[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
commit: 805bb1f5f38626dad04b06629c0ef515c3a2 Author: Pacho Ramos gentoo org> AuthorDate: Sun Mar 8 18:46:56 2020 + Commit: Pacho Ramos gentoo org> CommitDate: Sun Mar 8 18:46:56 2020 + 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 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 000..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 + // John Stone +@@ -48,7 +51,7 @@ + #include + + // +-// 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 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*)input), ++ thrust::device_ptr((myuint2*)input + numElements), ++ thrust::device_ptr((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, unsig
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
commit: 4c03ac229acd7c3f5fd7aa110148ac5172268d4e Author: Pacho Ramos gentoo org> AuthorDate: Sun Dec 15 15:31:06 2019 + Commit: Pacho Ramos gentoo org> CommitDate: Sun Dec 15 15:31:29 2019 + 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 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 000..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 05:46:34.0 +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 19:30:23.0 +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 ($i); diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild new file mode 100644 index 000..02ad806afbe --- /dev/null +++ b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild @@ -0,0 +1,266 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +PYTHON_COMPAT=( python2_7 ) + +inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg + +DESCRIPTION="Visual Molecular Dynamics" +HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"; +SRC_URI=" + https://dev.gentoo.org/~jlec/distfiles/${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
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
commit: 8c9499c1d811547d4d69f60d5b78ae7edacdd922 Author: Pacho Ramos gentoo org> AuthorDate: Sun May 2 19:22:03 2021 + Commit: Pacho Ramos gentoo org> CommitDate: Sun May 2 19:22:23 2021 + 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 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..000 --- 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.old2020-09-09 18:05:55.778655084 +0200 -+++ b/configure2020-09-09 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 c
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
commit: 8790988057a312f5e5cfa1d6f0acf4c681619321 Author: Pacho Ramos gentoo org> AuthorDate: Wed Sep 9 17:03:02 2020 + Commit: Pacho Ramos gentoo org> CommitDate: Wed Sep 9 17:03:02 2020 + 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 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 000..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.old2020-09-09 18:05:55.778655084 +0200 b/configure2020-09-09 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', 'LIN
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/files/, sci-chemistry/vmd/
commit: 644a181b8ab3d796f3a489edc77bf21be545e05f Author: Michał Górny gentoo org> AuthorDate: Sat Sep 19 11:49:58 2020 + Commit: Michał Górny gentoo org> CommitDate: Sat Sep 19 12:29:09 2020 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=644a181b sci-chemistry/vmd: Remove old Signed-off-by: Michał Górny 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..000 --- a/sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch +++ /dev/null @@ -1,13 +0,0 @@ a/configure.old2019-05-16 17:26:05.347560700 +0200 -+++ b/configure2019-05-16 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..000 --- 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 - // John Stone -@@ -48,7 +51,7 @@ - #include - - // --// Restrict macro