Software/VMD: vmd-1.9.3_configure.patch

--- vmd-1.9.3/configure 2017-04-19 14:50:19.592820000 +0200
@@ -459,14 +459,14 @@
 $arch_echo        = "echo";
 $arch_tar         = "tar";
 $arch_compress    = "compress";
-$arch_gnucompress = "/usr/local/bin/gzip";
+$arch_gnucompress = "gzip";
 $arch_latex       = "latex";
 $arch_compilerc   = $arch_echo;
 $arch_rcflags     = "No resource compiler required on this platform.";
 
 $arch_cc          = "cc";
 $arch_ccpp        = "CC";
-$arch_nvcc        = "/usr/local/cuda-8.0/bin/nvcc";
+$arch_nvcc        = "nvcc";
 $arch_nvccflags   = "--ptxas-options=-v " . 
                     "-gencode arch=compute_30,code=compute_30 " .
                     "-gencode arch=compute_30,code=sm_35 " .
@@ -508,9 +508,9 @@
 ################ Plugin options
 #
 $plugin_dir    = "../plugins";
-$plugin_include = "-I$plugin_dir/include";
-$plugin_library = "";
-$plugin_libs    = "";
+$plugin_include = "-I$plugin_dir/include -I$ENV{EBROOTEXPAT}/include";
+$plugin_library = "-L$ENV{EBROOTEXPAT}/lib";
+$plugin_libs    = "-lexpat";
 $plugin_defines = "";
 @plugin_cc      = ();
 @plugin_cu      = ();
@@ -538,8 +538,8 @@
 # OpenGL libraries. Note that these options require -I and -L in front of
 # the include and library directory names
 $opengl_dep_dir         = "";
-$opengl_dep_include     = "";
-$opengl_dep_library     = "";
+$opengl_dep_include     = "-I/usr/include/GL";
+$opengl_dep_library     = "-L/usr/lib64/nvidia";
 if ($config_opengl_dispatch) {
   # version of OpenGL libs that can do dispatch, allowing use of 
   # EGL for window management, but full GL or GLES etc for drawing
@@ -645,9 +645,9 @@
 #
 # FLTK-based OpenGL graphics windows 
 #
-$fltkopengl_dir         = "";
-$fltkopengl_include     = "";
-$fltkopengl_library     = "";
+$fltkopengl_dir         = $ENV{EBROOTFLTK};
+$fltkopengl_include     = "-I$fltkopengl_dir/include";
+$fltkopengl_library     = "-L$fltkopengl_dir/lib";
 if ($config_arch eq "MACOSX" ||
     $config_arch eq "MACOSXX86" || 
     $config_arch eq "MACOSXX86_64") {
@@ -667,9 +667,9 @@
 ################ FLTK GUI
 $fltk_defines     = "-DVMDGUI -DVMDFLTK";
 $fltk_dir         = "$vmd_library_dir/fltk";
-$fltk_include     = "-I$fltk_dir/include";
-$fltk_library     = "-L$fltk_dir/$config_arch";
-$fltk_libs        = "-lfltk -lX11";
+$fltk_include     = "-I$fltk_dir/include -I$ENV{EBROOTX11}/include -I$ENV{EBROOTFONTCONFIG}/include";
+$fltk_library     = "-L$fltk_dir/$config_arch -L$ENV{EBROOTX11}/lib -L$ENV{EBROOTFONTCONFIG}/lib";
+$fltk_libs        = "-lfltk -lX11 -lXfixes -lXext -lXrender -lXcursor -lXinerama -lXft -lfontconfig";
 #@fltk_cc          = ('forms_ui.c');
 @fltk_cu          = ();
 @fltk_ccpp        = ( 'ColorFltkMenu.C',
@@ -922,10 +922,10 @@
 #   This option enables the use of CUDA GPU acceleration functions.
 #######################
 $cuda_defines     = "-DVMDCUDA -DMSMPOT_CUDA";
-$cuda_dir         = "/usr/local/cuda-8.0";
-$cuda_include     = "";
-$cuda_library     = "";
-$cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static";
+$cuda_dir         = $ENV{EBROOTCUDA};
+$cuda_include     = "-I$cuda_dir/include";
+$cuda_library     = "-L$cuda_dir/lib64";
+$cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static -lrt";
 @cuda_cc          = ();
 @cuda_cu         = ('msmpot_cuda.cu',
                      'msmpot_cuda_latcut.cu',
@@ -1079,9 +1079,9 @@
 } else {
   $libospray_defines     = "-DVMDLIBOSPRAY ";
 }
