* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
@ 2019-12-15 15:31 Pacho Ramos
0 siblings, 0 replies; 5+ messages in thread
From: Pacho Ramos @ 2019-12-15 15:31 UTC (permalink / raw
To: gentoo-commits
commit: 4c03ac229acd7c3f5fd7aa110148ac5172268d4e
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 15 15:31:06 2019 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun Dec 15 15:31:29 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4c03ac22
sci-chemistry/vmd: Fix /tmp PATH, open .pdb files as pymol does
Package-Manager: Portage-2.3.81, Repoman-2.3.19
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch | 22 ++
sci-chemistry/vmd/vmd-1.9.3-r2.ebuild | 266 +++++++++++++++++++++++++
2 files changed, 288 insertions(+)
diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch
new file mode 100644
index 00000000000..22712abf30b
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch
@@ -0,0 +1,22 @@
+--- a/scripts/vmd/vmdinit.tcl~ 2016-10-27 05:46:34.000000000 +0200
++++ b/scripts/vmd/vmdinit.tcl 2019-12-03 16:29:01.894002827 +0100
+@@ -197,7 +197,7 @@
+ set env(TMPDIR) /tmp
+ }
+ default {
+- set env(TMPDIR) /usr/tmp
++ set env(TMPDIR) /tmp
+ }
+ }
+ }
+--- a/scripts/vmd/chemical2vmd~ 2000-07-03 19:30:23.000000000 +0200
++++ b/scripts/vmd/chemical2vmd 2019-12-03 16:28:49.316861178 +0100
+@@ -61,7 +61,7 @@
+
+
+ # Make a temp. file to store the load command
+-$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'};
++$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'};
+ sub tmpfile {
+ local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$;
+ local ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
new file mode 100644
index 00000000000..02ad806afbe
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
@@ -0,0 +1,266 @@
+# 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 xdg
+
+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/chemical-mime-data
+ 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() {
+ xdg_src_prepare
+
+ 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
+ eapply "${FILESDIR}"/${P}-tmpdir.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
+ # Open PDB files with VMD
+ echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
+ domenu "${WORKDIR}"/vmd.desktop
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
@ 2020-03-08 18:47 Pacho Ramos
0 siblings, 0 replies; 5+ messages in thread
From: Pacho Ramos @ 2020-03-08 18:47 UTC (permalink / raw
To: gentoo-commits
commit: 805bb1f57777f38626dad04b06629c0ef515c3a2
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 8 18:46:56 2020 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun Mar 8 18:46:56 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=805bb1f5
sci-chemistry/vmd: Fix support for current CUDA versions
Package-Manager: Portage-2.3.93, Repoman-2.3.20
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch | 426 +++++++++++++++++++++++++++
sci-chemistry/vmd/vmd-1.9.3-r5.ebuild | 272 +++++++++++++++++
2 files changed, 698 insertions(+)
diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch b/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch
new file mode 100644
index 00000000000..258efb777ca
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch
@@ -0,0 +1,426 @@
+--- a/src/CUDAMarchingCubes.cu 2018-03-30 18:52:25.467189457 +0300
++++ b/src/CUDAMarchingCubes.cu 2018-03-30 18:52:02.387136244 +0300
+@@ -10,7 +10,7 @@
+ *
+ * $RCSfile: CUDAMarchingCubes.cu,v $
+ * $Author: johns $ $Locker: $ $State: Exp $
+- * $Revision: 1.30 $ $Date: 2016/11/28 03:04:58 $
++ * $Revision: 1.32 $ $Date: 2018/02/15 05:15:02 $
+ *
+ ***************************************************************************
+ * DESCRIPTION:
+@@ -25,14 +25,17 @@
+ //
+ // Description: This class computes an isosurface for a given density grid
+ // using a CUDA Marching Cubes (MC) alorithm.
+-// The implementation is based on the MC demo from the
+-// Nvidia GPU Computing SDK, but has been improved
+-// and extended. This implementation achieves higher
+-// performance by reducing the number of temporary memory
+-// buffers, reduces the number of scan calls by using vector
+-// integer types, and allows extraction of per-vertex normals
+-// optionally computes per-vertex colors if provided with a
+-// volumetric texture map.
++//
++// The implementation is loosely based on the MC demo from
++// the Nvidia GPU Computing SDK, but the design has been
++// improved and extended in several ways.
++//
++// This implementation achieves higher performance
++// by reducing the number of temporary memory
++// buffers, reduces the number of scan calls by using
++// vector integer types, and allows extraction of
++// per-vertex normals and optionally computes
++// per-vertex colors if a volumetric texture map is provided.
+ //
+ // Author: Michael Krone <michael.krone@visus.uni-stuttgart.de>
+ // John Stone <johns@ks.uiuc.edu>
+@@ -48,7 +51,7 @@
+ #include <thrust/functional.h>
+
+ //
+-// Restrict macro to make it easy to do perf tuning tess
++// Restrict macro to make it easy to do perf tuning tests
+ //
+ #if 0
+ #define RESTRICT __restrict__
+@@ -171,6 +174,11 @@
+ texture<float, 3, cudaReadModeElementType> volumeTex;
+
+ // sample volume data set at a point p, p CAN NEVER BE OUT OF BOUNDS
++// XXX The sampleVolume() call underperforms vs. peak memory bandwidth
++// because we don't strictly enforce coalescing requirements in the
++// layout of the input volume presently. If we forced X/Y dims to be
++// warp-multiple it would become possible to use wider fetches and
++// a few other tricks to improve global memory bandwidth
+ __device__ float sampleVolume(const float * RESTRICT data,
+ uint3 p, uint3 gridSize) {
+ return data[(p.z*gridSize.x*gridSize.y) + (p.y*gridSize.x) + p.x];
+@@ -592,6 +600,30 @@
+ cudaBindTextureToArray(volumeTex, d_vol, desc);
+ }
+
++#if CUDART_VERSION >= 9000
++//
++// XXX CUDA 9.0RC breaks the usability of Thrust scan() prefix sums when
++// used with the built-in uint2 vector integer types. To workaround
++// the problem we have to define our own type and associated conversion
++// routines etc.
++//
++
++// XXX workaround for uint2 breakage in CUDA 9.0RC
++struct myuint2 : uint2 {
++ __host__ __device__ myuint2() : uint2(make_uint2(0, 0)) {}
++ __host__ __device__ myuint2(int val) : uint2(make_uint2(val, val)) {}
++ __host__ __device__ myuint2(uint2 val) : uint2(make_uint2(val.x, val.y)) {}
++};
++
++void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) {
++ const uint2 zero = make_uint2(0, 0);
++ thrust::exclusive_scan(thrust::device_ptr<myuint2>((myuint2*)input),
++ thrust::device_ptr<myuint2>((myuint2*)input + numElements),
++ thrust::device_ptr<myuint2>((myuint2*)output),
++ (myuint2) zero);
++}
++
++#else
+
+ void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) {
+ const uint2 zero = make_uint2(0, 0);
+@@ -601,6 +633,7 @@
+ zero);
+ }
+
++#endif
+
+ void ThrustScanWrapperArea(float* output, float* input, unsigned int numElements) {
+ thrust::inclusive_scan(thrust::device_ptr<float>(input),
+@@ -639,11 +672,9 @@
+ }
+
+
+-///////////////////////////////////////////////////////////////////////////////
+ //
+ // class CUDAMarchingCubes
+ //
+-///////////////////////////////////////////////////////////////////////////////
+
+ CUDAMarchingCubes::CUDAMarchingCubes() {
+ // initialize values
+@@ -713,9 +744,6 @@
+ }
+
+
+-////////////////////////////////////////////////////////////////////////////////
+-//! Run the Cuda part of the computation
+-////////////////////////////////////////////////////////////////////////////////
+ void CUDAMarchingCubes::computeIsosurfaceVerts(float3* vertOut, unsigned int maxverts, dim3 & grid3) {
+ // check if data is available
+ if (!this->setdata)
+
+--- a/src/CUDAMDFF.cu 2016-12-01 10:11:56.000000000 +0300
++++ b/src/CUDAMDFF.cu 2018-03-30 18:56:44.352937599 +0300
+@@ -11,7 +11,7 @@
+ *
+ * $RCSfile: CUDAMDFF.cu,v $
+ * $Author: johns $ $Locker: $ $State: Exp $
+- * $Revision: 1.75 $ $Date: 2015/04/07 20:41:26 $
++ * $Revision: 1.78 $ $Date: 2018/02/19 07:10:37 $
+ *
+ ***************************************************************************
+ * DESCRIPTION:
+@@ -28,12 +28,16 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <cuda.h>
+-#include <float.h> // FLT_MAX etc
+-
++#if CUDART_VERSION >= 9000
++#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0
++#endif
+ #if CUDART_VERSION < 4000
+ #error The VMD MDFF feature requires CUDA 4.0 or later
+ #endif
+
++#include <float.h> // FLT_MAX etc
++
++
+ #include "Inform.h"
+ #include "utilities.h"
+ #include "WKFThreads.h"
+@@ -588,6 +592,43 @@
+ }
+
+
++
++// #define VMDUSESHUFFLE 1
++#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000
++// New warp shuffle-based CC sum reduction for Kepler and later GPUs.
