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277 lines
11 KiB
277 lines
11 KiB
--- a/bin/vmd.sh.old 2020-09-09 18:02:09.135798193 +0200
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+++ b/bin/vmd.sh 2020-09-09 18:37:22.355511675 +0200
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@@ -436,6 +436,7 @@
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# set the path to a few external programs
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# Stride -- used to generate cartoon representations etc.
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+export STRIDE_BIN="gentoo-stride"
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if [ -z "$STRIDE_BIN" ]
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then
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if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
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@@ -446,6 +447,7 @@
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fi
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# Surf -- used to generate molecular surfaces
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+export SURF_BIN="gentoo-surf"
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if [ -z "$SURF_BIN" ]
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then
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if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
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@@ -456,6 +458,7 @@
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fi
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# Tachyon -- used to generate ray traced graphics
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+export TACHYON_BIN="gentoo-tachyon"
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if [ -z "$TACHYON_BIN" ]
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then
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if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
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--- a/configure.old 2020-09-09 18:05:55.778655084 +0200
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+++ b/configure 2020-09-09 18:38:01.607083112 +0200
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@@ -13,11 +13,10 @@
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$install_name = "vmd";
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# Directory where VMD startup script is installed, should be in users' paths.
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-$install_bin_dir="/usr/local/bin";
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+$install_bin_dir="gentoo-bindir";
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# Directory where VMD files and executables are installed
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-$install_library_dir="/usr/local/lib/$install_name";
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-
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+$install_library_dir="gentoo-libdir/$install_name";
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# optionally override hard-coded defaults above with environment variables
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if ($ENV{VMDINSTALLNAME}) {
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@@ -143,29 +142,6 @@
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# Configure script code begins here
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############################################################################
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-## Test for existence of a properly compiled plugin tree
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-if (!(-e "plugins")) {
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- print "\n";
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- print "VMD plugin directory not found.\n";
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- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
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- print "into a 'plugins' directory linked or located in this directory.\n";
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- print "Be sure your PLUGINDIR environment variable is set before running\n";
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- print "'make distrib' in the plugin build area.\n";
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- print "\n";
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- die "Halting configuration until VMD plugins are built.\n";
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-} else {
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- if (!(-e "plugins/include/vmdplugin.h")) {
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- print "\n";
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- print "VMD plugin include files or directory not found.\n";
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- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
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- print "into a 'plugins' directory linked or located in this directory.\n";
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- print "Be sure your PLUGINDIR environment variable is set before running\n";
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- print "'make distrib' in the plugin build area.\n";
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- print "\n";
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- die "Halting configuration until VMD plugins are built.\n";
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- }
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-}
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-
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#################### Parse command line options ###########
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# list of allowed architectures
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@archlist=('AIX6_64', 'ANDROIDARMV7A', 'BLUEGENEQ', 'BLUEWATERS', 'CRAY_XC', 'CRAY_XK', 'FREEBSD', 'FREEBSDAMD64', 'LINUX', 'LINUXAMD64', 'LINUXARM64', 'LINUXCARMA', 'LINUXPPC64', 'MACOSX', 'MACOSXX86', 'MACOSXX86_64', 'OPENPOWER', 'SUMMIT', 'SUMMITDEV', 'SOLARIS2', 'SOLARIS2_64', 'SOLARISX86', 'SOLARISX86_64', 'WIN32', 'WIN64');
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@@ -493,7 +469,7 @@
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$arch_cc = "cc";
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$arch_ccpp = "CC";
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-$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc";
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+$arch_nvcc = "gentoo-nvcc";
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$arch_nvccflags = "-lineinfo --ptxas-options=-v " .
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"-gencode arch=compute_30,code=compute_30 " .
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"-gencode arch=compute_30,code=sm_35 " .
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@@ -537,7 +513,7 @@
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################ Plugin options
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#
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-$plugin_dir = "../plugins";
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+$plugin_dir = "gentoo-plugindir";
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$plugin_include = "-I$plugin_dir/include";
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$plugin_library = "";
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$plugin_libs = "";
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@@ -550,7 +526,7 @@
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@plugin_extra = ();
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if ($config_staticplugin) {
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- $molfile_dir = "$plugin_dir/$config_arch/molfile";
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+ $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
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$plugin_include .= " -I$molfile_dir";
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$plugin_library .= " -L$molfile_dir";
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$plugin_libs .= " -lmolfile_plugin";
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@@ -715,8 +691,8 @@
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################ FLTK GUI
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$fltk_defines = "-DVMDGUI -DVMDFLTK";
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$fltk_dir = "$vmd_library_dir/fltk";
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-$fltk_include = "-I$fltk_dir/include";
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-$fltk_library = "-L$fltk_dir/$config_arch";
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+$fltk_include = "-Igentoo-fltk-include";
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+$fltk_library = "-Lgentoo-fltk-libs";
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$fltk_libs = "-lfltk -lX11";
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#@fltk_cc = ('forms_ui.c');
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@fltk_cu = ();
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@@ -777,8 +753,8 @@
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if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; }
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$tcl_library = "-L$stock_tcl_library_dir";
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if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; }
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-$tcl_libs = "-ltcl8.5";
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-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; }
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+$tcl_libs = "-ltcl";
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+if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
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@tcl_cc = ();
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@tcl_cu = ();
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@@ -1289,8 +1265,8 @@
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# This may be commented out if not required.