-$libospray_dir         = "/usr/local/ospray-1.1.1.x86_64.linux";
-$libospray_include     = "-I$libospray_dir/include -I$libospray_dir/ospray/include ";
-$libospray_library     = "-L$libospray_dir/lib ";
+$libospray_dir         = $ENV{EBROOTOSPRAY};
+$libospray_include     = "-I$libospray_dir/include -I$libospray_dir/include/ospray -I$ENV{EBROOTEMBREE}/include -I$ENV{EBROOTEMBREE}/include/embree -I$ENV{EBROOTTBB}/tbb/include -I$ENV{EBROOTTBB}/tbb/include/tbb";
+$libospray_library     = "-L$libospray_dir/lib64 -L$ENV{EBROOTEMBREE}/lib64 -L$ENV{EBROOTTBB}/tbb/lib";
 $libospray_libs        = "-lospray -lospray_common -lembree -ltbb -ltbbmalloc ";
 # Both OptiX and OSPRay renderers use the Tachyon glwin code, 
 # so we have to make sure we don't build/link it twice
@@ -1119,9 +1119,9 @@
 # OPTIONAL COMPONENT: PNG image I/O
 # This may be commented out if not required.
 $libpng_defines     = "-DVMDLIBPNG";
-$libpng_dir         = "";
-$libpng_include     = "";
-$libpng_library     = "";
+$libpng_dir         = $ENV{EBROOTLIBPNG};
+$libpng_include     = "-I$libpng_dir/include";
+$libpng_library     = "-L$libpng_dir/lib -L$ENV{EBROOTZLIB}";
 $libpng_libs        = "-lpng -lz";
 @libpng_cc          = ();
 @libpng_cu          = ();
@@ -1159,9 +1159,9 @@
 # OPTIONAL COMPONENT: Xinerama full-screen mode handling support
 # This may be commented out if not required.
 $xinerama_defines     = "-DVMDXINERAMA";
-$xinerama_dir         = "";
-$xinerama_include     = "";
-$xinerama_library     = "";
+$xinerama_dir         = $ENV{EBROOTX11};
+$xinerama_include     = "-I$xinerama_dir/include";
+$xinerama_library     = "-L$xinerama_dir/lib";
 $xinerama_libs        = "-lXinerama";
 @xinerama_cc          = ();
 @xinerama_cu          = ();
@@ -1172,9 +1172,9 @@
 # OPTIONAL COMPONENT: XInput based Spaceball, Dial box 6DOF input support
 # This may be commented out if not required.
 $xinput_defines     = "-DVMDXINPUT";
-$xinput_dir         = "";
-$xinput_include     = "";
-$xinput_library     = "";
+$xinput_dir         = $ENV{EBROOTX11};
+$xinput_include     = "-I$xinput_dir/include";
+$xinput_library     = "-L$xinput_dir/lib";
 $xinput_libs        = "-lXi";
 @xinput_cc          = ();
 @xinput_cu          = ();
@@ -1377,18 +1377,18 @@
 # If left blank, standard system  directories will be searched.
 #$stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "/usr/local/include";
 #$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
-$stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
-$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
+$stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.7";
+$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.7/config";
 
 #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
 #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
 $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$vmd_library_dir/numpy/lib_$config_arch/include";
-$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include";
+$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.7/site-packages/numpy/core/include";
 
 $python_defines     = "-DVMDPYTHON";
 $python_include     = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
 $python_library     = "-L$stock_python_library_dir";
-$python_libs        = "-lpython2.5 -lpthread";
+$python_libs        = "-lpython2.7 -lpthread";
 @python_h           = ('PythonTextInterp.h',
                        'VMDTkinterMenu.h',
                       'py_commands.h',