diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/vmd/Manifest | 1 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.3-configure-libtachyon.patch | 13 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.3-cuda.patch | 426 | ||||
| -rw-r--r-- | sci-chemistry/vmd/files/vmd-1.9.3-tmpdir.patch | 22 | ||||
| -rw-r--r-- | sci-chemistry/vmd/vmd-1.9.3-r5.ebuild | 272 |
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 -} |