sci-chemistry/vmd: Remove old

Signed-off-by: Michał Górny <mgorny@gentoo.org>

5 files changed, 0 insertions, 734 deletions

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 62f7ae61617b..f2c96b248550 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 b71cd97210a8..000000000000
--- 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 258efb777caf..000000000000
--- 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 22712abf30b8..000000000000
--- 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 ($i);
diff --git a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
deleted file mode 100644
index a4e0e6db49b0..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.3-r5.ebuild
+++ /dev/null
@@ -1,272 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python2_7 )
-
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${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
-}