++inline __device__ void cc_sumreduction(int tid, int totaltb,
++ float4 &total_cc_sums,
++ float &total_lcc,
++ int &total_lsize,
++ float4 *tb_cc_sums,
++ float *tb_lcc,
++ int *tb_lsize) {
++ total_cc_sums = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
++ total_lcc = 0.0f;
++ total_lsize = 0;
++
++ // use precisely one warp to do the final reduction
++ if (tid < warpSize) {
++ for (int i=tid; i<totaltb; i+=warpSize) {
++ total_cc_sums += tb_cc_sums[i];
++ total_lcc += tb_lcc[i];
++ total_lsize += tb_lsize[i];
++ }
++
++ // perform intra-warp parallel reduction...
++ // general loop version of parallel sum-reduction
++ for (int mask=warpSize/2; mask>0; mask>>=1) {
++ total_cc_sums.x += __shfl_xor_sync(0xffffffff, total_cc_sums.x, mask);
++ total_cc_sums.y += __shfl_xor_sync(0xffffffff, total_cc_sums.y, mask);
++ total_cc_sums.z += __shfl_xor_sync(0xffffffff, total_cc_sums.z, mask);
++ total_cc_sums.w += __shfl_xor_sync(0xffffffff, total_cc_sums.w, mask);
++ total_lcc += __shfl_xor_sync(0xffffffff, total_lcc, mask);
++ total_lsize += __shfl_xor_sync(0xffffffff, total_lsize, mask);
++ }
++ }
++}
++#else
++// shared memory based CC sum reduction
+ inline __device__ void cc_sumreduction(int tid, int totaltb,
+ float4 &total_cc_sums,
+ float &total_lcc,
+@@ -629,6 +670,7 @@
+ total_lcc = tb_lcc[0];
+ total_lsize = tb_lsize[0];
+ }
++#endif
+
+
+ inline __device__ void thread_cc_sum(float ref, float density,
+@@ -750,6 +792,92 @@
+ }
+
+
++#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000
++ // all threads write their local sums to shared memory...
++ __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ];
++ __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ];
++ __shared__ float tb_lcc_s[TOTALBLOCKSZ];
++ __shared__ int tb_lsize_s[TOTALBLOCKSZ];
++
++ tb_cc_means_s[tid] = thread_cc_means;
++ tb_cc_squares_s[tid] = thread_cc_squares;
++ tb_lcc_s[tid] = thread_lcc;
++ tb_lsize_s[tid] = thread_lsize;
++ __syncthreads(); // all threads must hit syncthreads call...
++
++ // use precisely one warp to do the thread-block-wide reduction
++ if (tid < warpSize) {
++ float2 tmp_cc_means = make_float2(0.0f, 0.0f);
++ float2 tmp_cc_squares = make_float2(0.0f, 0.0f);
++ float tmp_lcc = 0.0f;
++ int tmp_lsize = 0;
++ for (int i=tid; i<TOTALBLOCKSZ; i+=warpSize) {
++ tmp_cc_means += tb_cc_means_s[i];
++ tmp_cc_squares += tb_cc_squares_s[i];
++ tmp_lcc += tb_lcc_s[i];
++ tmp_lsize += tb_lsize_s[i];
++ }
++
++ // perform intra-warp parallel reduction...
++ // general loop version of parallel sum-reduction
++ for (int mask=warpSize/2; mask>0; mask>>=1) {
++ tmp_cc_means.x += __shfl_xor_sync(0xffffffff, tmp_cc_means.x, mask);
++ tmp_cc_means.y += __shfl_xor_sync(0xffffffff, tmp_cc_means.y, mask);
++ tmp_cc_squares.x += __shfl_xor_sync(0xffffffff, tmp_cc_squares.x, mask);
++ tmp_cc_squares.y += __shfl_xor_sync(0xffffffff, tmp_cc_squares.y, mask);
++ tmp_lcc += __shfl_xor_sync(0xffffffff, tmp_lcc, mask);
++ tmp_lsize += __shfl_xor_sync(0xffffffff, tmp_lsize, mask);
++ }
++
++ // write per-thread-block partial sums to global memory,
++ // if a per-thread-block CC output array is provided, write the
++ // local CC for this thread block out, and finally, check if we
++ // are the last thread block to finish, and finalize the overall
++ // CC results for the entire grid of thread blocks.
++ if (tid == 0) {
++ unsigned int bid = blockIdx.z * gridDim.x * gridDim.y +
++ blockIdx.y * gridDim.x + blockIdx.x;
++
++ tb_cc_sums[bid] = make_float4(tmp_cc_means.x, tmp_cc_means.y,
++ tmp_cc_squares.x, tmp_cc_squares.y);
++ tb_lcc[bid] = tmp_lcc;
++ tb_lsize[bid] = tmp_lsize;
++
++ if (tb_CC != NULL) {
++ float cc = calc_cc(tb_cc_means_s[0].x, tb_cc_means_s[0].y,
++ tb_cc_squares_s[0].x, tb_cc_squares_s[0].y,
++ tb_lsize_s[0], tb_lcc_s[0]);
++
++ // write local per-thread-block CC to global memory
++ tb_CC[bid] = cc;
++ }
++
++ __threadfence();
++
++ unsigned int value = atomicInc(&tbcatomic[0], totaltb);
++ isLastBlockDone = (value == (totaltb - 1));
++ }
++ }
++ __syncthreads();
++
++ if (isLastBlockDone) {
++ float4 total_cc_sums;
++ float total_lcc;
++ int total_lsize;
++ cc_sumreduction(tid, totaltb, total_cc_sums, total_lcc, total_lsize,
++ tb_cc_sums, tb_lcc, tb_lsize);
++
++ if (tid == 0) {
++ tb_cc_sums[totaltb] = total_cc_sums;
++ tb_lcc[totaltb] = total_lcc;
++ tb_lsize[totaltb] = total_lsize;
++ }
++
++ reset_atomic_counter(&tbcatomic[0]);
++ }
++
++#else
++
+ // all threads write their local sums to shared memory...
+ __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ];
+ __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ];
+@@ -794,6 +922,7 @@
+ }
+ __syncthreads(); // all threads must hit syncthreads call...
+ }
++//#endif
+
+ // write per-thread-block partial sums to global memory,
+ // if a per-thread-block CC output array is provided, write the
+@@ -847,6 +976,7 @@
+ }
+ #endif
+ }
++#endif
+ }
+
+
+
+--- a/src/CUDAQuickSurf.cu 2016-12-01 10:11:56.000000000 +0300
++++ b/src/CUDAQuickSurf.cu 2018-03-30 19:01:38.777196233 +0300
+@@ -11,7 +11,7 @@
+ *
+ * $RCSfile: CUDAQuickSurf.cu,v $
+ * $Author: johns $ $Locker: $ $State: Exp $
+- * $Revision: 1.81 $ $Date: 2016/04/20 04:57:46 $
++ * $Revision: 1.84 $ $Date: 2018/02/15 04:59:15 $
+ *
+ ***************************************************************************
+ * DESCRIPTION:
+@@ -22,6 +22,9 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <cuda.h>
++#if CUDART_VERSION >= 9000
++#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0
++#endif
+
+ #if CUDART_VERSION < 4000
+ #error The VMD QuickSurf feature requires CUDA 4.0 or later
+@@ -130,14 +133,14 @@
+ #define GUNROLL 1
+ #endif
+
+-#if __CUDA_ARCH__ >= 300
+ #define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
+-#define MINBLOCKDENS 1
++#if __CUDA_ARCH__ >= 600
++#define MINBLOCKDENS 16
++#elif __CUDA_ARCH__ >= 300
++#define MINBLOCKDENS 16
+ #elif __CUDA_ARCH__ >= 200
+-#define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
+ #define MINBLOCKDENS 1
+ #else
+-#define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
+ #define MINBLOCKDENS 1
+ #endif
+
+@@ -150,7 +153,7 @@
+ //
+ template<class DENSITY, class VOLTEX>
+ __global__ static void
+-// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
++__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
+ gaussdensity_fast_tex_norm(int natoms,
+ const float4 * RESTRICT sorted_xyzr,
+ const float4 * RESTRICT sorted_color,
+@@ -217,6 +220,8 @@
+ for (yab=yabmin; yab<=yabmax; yab++) {
+ for (xab=xabmin; xab<=xabmax; xab++) {
+ int abcellidx = zab * acplanesz + yab * acncells.x + xab;
++ // this biggest latency hotspot in the kernel, if we could improve
++ // packing of the grid cell map, we'd likely improve performance
+ uint2 atomstartend = cellStartEnd[abcellidx];
+ if (atomstartend.x != GRID_CELL_EMPTY) {
+ unsigned int atomid;
+@@ -296,7 +301,7 @@
+
+
+ __global__ static void
+-// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
++__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
+ gaussdensity_fast_tex3f(int natoms,
+ const float4 * RESTRICT sorted_xyzr,
+ const float4 * RESTRICT sorted_color,
+@@ -363,6 +368,8 @@
+ for (yab=yabmin; yab<=yabmax; yab++) {
+ for (xab=xabmin; xab<=xabmax; xab++) {
+ int abcellidx = zab * acplanesz + yab * acncells.x + xab;
++ // this biggest latency hotspot in the kernel, if we could improve
++ // packing of the grid cell map, we'd likely improve performance
+ uint2 atomstartend = cellStartEnd[abcellidx];
+ if (atomstartend.x != GRID_CELL_EMPTY) {
+ unsigned int atomid;
+@@ -550,7 +557,6 @@
+
+ // per-GPU handle with various memory buffer pointers, etc.
