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-rw-r--r--sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch276
1 files changed, 276 insertions, 0 deletions
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
new file mode 100644
index 000000000000..ca74b868d8f4
--- /dev/null
+++ b/sci-chemistry/vmd/files/vmd-1.9.4-gentoo-paths.patch
@@ -0,0 +1,276 @@
+--- a/bin/vmd.sh.old 2020-09-09 18:02:09.135798193 +0200
++++ b/bin/vmd.sh 2020-09-09 18:37:22.355511675 +0200
+@@ -436,6 +436,7 @@
+
+ # set the path to a few external programs
+ # Stride -- used to generate cartoon representations etc.
++export STRIDE_BIN="gentoo-stride"
+ if [ -z "$STRIDE_BIN" ]
+ then
+ if [ -x "$MASTERVMDDIR/stride_$ARCH" ]
+@@ -446,6 +447,7 @@
+ fi
+
+ # Surf -- used to generate molecular surfaces
++export SURF_BIN="gentoo-surf"
+ if [ -z "$SURF_BIN" ]
+ then
+ if [ -x "$MASTERVMDDIR/surf_$ARCH" ]
+@@ -456,6 +458,7 @@
+ fi
+
+ # Tachyon -- used to generate ray traced graphics
++export TACHYON_BIN="gentoo-tachyon"
+ if [ -z "$TACHYON_BIN" ]
+ then
+ if [ -x "$MASTERVMDDIR/tachyon_$ARCH" ]
+--- a/configure.old 2020-09-09 18:05:55.778655084 +0200
++++ b/configure 2020-09-09 18:38:01.607083112 +0200
+@@ -13,11 +13,10 @@
+ $install_name = "vmd";
+
+ # Directory where VMD startup script is installed, should be in users' paths.
+-$install_bin_dir="/usr/local/bin";
++$install_bin_dir="gentoo-bindir";
+
+ # Directory where VMD files and executables are installed
+-$install_library_dir="/usr/local/lib/$install_name";
+-
++$install_library_dir="gentoo-libdir/$install_name";
+
+ # optionally override hard-coded defaults above with environment variables
+ if ($ENV{VMDINSTALLNAME}) {
+@@ -143,29 +142,6 @@
+ # Configure script code begins here
+ ############################################################################
+
+-## Test for existence of a properly compiled plugin tree
+-if (!(-e "plugins")) {
+- print "\n";
+- print "VMD plugin directory not found.\n";
+- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+- print "into a 'plugins' directory linked or located in this directory.\n";
+- print "Be sure your PLUGINDIR environment variable is set before running\n";
+- print "'make distrib' in the plugin build area.\n";
+- print "\n";
+- die "Halting configuration until VMD plugins are built.\n";
+-} else {
+- if (!(-e "plugins/include/vmdplugin.h")) {
+- print "\n";
+- print "VMD plugin include files or directory not found.\n";
+- print "Please compile the VMD plugins and do 'make distrib' to copy them\n";
+- print "into a 'plugins' directory linked or located in this directory.\n";
+- print "Be sure your PLUGINDIR environment variable is set before running\n";
+- print "'make distrib' in the plugin build area.\n";
+- print "\n";
+- die "Halting configuration until VMD plugins are built.\n";
+- }
+-}
+-
+ #################### Parse command line options ###########
+ # list of allowed architectures
+ @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');
+@@ -493,7 +469,7 @@
+
+ $arch_cc = "cc";
+ $arch_ccpp = "CC";
+-$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc";
++$arch_nvcc = "gentoo-nvcc";
+ $arch_nvccflags = "-lineinfo --ptxas-options=-v " .
+ "-gencode arch=compute_30,code=compute_30 " .
+ "-gencode arch=compute_30,code=sm_35 " .
