 deletions(-) create mode 100644 sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch create mode 100644 sci-chemistry/vmd/vmd-1.9.3-r1.ebuild diff --git a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch index ce842448decf..67eb11bbd36b 100644 --- a/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch +++ b/sci-chemistry/vmd/files/vmd-1.9.1-cuda-device_ptr.patch @@ -4,8 +4,8 @@ diff --git a/vmd-1.9.1/src/CUDAMarchingCubes.cu b/vmd-1.9.1/src/CUDAMarchingCubes.cu index 5bfe7bf..36faaf0 100755 ---- a/vmd-1.9.1/src/CUDAMarchingCubes.cu -+++ b/vmd-1.9.1/src/CUDAMarchingCubes.cu +--- a/src/CUDAMarchingCubes.cu ++++ b/src/CUDAMarchingCubes.cu @@ -45,6 +45,7 @@ #include "CUDAMarchingCubes.h" #include @@ -16,8 +16,8 @@ index 5bfe7bf..36faaf0 100755 // (limited by shared memory size) diff --git a/vmd-1.9.1/src/CUDAQuickSurf.cu b/vmd-1.9.1/src/CUDAQuickSurf.cu index a21ebde..56a42c8 100755 ---- a/vmd-1.9.1/src/CUDAQuickSurf.cu -+++ b/vmd-1.9.1/src/CUDAQuickSurf.cu +--- a/src/CUDAQuickSurf.cu ++++ b/src/CUDAQuickSurf.cu @@ -22,6 +22,7 @@ #include #include diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch new file mode 100644 index 000000000000..b71cd97210a8 --- /dev/null +++ b/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch @@ -0,0 +1,13 @@ +--- a/configure.old 2019-05-16 17:26:05.347560700 +0200 ++++ b/configure 2019-05-16 17:30:25.478455770 +0200 +@@ -1105,8 +1105,8 @@ + # This may be commented out if not required. + $libtachyon_defines = "-DVMDLIBTACHYON"; + $libtachyon_dir = "$vmd_library_dir/tachyon"; +-$libtachyon_include = "-I$libtachyon_dir/include"; +-$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch"; ++$libtachyon_include = "-Igentoo-libtachyon-include"; ++$libtachyon_library = "-Lgentoo-libtachyon-libs"; + $libtachyon_libs = "-ltachyon"; + @libtachyon_cc = (); + @libtachyon_cu = (); diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild new file mode 100644 index 000000000000..392e380ece15 --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild @@ -0,0 +1,262 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +PYTHON_COMPAT=( python2_7 ) + +inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz + ${P}.src.tar +" + +SLOT="0" +LICENSE="vmd" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda gromacs msms povray sqlite tachyon xinerama" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RESTRICT="fetch" + +# currently, tk-8.5* with USE=truetype breaks some +# tk apps such as Sequence Viewer or Timeline. +CDEPEND=" + >=dev-lang/tk-8.6.1:0= + dev-lang/perl + dev-libs/expat + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/netcdf:0= + virtual/opengl + >=x11-libs/fltk-1.1.10-r2:1 + x11-libs/libXft + x11-libs/libXi + ${PYTHON_DEPS} + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) + gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) + sqlite? ( dev-db/sqlite:3= ) + tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) + xinerama? ( x11-libs/libXinerama ) +" +DEPEND="${CDEPEND}" +BDEPEND=" + virtual/pkgconfig + dev-lang/swig +" +RDEPEND="${CDEPEND} + sci-biology/stride + sci-chemistry/surf + x11-terms/xterm + msms? ( sci-chemistry/msms-bin ) + povray? ( media-gfx/povray ) +" + +VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" +# Binary only plugin!! +QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf1.1/bin/intersurf.so" +QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil" +QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil" + +pkg_nofetch() { + elog "Please download ${P}.src.tar from" + elog "${VMD_DOWNLOAD}" + elog "after agreeing to the license and get" + elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz" + elog "Place both into your DISTDIR directory" + elog + elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources" + elog "file may get downloaded as a compressed tarball or not. In that case" + elog "you will need to ensure you uncompress the file and rename it" + elog "as ${P}.src.tar" +} + +src_prepare() { + default + + use cuda && cuda_sanitize + + eapply "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch + + cd "${WORKDIR}"/plugins || die + + eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch + + [[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile) + + sed \ + -e "s:CC = gcc:CC = $(tc-getCC):" \ + -e "s:CXX = g++:CXX = $(tc-getCXX):" \ + -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ + -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ + -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ + -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ + -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ + -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ + -e "s:-ltcl8.5:-ltcl:" \ + -i Make-arch || die "Failed to set up plugins Makefile" + + sed \ + -e '/^AR /s:=:?