+ typedef struct {
+- /// max grid sizes and attributes the current allocations will support
+ int verbose;
+ long int natoms;
+ int colorperatom;
+@@ -561,18 +567,18 @@
+ int gy;
+ int gz;
+
+- CUDAMarchingCubes *mc; ///< Marching cubes class used to extract surface
++ CUDAMarchingCubes *mc;
+
+- float *devdensity; ///< density map stored in GPU memory
+- void *devvoltexmap; ///< volumetric texture map
+- float4 *xyzr_d; ///< atom coords and radii
+- float4 *sorted_xyzr_d; ///< cell-sorted coords and radii
+- float4 *color_d; ///< colors
+- float4 *sorted_color_d; ///< cell-sorted colors
+-
+- unsigned int *atomIndex_d; ///< cell index for each atom
+- unsigned int *atomHash_d; ///<
+- uint2 *cellStartEnd_d; ///< cell start/end indices
++ float *devdensity;
++ void *devvoltexmap;
++ float4 *xyzr_d;
++ float4 *sorted_xyzr_d;
++ float4 *color_d;
++ float4 *sorted_color_d;
++
++ unsigned int *atomIndex_d;
++ unsigned int *atomHash_d;
++ uint2 *cellStartEnd_d;
+
+ void *safety;
+ float3 *v3f_d;
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
new file mode 100644
index 00000000000..a4e0e6db49b
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
@@ -0,0 +1,272 @@
+# Copyright 1999-2020 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 xdg
+
+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
+ $(python_gen_cond_dep '
+ || (
+ dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+ dev-python/numpy[${PYTHON_MULTI_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/chemical-mime-data
+ 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() {
+ xdg_src_prepare
+
+ use cuda && cuda_sanitize
+
+ # Compat with newer CUDA versions (from Arch)
+ eapply "${FILESDIR}"/${P}-cuda.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
+ eapply "${FILESDIR}"/${P}-tmpdir.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
+ # Open PDB files with VMD
+ echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
+ domenu "${WORKDIR}"/vmd.desktop
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
@ 2020-09-09 17:03 Pacho Ramos
0 siblings, 0 replies; 5+ messages in thread
From: Pacho Ramos @ 2020-09-09 17:03 UTC (permalink / raw
To: gentoo-commits
commit: 8790988057a312f5e5cfa1d6f0acf4c681619321
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 9 17:03:02 2020 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Wed Sep 9 17:03:02 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=87909880
sci-chemistry/vmd: Bump to 1.9.4_alpha43
Bug: https://bugs.gentoo.org/735462
Package-Manager: Portage-3.0.4, Repoman-3.0.1
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-chemistry/vmd/Manifest | 1 +
.../vmd/files/vmd-1.9.4-gentoo-paths.patch | 276 +++++++++++++++++++++
sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch | 11 +
sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 265 ++++++++++++++++++++
4 files changed, 553 insertions(+)
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 977dcfa66a2..62f7ae61617 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,2 +1,3 @@
DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba
+DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
new file mode 100644
index 00000000000..ca74b868d8f
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
@@ -0,0 +1,276 @@
+--- a/bin/vmd.sh.old 2020-09-09 18:02:09.135798193 +0200
++++ b/bin/vmd.sh 2020-09-09 18:37:22.355511675 +0200
+@@ -436,6 +436,7 @@
+
+ # set the path to a few external programs
+ # Stride -- used to generate cartoon representations etc.
++export STRIDE_BIN="gentoo-stride"
+ if [ -z "$STRIDE_BIN" ]
+ then
+ if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
+@@ -446,6 +447,7 @@
+ fi
+
+ # Surf -- used to generate molecular surfaces
++export SURF_BIN="gentoo-surf"
+ if [ -z "$SURF_BIN" ]
+ then
+ if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
+@@ -456,6 +458,7 @@
+ fi
+
+ # Tachyon -- used to generate ray traced graphics
++export TACHYON_BIN="gentoo-tachyon"
+ if [ -z "$TACHYON_BIN" ]
+ then
+ if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
+--- a/configure.old 2020-09-09 18:05:55.778655084 +0200
++++ b/configure 2020-09-09 18:38:01.607083112 +0200
+@@ -13,11 +13,10 @@
+ $install_name = "vmd";
+
+ # Directory where VMD startup script is installed, should be in users' paths.
+-$install_bin_dir="/usr/local/bin";
++$install_bin_dir="gentoo-bindir";
+
+ # Directory where VMD files and executables are installed
+-$install_library_dir="/usr/local/lib/$install_name";
+-
++$install_library_dir="gentoo-libdir/$install_name";
+
+ # optionally override hard-coded defaults above with environment variables
+ if ($ENV{VMDINSTALLNAME}) {
+@@ -143,29 +142,6 @@
+ # Configure script code begins here
+ ############################################################################
+
+-## Test for existence of a properly compiled plugin tree
+-if (!(-e "plugins")) {
+- print "\n";
+- print "VMD plugin directory not found.\n";
+- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+- print "into a 'plugins' directory linked or located in this directory.\n";
+- print "Be sure your PLUGINDIR environment variable is set before running\n";
+- print "'make distrib' in the plugin build area.\n";
+- print "\n";
+- die "Halting configuration until VMD plugins are built.\n";
+-} else {
+- if (!(-e "plugins/include/vmdplugin.h")) {
+- print "\n";
+- print "VMD plugin include files or directory not found.\n";
+- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+- print "into a 'plugins' directory linked or located in this directory.\n";
+- print "Be sure your PLUGINDIR environment variable is set before running\n";
+- print "'make distrib' in the plugin build area.\n";
+- print "\n";
+- die "Halting configuration until VMD plugins are built.\n";
+- }
+-}
+-
+ #################### Parse command line options ###########
+ # list of allowed architectures
+ @archlist=('AIX6_64', 'ANDROIDARMV7A', 'BLUEGENEQ', 'BLUEWATERS', 'CRAY_XC', 'CRAY_XK', 'FREEBSD', 'FREEBSDAMD64', 'LINUX', 'LINUXAMD64', 'LINUXARM64', 'LINUXCARMA', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'OPENPOWER', 'SUMMIT', 'SUMMITDEV', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
+@@ -493,7 +469,7 @@
+
+ $arch_cc = "cc";
+ $arch_ccpp = "CC";
+-$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc";
++$arch_nvcc = "gentoo-nvcc";
+ $arch_nvccflags = "-lineinfo --ptxas-options=-v " .
+ "-gencode arch=compute_30,code=compute_30 " .
+ "-gencode arch=compute_30,code=sm_35 " .