+@@ -537,7 +513,7 @@
+
+ ################ Plugin options
+ #
+-$plugin_dir = "../plugins";
++$plugin_dir = "gentoo-plugindir";
+ $plugin_include = "-I$plugin_dir/include";
+ $plugin_library = "";
+ $plugin_libs = "";
+@@ -550,7 +526,7 @@
+ @plugin_extra = ();
+
+ if ($config_staticplugin) {
+- $molfile_dir = "$plugin_dir/$config_arch/molfile";
++ $molfile_dir = "$plugin_dir/compile/lib_LINUX/molfile";
+ $plugin_include .= " -I$molfile_dir";
+ $plugin_library .= " -L$molfile_dir";
+ $plugin_libs .= " -lmolfile_plugin";
+@@ -715,8 +691,8 @@
+ ################ 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_include = "-Igentoo-fltk-include";
++$fltk_library = "-Lgentoo-fltk-libs";
+ $fltk_libs = "-lfltk -lX11";
+ #@fltk_cc = ('forms_ui.c');
+ @fltk_cu = ();
+@@ -777,8 +753,8 @@
+ if ($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 = "-ltcl";
++if ($config_tk) { $tcl_libs = "-ltk -lX11 " . $tcl_libs; }
+
+ @tcl_cc = ();
+ @tcl_cu = ();
+@@ -1289,8 +1265,8 @@
+ # 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 = ();
+@@ -1541,8 +1517,8 @@
+ #######################
+ $netcdf_defines = "";
+ $netcdf_dir = "$vmd_library_dir/netcdf";
+-$netcdf_include = "-I$netcdf_dir/include";
+-$netcdf_library = "-L$netcdf_dir/lib_$config_arch";
++$netcdf_include = "-Igentoo-netcdf-include";
++$netcdf_library = "-Lgentoo-netcdf-libs";
+ $netcdf_libs = "-lnetcdf";
+ @netcdf_cc = ();
+ @netcdf_cu = ();
+@@ -1595,6 +1571,7 @@
+ #$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";
++$stock_python_library=$ENV{"PYTHON_LIBRARY"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/config";
+
+ #$stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "/usr/local/include";
+ #$stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib";
+@@ -1604,7 +1581,7 @@
+ $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 = "$stock_python_library -lpthread";
+ @python_h = ('PythonTextInterp.h',
+ 'VMDTkinterMenu.h',
+ 'py_commands.h',
+@@ -2350,8 +2327,8 @@
+
+ # XFree 4.0 Direct Rendering Interface and GLX
+ $opengl_dep_dir = "/usr/X11R6";
+- $opengl_dep_include = "-I$opengl_dep_dir/include";
+- $opengl_dep_library = "-L$opengl_dep_dir/lib";
++ $opengl_dep_include = "-Igentoo-opengl-include";
++ $opengl_dep_library = "-Lgentoo-opengl-libs";
+ $opengl_dep_libs = "-lGL";
+ # $opengl_dep_libs = "-L/usr/X11R6/lib -lGL -lXext -lX11";
+
+@@ -2381,15 +2358,15 @@
+ $arch_lopts .= "-i-static ";
+ } else {
+ # compling with GCC
+- $arch_cc = "gcc";
+- $arch_ccpp = "g++";
++ $arch_cc = "gentoo-gcc";
++ $arch_ccpp = "gentoo-g++";
+ $arch_depend_flag = "-MM";
+- $arch_shld = "g++ -shared";
++ $arch_shld = "gentoo-g++ -shared";
+ $arch_shlibname = "so";
+ $arch_shcppopts = "-fPIC";
+- $arch_shldopts = "";
+- $arch_opt_flag = "-m32 -fno-for-scope -Wno-deprecated -Wall -Wno-unknown-pragmas -O3";
+- $arch_copts = "-m32 -Wall -Wno-unknown-pragmas -O3";
++ $arch_shldopts = "gentoo-ldflags";
++ $arch_opt_flag = "gentoo-cflags";
++ $arch_copts = "gentoo-cflags";
+
+ if ($config_static) {
+ $arch_lopts = "-static";
+@@ -2407,14 +2384,13 @@
+
+ $arch_cppopts = "";
+ if ($config_cuda) {
+- $arch_nvcc = "/usr/local/cuda-4.0/bin/nvcc";
+ $arch_nvccflags = "--ptxas-options=-v " .
+ "-gencode arch=compute_13,code=sm_13 " .
+ "-gencode arch=compute_20,code=sm_20 " .
+ "-gencode arch=compute_20,code=compute_20 " .