=:g' \ + -e '/^RANLIB /s:=:?=:g' \ + -i ../plugins/*/Makefile || die + + tc-export AR RANLIB + + sed \ + -e "s:\$(CXXFLAGS)::g" \ + -i hesstrans/Makefile || die + + # prepare vmd itself + cd "${S}" || die + + eapply -p2 "${WORKDIR}"/${P}-gentoo-base.patch + eapply "${FILESDIR}"/${P}-configure-libtachyon.patch + + # PREFIX + sed \ + -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ + -i configure || die + + sed \ + -e "s:gentoo-bindir:${ED}/usr/bin:g" \ + -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ + -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ + -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-gcc:$(tc-getCC):g" \ + -e "s:gentoo-g++:$(tc-getCXX):g" \ + -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ + -e "s:gentoo-cflags:${CFLAGS}:g" \ + -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ + -e "s:gentoo-nvflags::g" \ + -e "s:gentoo-ldflags:${LDFLAGS}:g" \ + -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ + -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ + -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ + -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ + -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ + -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ + -i configure || die + + if use cuda; then + sed \ + -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ + -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ + -i configure src/Makefile || die + sed \ + -e '/compute_/d' \ + -i configure || die + sed \ + -e 's:-gencode .*code=sm_..::' \ + -i src/Makefile || die + fi + + sed \ + -e "s:LINUXPPC:LINUX:g" \ + -e "s:LINUXALPHA:LINUX:g" \ + -e "s:LINUXAMD64:LINUX:g" \ + -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ + -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ + -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ + -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" + + EMAKEOPTS=( + TCLINC="-I${EPREFIX}/usr/include" + TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" + TCLLDFLAGS="-shared" + NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" + NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" + NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" + NETCDFDYNAMIC=1 + EXPATINC="-I${EPREFIX}/usr/include" + EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" + EXPATLDFLAGS="-shared" + EXPATDYNAMIC=1 + ) + if use gromacs; then + EMAKEOPTS+=( + TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" + TNGINC="-I${EPREFIX}/usr/include" + TNGLDFLAGS="-shared" + TNGDYNAMIC=1 + ) + fi + if use sqlite; then + EMAKEOPTS+=( + SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" + SQLITEINC="-I${EPREFIX}/usr/include" + SQLITELDFLAGS="-shared" + SQLITEDYNAMIC=1 + ) + fi +} + +src_configure() { + local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" + rm -f configure.options && echo $myconf >> configure.options + + use cuda && myconf+=" CUDA" +# use mpi && myconf+=" MPI" + use tachyon && myconf+=" LIBTACHYON" + use xinerama && myconf+=" XINERAMA" + + export \ + PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ + PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ + PYTHON_LIBRARY="$(python_get_LIBS)" \ + NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ + NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" + + perl ./configure LINUX \ + ${myconf} || die +} + +src_compile() { + # build plugins + cd "${WORKDIR}"/plugins || die + + emake \ + ${EMAKEOPTS[@]} \ + LINUX + + # build vmd + cd "${S}"/src || die + emake +} + +src_install() { + # install plugins + cd "${WORKDIR}"/plugins || die + emake \ + PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ + distrib + + # install vmd + cd "${S}"/src || die + emake install + + # install docs + cd "${S}" || die + dodoc Announcement README doc/ig.pdf doc/ug.pdf + + # remove some of the things we don't want and need in + # /usr/lib + cd "${ED}"/usr/$(get_libdir)/vmd || die + rm -fr doc README Announcement LICENSE || \ + die "failed to clean up /usr/lib/vmd directory" + + # adjust path in vmd wrapper + sed \ + -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ + -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ + || die "failed to set up vmd wrapper script" + + # install icon and generate desktop entry + insinto /usr/share/pixmaps + doins "${WORKDIR}"/vmd.png + eprefixify "${WORKDIR}"/vmd.desktop + sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die + domenu "${WORKDIR}"/vmd.desktop +} -- cgit v1.2.3-65-gdbad