+@@ -537,7 +513,7 @@
+
+ ################ Plugin options
+ #
+-$plugin_dir = "../plugins";
++$plugin_dir = "gentoo-plugindir";
+ $plugin_include = "-I$plugin_dir/include";
+ $plugin_library = "";
+ $plugin_libs = "";
+@@ -550,7 +526,7 @@
+ @plugin_extra = ();
+
+ if ($config_staticplugin) {
+- $molfile_dir = "$plugin_dir/$config_arch/molfile";
++ $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
+ $plugin_include .= " -I$molfile_dir";
+ $plugin_library .= " -L$molfile_dir";
+ $plugin_libs .= " -lmolfile_plugin";
+@@ -715,8 +691,8 @@
+ ################ FLTK GUI
+ $fltk_defines = "-DVMDGUI -DVMDFLTK";
+ $fltk_dir = "$vmd_library_dir/fltk";
+-$fltk_include = "-I$fltk_dir/include";
+-$fltk_library = "-L$fltk_dir/$config_arch";
++$fltk_include = "-Igentoo-fltk-include";
++$fltk_library = "-Lgentoo-fltk-libs";
+ $fltk_libs = "-lfltk -lX11";
+ #@fltk_cc = ('forms_ui.c');
+ @fltk_cu = ();
+@@ -777,8 +753,8 @@
+ if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
+ $tcl_library = "-L$stock_tcl_library_dir";
+ if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
+-$tcl_libs = "-ltcl8.5";
+-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
++$tcl_libs = "-ltcl";
++if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
+
+ @tcl_cc = ();
+ @tcl_cu = ();
+@@ -1289,8 +1265,8 @@
+ # 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 = ();
+@@ -1541,8 +1517,8 @@
+ #######################
+ $netcdf_defines = "";
+ $netcdf_dir = "$vmd_library_dir/netcdf";
+-$netcdf_include = "-I$netcdf_dir/include";
+-$netcdf_library = "-L$netcdf_dir/lib_$config_arch";
++$netcdf_include = "-Igentoo-netcdf-include";
++$netcdf_library = "-Lgentoo-netcdf-libs";
+ $netcdf_libs = "-lnetcdf";
+ @netcdf_cc = ();
+ @netcdf_cu = ();
+@@ -1595,6 +1571,7 @@
+ #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
+ $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
+ $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
++$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
+
+ #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
+ #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
+@@ -1604,7 +1581,7 @@
+ $python_defines = "-DVMDPYTHON";
+ $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
+ $python_library = "-L$stock_python_library_dir";
+-$python_libs = "-lpython2.5 -lpthread";
++$python_libs = "$stock_python_library -lpthread";
+ @python_h = ('PythonTextInterp.h',
+ 'VMDTkinterMenu.h',
+ 'py_commands.h',
+@@ -2350,8 +2327,8 @@
+
+ # XFree 4.0 Direct Rendering Interface and GLX
+ $opengl_dep_dir = "/usr/X11R6";
+- $opengl_dep_include = "-I$opengl_dep_dir/include";
+- $opengl_dep_library = "-L$opengl_dep_dir/lib";
++ $opengl_dep_include = "-Igentoo-opengl-include";
++ $opengl_dep_library = "-Lgentoo-opengl-libs";
+ $opengl_dep_libs = "-lGL";
+ # $opengl_dep_libs = "-L/usr/X11R6/lib -lGL -lXext -lX11";
+
+@@ -2381,15 +2358,15 @@
+ $arch_lopts .= "-i-static ";
+ } else {
+ # compling with GCC
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "gentoo-gcc";
++ $arch_ccpp = "gentoo-g++";
+ $arch_depend_flag = "-MM";
+- $arch_shld = "g++ -shared";
++ $arch_shld = "gentoo-g++ -shared";
+ $arch_shlibname = "so";
+ $arch_shcppopts = "-fPIC";
+- $arch_shldopts = "";
+- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
+- $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3";
++ $arch_shldopts = "gentoo-ldflags";
++ $arch_opt_flag = "gentoo-cflags";
++ $arch_copts = "gentoo-cflags";
+
+ if ($config_static) {
+ $arch_lopts = "-static";
+@@ -2407,14 +2384,13 @@
+
+ $arch_cppopts = "";
+ if ($config_cuda) {
+- $arch_nvcc = "/usr/local/cuda-4.0/bin/nvcc";
+ $arch_nvccflags = "--ptxas-options=-v " .
+ "-gencode arch=compute_13,code=sm_13 " .
+ "-gencode arch=compute_20,code=sm_20 " .
+ "-gencode arch=compute_20,code=compute_20 " .
+ "--ftz=true ";
+- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
+- $cuda_library = "-L/usr/local/cuda-4.0/lib";
++ $arch_nvccflags .= "gentoo-nvflags $cuda_include";
++ $cuda_library = "-Lgentoo-cuda-lib";
+ $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
+ }
+ # this is to make tcl happy
+@@ -2513,7 +2489,7 @@
+
+ if ($config_cuda) {
+ $arch_nvccflags .= " --machine 64 -O3 $cuda_include";
+- $cuda_library = "-L/usr/local/cuda-10.2/lib64";
++ $cuda_library = "-Lgentoo-cuda-lib";
+ }
+
+ $arch_lex = "flex"; # has problems with vendor lex
+@@ -3502,11 +3478,11 @@
+ DEFINES = $DEFINES
+
+ # compiler and compiler directives
+-CC = $arch_cc
+-CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CC = gentoo-gcc
++CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+
+-CCPP = $arch_ccpp
+-CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CCPP = gentoo-g++
++CPPFLAGS = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+
+ NVCC = $arch_nvcc
+ NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+@@ -3555,7 +3531,7 @@
+ $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX)
+ \$(ECHO) "Linking " \$\@ "..."; \\
+ \$(CD) $vmd_arch_dir ; \\
+- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
++ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
+ \$(COMPILERC) \$(RCFLAGS)
+
+ install:
+@@ -3596,8 +3572,7 @@
+ -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
+ \$(CD) $vmd_bin_dir ; \\
+ if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
+- if [ ! -x "/bin/csh" ]; then \\
+- \$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
++ if [ -x "/bin/bash" ]; then \\
+ \$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
+ \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
+ \$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
+--- a/src/Makefile.old 2020-09-09 18:22:46.234818925 +0200
++++ b/src/Makefile 2020-09-09 18:37:22.356511690 +0200
+@@ -647,7 +647,7 @@
+ vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX)
+ $(ECHO) "Linking " $@ "..."; \
+ $(CD) ../LINUXAMD64 ; \
+- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
++ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
+ $(COMPILERC) $(RCFLAGS)
+
+ install:
+@@ -660,10 +660,6 @@
+ if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
+ $(MAKEDIR) "/usr/local/lib/vmd"/doc; \
+ fi
+- -$(COPY) ../Announcement "/usr/local/lib/vmd"
+- -$(COPY) ../README "/usr/local/lib/vmd"
+- -$(COPY) ../LICENSE "/usr/local/lib/vmd"
+- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc
+ if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
+ $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
+ -$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
new file mode 100644
index 00000000000..295811db058
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
@@ -0,0 +1,11 @@
+--- a/scripts/vmd/chemical2vmd.old 2020-09-09 18:40:56.795215443 +0200
++++ b/scripts/vmd/chemical2vmd 2020-09-09 18:41:09.648348701 +0200
+@@ -61,7 +61,7 @@
+
+
+ # Make a temp. file to store the load command
+-$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'};
++$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'};
+ sub tmpfile {
+ local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$;
+ local ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
new file mode 100644
index 00000000000..29d0417b34e
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -0,0 +1,265 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python3_{6..9} )
+
+inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+
+MY_PV="${PV/_alpha/a}"
+MY_P="${PN}-${MY_PV}"
+SRC_URI="
+ ${MY_P}.src.tar
+ https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
+"
+
+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"
+
+CDEPEND="
+ >=dev-lang/tk-8.6.1:0=
+ dev-lang/perl
+ dev-libs/expat
+ $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_MULTI_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="${CDEPEND}
+ sci-biology/stride
+ sci-chemistry/chemical-mime-data
+ sci-chemistry/surf
+ x11-terms/xterm
+ msms? ( sci-chemistry/msms-bin )
+ povray? ( media-gfx/povray )
+"
+
+S="${WORKDIR}/${MY_P}"
+
+VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
+# Binary only plugin!!
+QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/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 ${P}.src.tar"
+}
+
+src_prepare() {
+ xdg_src_prepare
+
+ use cuda && cuda_sanitize
+
+ cd "${WORKDIR}"/plugins || die
+
+ 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 "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch
+ eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.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
+ # Open PDB files with VMD
+ echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
+ domenu "${WORKDIR}"/vmd.desktop
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
@ 2020-09-19 12:29 Michał Górny
0 siblings, 0 replies; 5+ messages in thread
From: Michał Górny @ 2020-09-19 12:29 UTC (permalink / raw
To: gentoo-commits
commit: 644a181b8ab3d796f3a489edc77bf21be545e05f
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 19 11:49:58 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sat Sep 19 12:29:09 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=644a181b
sci-chemistry/vmd: Remove old
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-chemistry/vmd/Manifest | 1 -
.../vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 -
sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch | 426 ---------------------
sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch | 22 --
sci-chemistry/vmd/vmd-1.9.3-r5.ebuild | 272 -------------
5 files changed, 734 deletions(-)
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 62f7ae61617..f2c96b24855 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,3 +1,2 @@
DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
-DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba
DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
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
deleted file mode 100644
index b71cd97210a..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- 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/files/vmd-1.9.3-cuda.patch b/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch
deleted file mode 100644
index 258efb777ca..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch
+++ /dev/null
@@ -1,426 +0,0 @@
---- a/src/CUDAMarchingCubes.cu 2018-03-30 18:52:25.467189457 +0300
-+++ b/src/CUDAMarchingCubes.cu 2018-03-30 18:52:02.387136244 +0300
-@@ -10,7 +10,7 @@
- *
- * $RCSfile: CUDAMarchingCubes.cu,v $
- * $Author: johns $ $Locker: $ $State: Exp $
-- * $Revision: 1.30 $ $Date: 2016/11/28 03:04:58 $
-+ * $Revision: 1.32 $ $Date: 2018/02/15 05:15:02 $
- *
- ***************************************************************************
- * DESCRIPTION:
-@@ -25,14 +25,17 @@
- //
- // Description: This class computes an isosurface for a given density grid
- // using a CUDA Marching Cubes (MC) alorithm.
--// The implementation is based on the MC demo from the
--// Nvidia GPU Computing SDK, but has been improved
--// and extended. This implementation achieves higher
--// performance by reducing the number of temporary memory
--// buffers, reduces the number of scan calls by using vector
--// integer types, and allows extraction of per-vertex normals
--// optionally computes per-vertex colors if provided with a
--// volumetric texture map.
-+//
-+// The implementation is loosely based on the MC demo from
-+// the Nvidia GPU Computing SDK, but the design has been
-+// improved and extended in several ways.
-+//
-+// This implementation achieves higher performance
-+// by reducing the number of temporary memory
-+// buffers, reduces the number of scan calls by using
-+// vector integer types, and allows extraction of
-+// per-vertex normals and optionally computes
-+// per-vertex colors if a volumetric texture map is provided.
- //
- // Author: Michael Krone <michael.krone@visus.uni-stuttgart.de>
- // John Stone <johns@ks.uiuc.edu>
-@@ -48,7 +51,7 @@
- #include <thrust/functional.h>
-
- //
--// Restrict macro to make it easy to do perf tuning tess
-+// Restrict macro to make it easy to do perf tuning tests
- //
- #if 0
- #define RESTRICT __restrict__
-@@ -171,6 +174,11 @@
- texture<float, 3, cudaReadModeElementType> volumeTex;
-
- // sample volume data set at a point p, p CAN NEVER BE OUT OF BOUNDS
-+// XXX The sampleVolume() call underperforms vs. peak memory bandwidth
-+// because we don't strictly enforce coalescing requirements in the
-+// layout of the input volume presently. If we forced X/Y dims to be
-+// warp-multiple it would become possible to use wider fetches and
-+// a few other tricks to improve global memory bandwidth
- __device__ float sampleVolume(const float * RESTRICT data,
- uint3 p, uint3 gridSize) {
- return data[(p.z*gridSize.x*gridSize.y) + (p.y*gridSize.x) + p.x];
-@@ -592,6 +600,30 @@
- cudaBindTextureToArray(volumeTex, d_vol, desc);
- }
-
-+#if CUDART_VERSION >= 9000
-+//
-+// XXX CUDA 9.0RC breaks the usability of Thrust scan() prefix sums when
-+// used with the built-in uint2 vector integer types. To workaround
-+// the problem we have to define our own type and associated conversion
-+// routines etc.
-+//
-+
-+// XXX workaround for uint2 breakage in CUDA 9.0RC
-+struct myuint2 : uint2 {
-+ __host__ __device__ myuint2() : uint2(make_uint2(0, 0)) {}
-+ __host__ __device__ myuint2(int val) : uint2(make_uint2(val, val)) {}
-+ __host__ __device__ myuint2(uint2 val) : uint2(make_uint2(val.x, val.y)) {}
-+};
-+
-+void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) {
-+ const uint2 zero = make_uint2(0, 0);
-+ thrust::exclusive_scan(thrust::device_ptr<myuint2>((myuint2*)input),
-+ thrust::device_ptr<myuint2>((myuint2*)input + numElements),
-+ thrust::device_ptr<myuint2>((myuint2*)output),
-+ (myuint2) zero);
-+}
-+
-+#else
-
- void ThrustScanWrapperUint2(uint2* output, uint2* input, unsigned int numElements) {
- const uint2 zero = make_uint2(0, 0);
-@@ -601,6 +633,7 @@
- zero);
- }
-
-+#endif
-
- void ThrustScanWrapperArea(float* output, float* input, unsigned int numElements) {
- thrust::inclusive_scan(thrust::device_ptr<float>(input),
-@@ -639,11 +672,9 @@
- }
-
-
--///////////////////////////////////////////////////////////////////////////////
- //
- // class CUDAMarchingCubes
- //
--///////////////////////////////////////////////////////////////////////////////
-
- CUDAMarchingCubes::CUDAMarchingCubes() {
- // initialize values
-@@ -713,9 +744,6 @@
- }
-
-
--////////////////////////////////////////////////////////////////////////////////
--//! Run the Cuda part of the computation
--////////////////////////////////////////////////////////////////////////////////
- void CUDAMarchingCubes::computeIsosurfaceVerts(float3* vertOut, unsigned int maxverts, dim3 & grid3) {
- // check if data is available
- if (!this->setdata)
-
---- a/src/CUDAMDFF.cu 2016-12-01 10:11:56.000000000 +0300
-+++ b/src/CUDAMDFF.cu 2018-03-30 18:56:44.352937599 +0300
-@@ -11,7 +11,7 @@
- *
- * $RCSfile: CUDAMDFF.cu,v $
- * $Author: johns $ $Locker: $ $State: Exp $
-- * $Revision: 1.75 $ $Date: 2015/04/07 20:41:26 $
-+ * $Revision: 1.78 $ $Date: 2018/02/19 07:10:37 $
- *
- ***************************************************************************
- * DESCRIPTION:
-@@ -28,12 +28,16 @@
- #include <stdlib.h>
- #include <string.h>
- #include <cuda.h>
--#include <float.h> // FLT_MAX etc
--
-+#if CUDART_VERSION >= 9000
-+#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0
-+#endif
- #if CUDART_VERSION < 4000
- #error The VMD MDFF feature requires CUDA 4.0 or later
- #endif
-
-+#include <float.h> // FLT_MAX etc
-+
-+
- #include "Inform.h"
- #include "utilities.h"
- #include "WKFThreads.h"
-@@ -588,6 +592,43 @@
- }
-
-
-+
-+// #define VMDUSESHUFFLE 1
-+#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000
-+// New warp shuffle-based CC sum reduction for Kepler and later GPUs.
-+inline __device__ void cc_sumreduction(int tid, int totaltb,
-+ float4 &total_cc_sums,
-+ float &total_lcc,
-+ int &total_lsize,
-+ float4 *tb_cc_sums,
-+ float *tb_lcc,
-+ int *tb_lsize) {
-+ total_cc_sums = make_float4(0.0f, 0.0f, 0.0f, 0.0f);
-+ total_lcc = 0.0f;
-+ total_lsize = 0;
-+
-+ // use precisely one warp to do the final reduction
-+ if (tid < warpSize) {
-+ for (int i=tid; i<totaltb; i+=warpSize) {
-+ total_cc_sums += tb_cc_sums[i];
-+ total_lcc += tb_lcc[i];
-+ total_lsize += tb_lsize[i];
-+ }
-+
-+ // perform intra-warp parallel reduction...
-+ // general loop version of parallel sum-reduction
-+ for (int mask=warpSize/2; mask>0; mask>>=1) {
-+ total_cc_sums.x += __shfl_xor_sync(0xffffffff, total_cc_sums.x, mask);
-+ total_cc_sums.y += __shfl_xor_sync(0xffffffff, total_cc_sums.y, mask);
-+ total_cc_sums.z += __shfl_xor_sync(0xffffffff, total_cc_sums.z, mask);
-+ total_cc_sums.w += __shfl_xor_sync(0xffffffff, total_cc_sums.w, mask);
-+ total_lcc += __shfl_xor_sync(0xffffffff, total_lcc, mask);
-+ total_lsize += __shfl_xor_sync(0xffffffff, total_lsize, mask);
-+ }
-+ }
-+}
-+#else
-+// shared memory based CC sum reduction
- inline __device__ void cc_sumreduction(int tid, int totaltb,
- float4 &total_cc_sums,
- float &total_lcc,
-@@ -629,6 +670,7 @@
- total_lcc = tb_lcc[0];
- total_lsize = tb_lsize[0];
- }
-+#endif
-
-
- inline __device__ void thread_cc_sum(float ref, float density,
-@@ -750,6 +792,92 @@
- }
-
-
-+#if defined(VMDUSESHUFFLE) && __CUDA_ARCH__ >= 300 && CUDART_VERSION >= 9000
-+ // all threads write their local sums to shared memory...
