fix hardcoded stuff in VMD configure script
authors: Stephane Thiell (Stanford University), Kenneth Hoste (HPC-UGent)
--- vmd-1.9.3/configure.orig	2016-12-01 08:11:33.000000000 +0100
+++ vmd-1.9.3/configure	2017-03-23 13:36:41.501910996 +0100
@@ -466,7 +476,7 @@
 
 $arch_cc          = "cc";
 $arch_ccpp        = "CC";
-$arch_nvcc        = "/usr/local/cuda-8.0/bin/nvcc";
+$arch_nvcc        = "nvcc";
 $arch_nvccflags   = "--ptxas-options=-v " . 
                     "-gencode arch=compute_30,code=compute_30 " .
                     "-gencode arch=compute_30,code=sm_35 " .
@@ -581,17 +591,17 @@
 # location of Mesa library and include files; basically does the same
 # as OpenGL.  This is based on the default instructions from the Mesa
 # README; the include files should by default be in /usr/local/include/GL.
-$mesa_dir         = "$vmd_library_dir/Mesa";
+$mesa_dir         = $ENV{'EBROOTMESA'};
 $mesa_include     = "-I$mesa_dir/include";
 $mesa_library     = "-L$mesa_dir/lib_$config_arch";
 #$mesa_libs        = "-lMesaGL -lMesaGLU"; 
-$mesa_libs        = "-lMesaGL"; 
+$mesa_libs        = "-lGL -lGLU";
 $mesa_defines     = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL";
 @mesa_cc          = ();
 @mesa_cu          = ();
-@mesa_ccpp        = @opengl_ccpp;
-@mesa_h           = @opengl_h;
-@mesa_extra       = @opengl_extra;
+@mesa_ccpp        = ();
+@mesa_h           = ();
+@mesa_extra       = ();
 
 
 #
@@ -666,10 +676,10 @@
 
 ################ FLTK GUI
 $fltk_defines     = "-DVMDGUI -DVMDFLTK";
-$fltk_dir         = "$vmd_library_dir/fltk";
+$fltk_dir         = $ENV{'EBROOTFLTK'};
 $fltk_include     = "-I$fltk_dir/include";
 $fltk_library     = "-L$fltk_dir/$config_arch";
-$fltk_libs        = "-lfltk -lX11";
+$fltk_libs        = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama";
 #@fltk_cc          = ('forms_ui.c');
 @fltk_cu          = ();
 @fltk_ccpp        = ( 'ColorFltkMenu.C',
@@ -729,8 +739,8 @@
 if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
 $tcl_library      = "-L$stock_tcl_library_dir";
 if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
-$tcl_libs         = "-ltcl8.5";  
-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
+$tcl_libs         = "-ltcl8.6";  
+if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; }
 
 @tcl_cc           = ();
 @tcl_cu           = ();
@@ -922,7 +932,7 @@
 #   This option enables the use of CUDA GPU acceleration functions.
 #######################
 $cuda_defines     = "-DVMDCUDA -DMSMPOT_CUDA";
-$cuda_dir         = "/usr/local/cuda-8.0";
+$cuda_dir         = "$CUDA_HOME";
 $cuda_include     = "";
 $cuda_library     = "";
 $cuda_libs        = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static";
@@ -1042,7 +1052,7 @@
 # $liboptix_dir         = "/usr/local/encap/NVIDIA-OptiX-SDK-3.6.3-linux64";
 # $liboptix_dir         = "/usr/local/encap/NVIDIA-OptiX-SDK-3.8.0-linux64";
 # $liboptix_dir         = "/usr/local/encap/NVIDIA-OptiX-SDK-3.9.0-linux64";
-$liboptix_dir         = "/usr/local/encap/NVIDIA-OptiX-SDK-4.0.1-linux64";
+$liboptix_dir         = "$ENV{'EBROOTOPTIX'}";
 # NCSA Blue Waters
 # $liboptix_dir         = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.6.3-linux64";
 # $liboptix_dir         = "/u/sciteam/stonej/local/NVIDIA-OptiX-SDK-3.8.0-linux64";
@@ -1310,8 +1320,8 @@
 #######################
 $actc_defines     = "-DVMDACTC";
 $actc_dir         = "$vmd_library_dir/actc";
-$actc_include     = "-I$actc_dir/include";
-$actc_library     = "-L$actc_dir/lib_$config_arch";
+$actc_include     = "-I$actc_dir";
+$actc_library     = "-L$actc_dir";
 $actc_libs        = "-lactc";
 @actc_cc          = ();
 @actc_cu          = ();
@@ -1388,7 +1398,7 @@
 $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',
@@ -2173,7 +2183,7 @@
 
       if ($config_static) {
         $arch_lopts       = "-static";
-        $mesa_libs        = "-lMesaGL -L/usr/X11R6/lib -lXext -lX11";
+        $mesa_libs        = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11";
       } else {
         $arch_lopts       = "";
        # -rpath causes problems for people running Chromium..
@@ -2303,7 +2313,7 @@
     # they likely serve no useful purpose going forward.
     if (!$config_opengl_dispatch) {
       $opengl_dep_libs	= "-L/usr/X11R6/lib64 -lGL -lX11";
-      $mesa_libs          = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11";
+      $mesa_libs          = "-lGL -lGLU -L/usr/X11R6/lib64 -lXext -lX11";
     }
 
     # this is to make tcl happy