+ "--ftz=true ";
+- $arch_nvccflags .= " --machine 32 -O3 -Xcompiler \"-m32\" $cuda_include";
+- $cuda_library = "-L/usr/local/cuda-4.0/lib";
++ $arch_nvccflags .= "gentoo-nvflags $cuda_include";
++ $cuda_library = "-Lgentoo-cuda-lib";
+ $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart";
+ }
+ # this is to make tcl happy
+@@ -2513,7 +2489,7 @@
+
+ if ($config_cuda) {
+ $arch_nvccflags .= " --machine 64 -O3 $cuda_include";
+- $cuda_library = "-L/usr/local/cuda-10.2/lib64";
++ $cuda_library = "-Lgentoo-cuda-lib";
+ }
+
+ $arch_lex = "flex"; # has problems with vendor lex
+@@ -3502,11 +3478,11 @@
+ DEFINES = $DEFINES
+
+ # compiler and compiler directives
+-CC = $arch_cc
+-CFLAGS = $arch_copts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CC = gentoo-gcc
++CFLAGS = gentoo-cflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+
+-CCPP = $arch_ccpp
+-CPPFLAGS = $arch_opt_flag $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
++CCPP = gentoo-g++
++CPPFLAGS = gentoo-cxxflags $arch_cppopts -DARCH_$config_arch \$(DEFINES) \$(INCDIRS) $rpm_optflags
+
+ NVCC = $arch_nvcc
+ NVCCFLAGS = $arch_nvccflags -DARCH_$config_arch \$(DEFINES) \$(INCDIRS)
+@@ -3555,7 +3531,7 @@
+ $config_progname: y.tab.h \$(VMD_OBJS) \$(VMD_PTX)
+ \$(ECHO) "Linking " \$\@ "..."; \\
+ \$(CD) $vmd_arch_dir ; \\
+- \$(CCPP) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
++ \$(CCPP) \$(LDFLAGS) \$(CPPFLAGS) -I$vmd_src_dir -o \$\@ \$(VMD_OBJS) \$(LOADLIBES) ;
+ \$(COMPILERC) \$(RCFLAGS)
+
+ install:
+@@ -3596,8 +3572,7 @@
+ -\$(COPY) ../data/.vmdrc ../data/.vmdsensors ../data/vmd_completion.dat "$install_library_dir"
+ \$(CD) $vmd_bin_dir ; \\
+ if [ -f run_vmd_tmp ]; then \$(DELETE) run_vmd_tmp; fi ; \\
+- if [ ! -x "/bin/csh" ]; then \\
+- \$(ECHO) "Info: /bin/csh shell not found, installing Bourne shell startup script instead" ; \\
++ if [ -x "/bin/bash" ]; then \\
+ \$(ECHO) '#!/bin/sh' >> run_vmd_tmp ; \\
+ \$(ECHO) 'defaultvmddir="$install_library_dir"' >> run_vmd_tmp ; \\
+ \$(ECHO) 'vmdbasename=vmd' >> run_vmd_tmp ; \\
+--- a/src/Makefile.old 2020-09-09 18:22:46.234818925 +0200
++++ b/src/Makefile 2020-09-09 18:37:22.356511690 +0200
+@@ -647,7 +647,7 @@
+ vmd_LINUXAMD64: y.tab.h $(VMD_OBJS) $(VMD_PTX)
+ $(ECHO) "Linking " $@ "..."; \
+ $(CD) ../LINUXAMD64 ; \
+- $(CCPP) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
++ $(CCPP) $(LDFLAGS) $(CPPFLAGS) -I../src -o $@ $(VMD_OBJS) $(LOADLIBES) ;
+ $(COMPILERC) $(RCFLAGS)
+
+ install:
+@@ -660,10 +660,6 @@
+ if [ ! -d "/usr/local/lib/vmd"/doc ]; then \
+ $(MAKEDIR) "/usr/local/lib/vmd"/doc; \
+ fi
+- -$(COPY) ../Announcement "/usr/local/lib/vmd"
+- -$(COPY) ../README "/usr/local/lib/vmd"
+- -$(COPY) ../LICENSE "/usr/local/lib/vmd"
+- -$(COPY) ../doc/ug.pdf "/usr/local/lib/vmd"/doc
+ if [ -f /usr/local/lib/vmd/vmd_LINUXAMD64 ]; then \
+ $(MOVE) "/usr/local/lib/vmd/vmd_LINUXAMD64" "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; $(DELETE) "/usr/local/lib/vmd/OLD_vmd_LINUXAMD64" ; fi
+ -$(COPY) ../LINUXAMD64/vmd_LINUXAMD64 "/usr/local/lib/vmd"
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-09 12:08:31 +0000