-+ __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ];
-+ __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ];
-+ __shared__ float tb_lcc_s[TOTALBLOCKSZ];
-+ __shared__ int tb_lsize_s[TOTALBLOCKSZ];
-+
-+ tb_cc_means_s[tid] = thread_cc_means;
-+ tb_cc_squares_s[tid] = thread_cc_squares;
-+ tb_lcc_s[tid] = thread_lcc;
-+ tb_lsize_s[tid] = thread_lsize;
-+ __syncthreads(); // all threads must hit syncthreads call...
-+
-+ // use precisely one warp to do the thread-block-wide reduction
-+ if (tid < warpSize) {
-+ float2 tmp_cc_means = make_float2(0.0f, 0.0f);
-+ float2 tmp_cc_squares = make_float2(0.0f, 0.0f);
-+ float tmp_lcc = 0.0f;
-+ int tmp_lsize = 0;
-+ for (int i=tid; i<TOTALBLOCKSZ; i+=warpSize) {
-+ tmp_cc_means += tb_cc_means_s[i];
-+ tmp_cc_squares += tb_cc_squares_s[i];
-+ tmp_lcc += tb_lcc_s[i];
-+ tmp_lsize += tb_lsize_s[i];
-+ }
-+
-+ // perform intra-warp parallel reduction...
-+ // general loop version of parallel sum-reduction
-+ for (int mask=warpSize/2; mask>0; mask>>=1) {
-+ tmp_cc_means.x += __shfl_xor_sync(0xffffffff, tmp_cc_means.x, mask);
-+ tmp_cc_means.y += __shfl_xor_sync(0xffffffff, tmp_cc_means.y, mask);
-+ tmp_cc_squares.x += __shfl_xor_sync(0xffffffff, tmp_cc_squares.x, mask);
-+ tmp_cc_squares.y += __shfl_xor_sync(0xffffffff, tmp_cc_squares.y, mask);
-+ tmp_lcc += __shfl_xor_sync(0xffffffff, tmp_lcc, mask);
-+ tmp_lsize += __shfl_xor_sync(0xffffffff, tmp_lsize, mask);
-+ }
-+
-+ // write per-thread-block partial sums to global memory,
-+ // if a per-thread-block CC output array is provided, write the
-+ // local CC for this thread block out, and finally, check if we
-+ // are the last thread block to finish, and finalize the overall
-+ // CC results for the entire grid of thread blocks.
-+ if (tid == 0) {
-+ unsigned int bid = blockIdx.z * gridDim.x * gridDim.y +
-+ blockIdx.y * gridDim.x + blockIdx.x;
-+
-+ tb_cc_sums[bid] = make_float4(tmp_cc_means.x, tmp_cc_means.y,
-+ tmp_cc_squares.x, tmp_cc_squares.y);
-+ tb_lcc[bid] = tmp_lcc;
-+ tb_lsize[bid] = tmp_lsize;
-+
-+ if (tb_CC != NULL) {
-+ float cc = calc_cc(tb_cc_means_s[0].x, tb_cc_means_s[0].y,
-+ tb_cc_squares_s[0].x, tb_cc_squares_s[0].y,
-+ tb_lsize_s[0], tb_lcc_s[0]);
-+
-+ // write local per-thread-block CC to global memory
-+ tb_CC[bid] = cc;
-+ }
-+
-+ __threadfence();
-+
-+ unsigned int value = atomicInc(&tbcatomic[0], totaltb);
-+ isLastBlockDone = (value == (totaltb - 1));
-+ }
-+ }
-+ __syncthreads();
-+
-+ if (isLastBlockDone) {
-+ float4 total_cc_sums;
-+ float total_lcc;
-+ int total_lsize;
-+ cc_sumreduction(tid, totaltb, total_cc_sums, total_lcc, total_lsize,
-+ tb_cc_sums, tb_lcc, tb_lsize);
-+
-+ if (tid == 0) {
-+ tb_cc_sums[totaltb] = total_cc_sums;
-+ tb_lcc[totaltb] = total_lcc;
-+ tb_lsize[totaltb] = total_lsize;
-+ }
-+
-+ reset_atomic_counter(&tbcatomic[0]);
-+ }
-+
-+#else
-+
- // all threads write their local sums to shared memory...
- __shared__ float2 tb_cc_means_s[TOTALBLOCKSZ];
- __shared__ float2 tb_cc_squares_s[TOTALBLOCKSZ];
-@@ -794,6 +922,7 @@
- }
- __syncthreads(); // all threads must hit syncthreads call...
- }
-+//#endif
-
- // write per-thread-block partial sums to global memory,
- // if a per-thread-block CC output array is provided, write the
-@@ -847,6 +976,7 @@
- }
- #endif
- }
-+#endif
- }
-
-
-
---- a/src/CUDAQuickSurf.cu 2016-12-01 10:11:56.000000000 +0300
-+++ b/src/CUDAQuickSurf.cu 2018-03-30 19:01:38.777196233 +0300
-@@ -11,7 +11,7 @@
- *
- * $RCSfile: CUDAQuickSurf.cu,v $
- * $Author: johns $ $Locker: $ $State: Exp $
-- * $Revision: 1.81 $ $Date: 2016/04/20 04:57:46 $
-+ * $Revision: 1.84 $ $Date: 2018/02/15 04:59:15 $
- *
- ***************************************************************************
- * DESCRIPTION:
-@@ -22,6 +22,9 @@
- #include <stdlib.h>
- #include <string.h>
- #include <cuda.h>
-+#if CUDART_VERSION >= 9000
-+#include <cuda_fp16.h> // need to explicitly include for CUDA 9.0
-+#endif
-
- #if CUDART_VERSION < 4000
- #error The VMD QuickSurf feature requires CUDA 4.0 or later
-@@ -130,14 +133,14 @@
- #define GUNROLL 1
- #endif
-
--#if __CUDA_ARCH__ >= 300
- #define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
--#define MINBLOCKDENS 1
-+#if __CUDA_ARCH__ >= 600
-+#define MINBLOCKDENS 16
-+#elif __CUDA_ARCH__ >= 300
-+#define MINBLOCKDENS 16
- #elif __CUDA_ARCH__ >= 200
--#define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
- #define MINBLOCKDENS 1
- #else
--#define MAXTHRDENS ( GBLOCKSZX * GBLOCKSZY * GBLOCKSZZ )
- #define MINBLOCKDENS 1
- #endif
-
-@@ -150,7 +153,7 @@
- //
- template<class DENSITY, class VOLTEX>
- __global__ static void
--// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
-+__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
- gaussdensity_fast_tex_norm(int natoms,
- const float4 * RESTRICT sorted_xyzr,
- const float4 * RESTRICT sorted_color,
-@@ -217,6 +220,8 @@
- for (yab=yabmin; yab<=yabmax; yab++) {
- for (xab=xabmin; xab<=xabmax; xab++) {
- int abcellidx = zab * acplanesz + yab * acncells.x + xab;
-+ // this biggest latency hotspot in the kernel, if we could improve
-+ // packing of the grid cell map, we'd likely improve performance
- uint2 atomstartend = cellStartEnd[abcellidx];
- if (atomstartend.x != GRID_CELL_EMPTY) {
- unsigned int atomid;
-@@ -296,7 +301,7 @@
-
-
- __global__ static void
--// __launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
-+__launch_bounds__ ( MAXTHRDENS, MINBLOCKDENS )
- gaussdensity_fast_tex3f(int natoms,
- const float4 * RESTRICT sorted_xyzr,
- const float4 * RESTRICT sorted_color,
-@@ -363,6 +368,8 @@
- for (yab=yabmin; yab<=yabmax; yab++) {
- for (xab=xabmin; xab<=xabmax; xab++) {
- int abcellidx = zab * acplanesz + yab * acncells.x + xab;
-+ // this biggest latency hotspot in the kernel, if we could improve
-+ // packing of the grid cell map, we'd likely improve performance
- uint2 atomstartend = cellStartEnd[abcellidx];
- if (atomstartend.x != GRID_CELL_EMPTY) {
- unsigned int atomid;
-@@ -550,7 +557,6 @@
-
- // per-GPU handle with various memory buffer pointers, etc.
