[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