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$libtachyon_defines = "-DVMDLIBTACHYON";
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$libtachyon_dir = "$vmd_library_dir/tachyon";
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-$libtachyon_include = "-I$libtachyon_dir/include";
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-$libtachyon_library = "-L$libtachyon_dir/lib_$config_arch";
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+$libtachyon_include = "-Igentoo-libtachyon-include";
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+$libtachyon_library = "-Lgentoo-libtachyon-libs";
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$libtachyon_libs = "-ltachyon";
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@libtachyon_cc = ();
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@libtachyon_cu = ();
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@@ -1541,8 +1517,8 @@
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#######################
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$netcdf_defines = "";
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$netcdf_dir = "$vmd_library_dir/netcdf";
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-$netcdf_include = "-I$netcdf_dir/include";
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-$netcdf_library = "-L$netcdf_dir/lib_$config_arch";
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+$netcdf_include = "-Igentoo-netcdf-include";
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+$netcdf_library = "-Lgentoo-netcdf-libs";
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$netcdf_libs = "-lnetcdf";
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@netcdf_cc = ();
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@netcdf_cu = ();
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@@ -1595,6 +1571,7 @@
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#$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib";
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$stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "$vmd_library_dir/python/lib_$config_arch/include/python2.5";
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$stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
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+$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
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#$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
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#$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
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@@ -1604,7 +1581,7 @@
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$python_defines = "-DVMDPYTHON";
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$python_include = "-I$stock_python_include_dir -I$stock_numpy_include_dir -I$stock_numpy_library_dir";
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$python_library = "-L$stock_python_library_dir";
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-$python_libs = "-lpython2.5 -lpthread";
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+$python_libs = "$stock_python_library -lpthread";
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@python_h = ('PythonTextInterp.h',
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'VMDTkinterMenu.h',
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'py_commands.h',
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@@ -2350,8 +2327,8 @@
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# XFree 4.0 Direct Rendering Interface and GLX
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$opengl_dep_dir = "/usr/X11R6";
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- $opengl_dep_include = "-I$opengl_dep_dir/include";
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- $opengl_dep_library = "-L$opengl_dep_dir/lib";
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+ $opengl_dep_include = "-Igentoo-opengl-include";
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+ $opengl_dep_library = "-Lgentoo-opengl-libs";
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$opengl_dep_libs = "-lGL";
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# $opengl_dep_libs = "-L/usr/X11R6/lib -lGL -lXext -lX11";
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@@ -2381,15 +2358,15 @@
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$arch_lopts .= "-i-static ";
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} else {
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# compling with GCC
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- $arch_cc = "gcc";
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- $arch_ccpp = "g++";
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+ $arch_cc = "gentoo-gcc";
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+ $arch_ccpp = "gentoo-g++";
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$arch_depend_flag = "-MM";
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- $arch_shld = "g++ -shared";
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+ $arch_shld = "gentoo-g++ -shared";
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$arch_shlibname = "so";
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$arch_shcppopts = "-fPIC";
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- $arch_shldopts = "";
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- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
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- $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3";
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+ $arch_shldopts = "gentoo-ldflags";
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+ $arch_opt_flag = "gentoo-cflags";
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+ $arch_copts = "gentoo-cflags";
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if ($config_static) {
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$arch_lopts = "-static";
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@@ -2407,14 +2384,13 @@
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$arch_cppopts = "";
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if ($config_cuda) {
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- $arch_nvcc = "/usr/local/cuda-4.0/bin/nvcc";
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$arch_nvccflags = "--ptxas-options=-v " .
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"-gencode arch=compute_13,code=sm_13 " .
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"-gencode arch=compute_20,code=sm_20 " .
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"-gencode arch=compute_20,code=compute_20 " .
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"--ftz=true ";
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- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
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- $cuda_library = "-L/usr/local/cuda-4.0/lib";
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+ $arch_nvccflags .= "gentoo-nvflags $cuda_include";
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+ $cuda_library = "-Lgentoo-cuda-lib";
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$cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
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}
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# this is to make tcl happy
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@@ -2513,7 +2489,7 @@
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if ($config_cuda) {
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$arch_nvccflags .= " --machine 64 -O3 $cuda_include";
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- $cuda_library = "-L/usr/local/cuda-10.2/lib64";
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+ $cuda_library = "-Lgentoo-cuda-lib";
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}
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$arch_lex = "flex"; # has problems with vendor lex
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@@ -3502,11 +3478,11 @@
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DEFINES = $DEFINES
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# compiler and compiler directives
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-CC = $arch_cc
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-CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
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+CC = gentoo-gcc
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+CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
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-CCPP = $arch_ccpp
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-CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
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+CCPP = gentoo-g++
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+CPPFLAGS = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
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NVCC = $arch_nvcc
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NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
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@@ -3555,7 +3531,7 @@
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$config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX)
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\$(ECHO) "Linking " \$\@ "..."; \\
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\$(CD) $vmd_arch_dir ; \\
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- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
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+ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
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\$(COMPILERC) \$(RCFLAGS)
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install:
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@@ -3596,8 +3572,7 @@
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-\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
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\$(CD) $vmd_bin_dir ; \\
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if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
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- if [ ! -x "/bin/csh" ]; then \\
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- \$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
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+ if [ -x "/bin/bash" ]; then \\
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\$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
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\$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
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\$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
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--- a/src/Makefile.old 2020-09-09 18:22:46.234818925 +0200
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+++ b/src/Makefile 2020-09-09 18:37:22.356511690 +0200
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@@ -647,7 +647,7 @@
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vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX)
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$(ECHO) "Linking " $@ "..."; \
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$(CD) ../LINUXAMD64 ; \
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- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
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+ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
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$(COMPILERC) $(RCFLAGS)
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install:
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@@ -660,10 +660,6 @@
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if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
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$(MAKEDIR) "/usr/local/lib/vmd"/doc; \
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fi
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- -$(COPY) ../Announcement "/usr/local/lib/vmd"
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- -$(COPY) ../README "/usr/local/lib/vmd"
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- -$(COPY) ../LICENSE "/usr/local/lib/vmd"
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- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc
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if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
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$(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
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-$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
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