- typedef struct {
-- /// max grid sizes and attributes the current allocations will support
- int verbose;
- long int natoms;
- int colorperatom;
-@@ -561,18 +567,18 @@
- int gy;
- int gz;
-
-- CUDAMarchingCubes *mc; ///< Marching cubes class used to extract surface
-+ CUDAMarchingCubes *mc;
-
-- float *devdensity; ///< density map stored in GPU memory
-- void *devvoltexmap; ///< volumetric texture map
-- float4 *xyzr_d; ///< atom coords and radii
-- float4 *sorted_xyzr_d; ///< cell-sorted coords and radii
-- float4 *color_d; ///< colors
-- float4 *sorted_color_d; ///< cell-sorted colors
--
-- unsigned int *atomIndex_d; ///< cell index for each atom
-- unsigned int *atomHash_d; ///<
-- uint2 *cellStartEnd_d; ///< cell start/end indices
-+ float *devdensity;
-+ void *devvoltexmap;
-+ float4 *xyzr_d;
-+ float4 *sorted_xyzr_d;
-+ float4 *color_d;
-+ float4 *sorted_color_d;
-+
-+ unsigned int *atomIndex_d;
-+ unsigned int *atomHash_d;
-+ uint2 *cellStartEnd_d;
-
- void *safety;
- float3 *v3f_d;
diff --git a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch
deleted file mode 100644
index 22712abf30b..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/scripts/vmd/vmdinit.tcl~ 2016-10-27 05:46:34.000000000 +0200
-+++ b/scripts/vmd/vmdinit.tcl 2019-12-03 16:29:01.894002827 +0100
-@@ -197,7 +197,7 @@
- set env(TMPDIR) /tmp
- }
- default {
-- set env(TMPDIR) /usr/tmp
-+ set env(TMPDIR) /tmp
- }
- }
- }
---- a/scripts/vmd/chemical2vmd~ 2000-07-03 19:30:23.000000000 +0200
-+++ b/scripts/vmd/chemical2vmd 2019-12-03 16:28:49.316861178 +0100
-@@ -61,7 +61,7 @@
-
-
- # Make a temp. file to store the load command
--$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'};
-+$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'};
- sub tmpfile {
- local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$;
- local ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
deleted file mode 100644
index a4e0e6db49b..00000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
+++ /dev/null
@@ -1,272 +0,0 @@
-# Copyright 1999-2020 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 xdg
-
-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
- $(python_gen_cond_dep '
- || (
- dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
- dev-python/numpy[${PYTHON_MULTI_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/chemical-mime-data
- 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() {
- xdg_src_prepare
-
- use cuda && cuda_sanitize
-
- # Compat with newer CUDA versions (from Arch)
- eapply "${FILESDIR}"/${P}-cuda.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
- eapply "${FILESDIR}"/${P}-tmpdir.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
- # Open PDB files with VMD
- echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
- domenu "${WORKDIR}"/vmd.desktop
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
@ 2021-05-02 19:22 Pacho Ramos
0 siblings, 0 replies; 5+ messages in thread
From: Pacho Ramos @ 2021-05-02 19:22 UTC (permalink / raw
To: gentoo-commits
commit: 8c9499c1d811547d4d69f60d5b78ae7edacdd922
Author: Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun May 2 19:22:03 2021 +0000
Commit: Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun May 2 19:22:23 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8c9499c1
sci-chemistry/vmd: Drop old
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
sci-chemistry/vmd/Manifest | 3 -
.../vmd/files/vmd-1.9.4-gentoo-paths.patch | 276 --------------------
sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch | 11 -
sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 277 ---------------------
4 files changed, 567 deletions(-)
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index a94593a65fc..dbb4249c928 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,5 +1,2 @@
-DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
-DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc
-DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
deleted file mode 100644
index ca74b868d8f..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
+++ /dev/null
@@ -1,276 +0,0 @@
---- a/bin/vmd.sh.old 2020-09-09 18:02:09.135798193 +0200
-+++ b/bin/vmd.sh 2020-09-09 18:37:22.355511675 +0200
-@@ -436,6 +436,7 @@
-
- # set the path to a few external programs
- # Stride -- used to generate cartoon representations etc.
-+export STRIDE_BIN="gentoo-stride"
- if [ -z "$STRIDE_BIN" ]
- then
- if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
-@@ -446,6 +447,7 @@
- fi
-
- # Surf -- used to generate molecular surfaces
-+export SURF_BIN="gentoo-surf"
- if [ -z "$SURF_BIN" ]
- then
- if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
-@@ -456,6 +458,7 @@
- fi
-
- # Tachyon -- used to generate ray traced graphics
-+export TACHYON_BIN="gentoo-tachyon"
- if [ -z "$TACHYON_BIN" ]
- then
- if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
---- a/configure.old 2020-09-09 18:05:55.778655084 +0200
-+++ b/configure 2020-09-09 18:38:01.607083112 +0200
-@@ -13,11 +13,10 @@
- $install_name = "vmd";
-
- # Directory where VMD startup script is installed, should be in users' paths.
--$install_bin_dir="/usr/local/bin";
-+$install_bin_dir="gentoo-bindir";
-
- # Directory where VMD files and executables are installed
--$install_library_dir="/usr/local/lib/$install_name";
--
-+$install_library_dir="gentoo-libdir/$install_name";
-
- # optionally override hard-coded defaults above with environment variables
- if ($ENV{VMDINSTALLNAME}) {
-@@ -143,29 +142,6 @@
- # Configure script code begins here
- ############################################################################
-
--## Test for existence of a properly compiled plugin tree
--if (!(-e "plugins")) {
-- print "\n";
-- print "VMD plugin directory not found.\n";
-- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
-- print "into a 'plugins' directory linked or located in this directory.\n";
-- print "Be sure your PLUGINDIR environment variable is set before running\n";
-- print "'make distrib' in the plugin build area.\n";
-- print "\n";
-- die "Halting configuration until VMD plugins are built.\n";
--} else {
-- if (!(-e "plugins/include/vmdplugin.h")) {
-- print "\n";
-- print "VMD plugin include files or directory not found.\n";
-- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
-- print "into a 'plugins' directory linked or located in this directory.\n";
-- print "Be sure your PLUGINDIR environment variable is set before running\n";
-- print "'make distrib' in the plugin build area.\n";
-- print "\n";
-- die "Halting configuration until VMD plugins are built.\n";
-- }
--}
--
- #################### Parse command line options ###########
- # list of allowed architectures
- @archlist=('AIX6_64', 'ANDROIDARMV7A', 'BLUEGENEQ', 'BLUEWATERS', 'CRAY_XC', 'CRAY_XK', 'FREEBSD', 'FREEBSDAMD64', 'LINUX', 'LINUXAMD64', 'LINUXARM64', 'LINUXCARMA', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'OPENPOWER', 'SUMMIT', 'SUMMITDEV', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
-@@ -493,7 +469,7 @@
-
- $arch_cc = "cc";
- $arch_ccpp = "CC";
--$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc";
-+$arch_nvcc = "gentoo-nvcc";
- $arch_nvccflags = "-lineinfo --ptxas-options=-v " .
- "-gencode arch=compute_30,code=compute_30 " .
- "-gencode arch=compute_30,code=sm_35 " .
