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.kr...@visus.uni-stuttgart.de>
- // John Stone <jo...@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
-}