-@@ -537,7 +513,7 @@
-
- ################ Plugin options
- #
--$plugin_dir = "../plugins";
-+$plugin_dir = "gentoo-plugindir";
- $plugin_include = "-I$plugin_dir/include";
- $plugin_library = "";
- $plugin_libs = "";
-@@ -550,7 +526,7 @@
- @plugin_extra = ();
-
- if ($config_staticplugin) {
-- $molfile_dir = "$plugin_dir/$config_arch/molfile";
-+ $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
- $plugin_include .= " -I$molfile_dir";
- $plugin_library .= " -L$molfile_dir";
- $plugin_libs .= " -lmolfile_plugin";
-@@ -715,8 +691,8 @@
- ################ FLTK GUI
- $fltk_defines = "-DVMDGUI -DVMDFLTK";
- $fltk_dir = "$vmd_library_dir/fltk";
--$fltk_include = "-I$fltk_dir/include";
--$fltk_library = "-L$fltk_dir/$config_arch";
-+$fltk_include = "-Igentoo-fltk-include";
-+$fltk_library = "-Lgentoo-fltk-libs";
- $fltk_libs = "-lfltk -lX11";
- #@fltk_cc = ('forms_ui.c');
- @fltk_cu = ();
-@@ -777,8 +753,8 @@
- if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
- $tcl_library = "-L$stock_tcl_library_dir";
- if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
--$tcl_libs = "-ltcl8.5";
--if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
-+$tcl_libs = "-ltcl";
-+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
-
- @tcl_cc = ();
- @tcl_cu = ();
-@@ -1289,8 +1265,8 @@
- # 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 = ();
-@@ -1541,8 +1517,8 @@
- #######################
- $netcdf_defines = "";
- $netcdf_dir = "$vmd_library_dir/netcdf";
--$netcdf_include = "-I$netcdf_dir/include";
--$netcdf_library = "-L$netcdf_dir/lib_$config_arch";
-+$netcdf_include = "-Igentoo-netcdf-include";
-+$netcdf_library = "-Lgentoo-netcdf-libs";
- $netcdf_libs = "-lnetcdf";
- @netcdf_cc = ();
- @netcdf_cu = ();
-@@ -1595,6 +1571,7 @@
- #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
- $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
- $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
-+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
-
- #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
- #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
-@@ -1604,7 +1581,7 @@
- $python_defines = "-DVMDPYTHON";
- $python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
- $python_library = "-L$stock_python_library_dir";
--$python_libs = "-lpython2.5 -lpthread";
-+$python_libs = "$stock_python_library -lpthread";
- @python_h = ('PythonTextInterp.h',
- 'VMDTkinterMenu.h',
- 'py_commands.h',
-@@ -2350,8 +2327,8 @@
-
- # XFree 4.0 Direct Rendering Interface and GLX
- $opengl_dep_dir = "/usr/X11R6";
-- $opengl_dep_include = "-I$opengl_dep_dir/include";
-- $opengl_dep_library = "-L$opengl_dep_dir/lib";
-+ $opengl_dep_include = "-Igentoo-opengl-include";
-+ $opengl_dep_library = "-Lgentoo-opengl-libs";
- $opengl_dep_libs = "-lGL";
- # $opengl_dep_libs = "-L/usr/X11R6/lib -lGL -lXext -lX11";
-
-@@ -2381,15 +2358,15 @@
- $arch_lopts .= "-i-static ";
- } else {
- # compling with GCC
-- $arch_cc = "gcc";
-- $arch_ccpp = "g++";
-+ $arch_cc = "gentoo-gcc";
-+ $arch_ccpp = "gentoo-g++";
- $arch_depend_flag = "-MM";
-- $arch_shld = "g++ -shared";
-+ $arch_shld = "gentoo-g++ -shared";
- $arch_shlibname = "so";
- $arch_shcppopts = "-fPIC";
-- $arch_shldopts = "";
-- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
-- $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3";
-+ $arch_shldopts = "gentoo-ldflags";
-+ $arch_opt_flag = "gentoo-cflags";
-+ $arch_copts = "gentoo-cflags";
-
- if ($config_static) {
- $arch_lopts = "-static";
-@@ -2407,14 +2384,13 @@
-
- $arch_cppopts = "";
- if ($config_cuda) {
-- $arch_nvcc = "/usr/local/cuda-4.0/bin/nvcc";
- $arch_nvccflags = "--ptxas-options=-v " .
- "-gencode arch=compute_13,code=sm_13 " .
- "-gencode arch=compute_20,code=sm_20 " .
- "-gencode arch=compute_20,code=compute_20 " .
- "--ftz=true ";
-- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
-- $cuda_library = "-L/usr/local/cuda-4.0/lib";
-+ $arch_nvccflags .= "gentoo-nvflags $cuda_include";
-+ $cuda_library = "-Lgentoo-cuda-lib";
- $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
- }
- # this is to make tcl happy
-@@ -2513,7 +2489,7 @@
-
- if ($config_cuda) {
- $arch_nvccflags .= " --machine 64 -O3 $cuda_include";
-- $cuda_library = "-L/usr/local/cuda-10.2/lib64";
-+ $cuda_library = "-Lgentoo-cuda-lib";
- }
-
- $arch_lex = "flex"; # has problems with vendor lex
-@@ -3502,11 +3478,11 @@
- DEFINES = $DEFINES
-
- # compiler and compiler directives
--CC = $arch_cc
--CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CC = gentoo-gcc
-+CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-
--CCPP = $arch_ccpp
--CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-+CCPP = gentoo-g++
-+CPPFLAGS = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
-
- NVCC = $arch_nvcc
- NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
-@@ -3555,7 +3531,7 @@
- $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX)
- \$(ECHO) "Linking " \$\@ "..."; \\
- \$(CD) $vmd_arch_dir ; \\
-- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
-+ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
- \$(COMPILERC) \$(RCFLAGS)
-
- install:
-@@ -3596,8 +3572,7 @@
- -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
- \$(CD) $vmd_bin_dir ; \\
- if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
-- if [ ! -x "/bin/csh" ]; then \\
-- \$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
-+ if [ -x "/bin/bash" ]; then \\
- \$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
- \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
- \$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
---- a/src/Makefile.old 2020-09-09 18:22:46.234818925 +0200
-+++ b/src/Makefile 2020-09-09 18:37:22.356511690 +0200
-@@ -647,7 +647,7 @@
- vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX)
- $(ECHO) "Linking " $@ "..."; \
- $(CD) ../LINUXAMD64 ; \
-- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
-+ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
- $(COMPILERC) $(RCFLAGS)
-
- install:
-@@ -660,10 +660,6 @@
- if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
- $(MAKEDIR) "/usr/local/lib/vmd"/doc; \
- fi
-- -$(COPY) ../Announcement "/usr/local/lib/vmd"
-- -$(COPY) ../README "/usr/local/lib/vmd"
-- -$(COPY) ../LICENSE "/usr/local/lib/vmd"
-- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc
- if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
- $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
- -$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch b/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
deleted file mode 100644
index 295811db058..00000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4-tmpdir.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/scripts/vmd/chemical2vmd.old 2020-09-09 18:40:56.795215443 +0200
-+++ b/scripts/vmd/chemical2vmd 2020-09-09 18:41:09.648348701 +0200
-@@ -61,7 +61,7 @@
-
-
- # Make a temp. file to store the load command
--$ENV{'TMPDIR'} = '/usr/tmp' if !$ENV{'TMPDIR'};
-+$ENV{'TMPDIR'} = '/tmp' if !$ENV{'TMPDIR'};
- sub tmpfile {
- local ($tempfile) = $ENV{'TMPDIR'} . '/chemical2vmd.' . $$;
- local ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
deleted file mode 100644
index 417828a3209..00000000000
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ /dev/null
@@ -1,277 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-
-MY_PV="${PV/_alpha/a}"
-MY_P="${PN}-${MY_PV}"
-SRC_URI="
- ${MY_P}.src.tar
- https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz
- https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch
-"
-
-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"
-
-CDEPEND="
- >=dev-lang/tk-8.6.1:0=
- dev-lang/perl
- dev-libs/expat
- $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_MULTI_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="${CDEPEND}
- sci-biology/stride
- sci-chemistry/chemical-mime-data
- sci-chemistry/surf
- x11-terms/xterm
- msms? ( sci-chemistry/msms-bin )
- povray? ( media-gfx/povray )
-"
-
-S="${WORKDIR}/${MY_P}"
-
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-# Binary only plugin!!
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"
-
-pkg_nofetch() {
- elog "Please download ${MY_P}.src.tar from"
- elog "${VMD_DOWNLOAD}"
- elog "after agreeing to the license and get"
- elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz"
- elog "https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch"
- elog "Place them 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 "to ${MY_P}.src.tar"
-}
-
-src_prepare() {
- # Apply user patches from ${WORKDIR} to allow patching on patches
- # subdir too
- cd "${WORKDIR}"
- xdg_src_prepare
-
- # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
- # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
- eapply "${DISTDIR}"/${PN}-1.9.4-gentoo-plugins.patch
-
- use cuda && cuda_sanitize
-
- # Prepare plugins
- cd plugins || die
-
- 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 "${FILESDIR}"/${PN}-1.9.4-gentoo-paths.patch
-
- # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
- eapply "${FILESDIR}"/${PN}-1.9.4-tmpdir.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
- # Open PDB files with VMD
- echo "MimeType=chemical/x-pdb;" >> "${WORKDIR}"/vmd.desktop || die
- domenu "${WORKDIR}"/vmd.desktop
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
end of thread, other threads:[~2021-05-02 19:22 UTC | newest]
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2020-03-08 18:47 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/ Pacho Ramos
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2021-05-02 19:22 Pacho Ramos
2020-09-19 12:29 Michał Górny
2020-09-09 17:03 Pacho Ramos
2019-12-15 15:31 Pacho Ramos
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