gaussian-view/vmd: add deps on X11/GL libraries (#22322)

Both binary packages would otherwise require X11 and Mesa libraries to
be installed on the host to run. Make sure they use the Spack-provided
libraries by patching the `rpath` via `patchelf`.

var/spack/repos/builtin/packages/gaussian-view/package.py

@@ -44,6 +44,15 @@ class GaussianView(Package):
 
     conflicts('+gaussian-src', when='@:6.0.99')
 
+    depends_on('libx11', type=('run', 'link'))
+    depends_on('libxext', type=('run', 'link'))
+    depends_on('gl@3:', type=('run', 'link'))
+    depends_on('glu@1.3', type=('run', 'link'))
+    depends_on('libxrender', type=('run', 'link'))
+    depends_on('libsm', type=('run', 'link'))
+    depends_on('libice', type=('run', 'link'))
+    depends_on('patchelf', type='build')
+
     def url_for_version(self, version):
         return "file://{0}/gv{1}-linux-x86_64.tbz".format(
             os.getcwd(),
@@ -52,6 +61,18 @@ def url_for_version(self, version):
     def install(self, spec, prefix):
         install_tree('.', prefix)
 
+        # make sure the executable finds and uses the Spack-provided
+        # libraries, otherwise the executable may or may not run depending
+        # on what is installed on the host
+        # the $ORIGIN prefix is required for the executable to find its
+        # own bundled shared libraries
+        patchelf = which('patchelf')
+        rpath = '$ORIGIN:$ORIGIN/lib' + ':'.join(
+            self.spec[dep].libs.directories[0]
+            for dep in ['libx11', 'libxext', 'libxrender', 'libice', 'libsm',
+                        'gl', 'glu'])
+        patchelf('--set-rpath', rpath, join_path(self.prefix, 'gview.exe'))
+
     @run_after('install')
     def caveats(self):
         perm_script = 'spack_perms_fix.sh'

var/spack/repos/builtin/packages/libice/package.py

@@ -18,3 +18,8 @@ class Libice(AutotoolsPackage, XorgPackage):
     depends_on('xtrans')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries('libICE', self.prefix,
+                              shared=True, recursive=True)

var/spack/repos/builtin/packages/libsm/package.py

@@ -22,3 +22,8 @@ class Libsm(AutotoolsPackage, XorgPackage):
     depends_on('xtrans')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries('libSM', self.prefix,
+                              shared=True, recursive=True)

var/spack/repos/builtin/packages/libxext/package.py

@@ -20,3 +20,8 @@ class Libxext(AutotoolsPackage, XorgPackage):
     depends_on('xextproto@7.1.99:')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries('libXext', self.prefix,
+                              shared=True, recursive=True)

var/spack/repos/builtin/packages/libxinerama/package.py

@@ -21,3 +21,8 @@ class Libxinerama(AutotoolsPackage, XorgPackage):
     depends_on('xineramaproto@1.1.99.1:')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries('libXinerama', self.prefix,
+                              shared=True, recursive=True)

var/spack/repos/builtin/packages/libxrender/package.py

@@ -20,3 +20,8 @@ class Libxrender(AutotoolsPackage, XorgPackage):
     depends_on('renderproto@0.9:')
     depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries('libXrender', self.prefix,
+                              shared=True, recursive=True)

var/spack/repos/builtin/packages/vmd/package.py

@@ -27,6 +27,12 @@ class Vmd(Package):
 
     phases = ['configure', 'install']
 
+    depends_on('libx11', type=('run', 'link'))
+    depends_on('libxi', type=('run', 'link'))
+    depends_on('libxinerama', type=('run', 'link'))
+    depends_on('gl@3:', type=('run', 'link'))
+    depends_on('patchelf', type='build')
+
     def setup_build_environment(self, env):
         env.set('VMDINSTALLBINDIR', self.prefix.bin)
         env.set('VMDINSTALLLIBRARYDIR', self.prefix.lib64)
@@ -39,5 +45,15 @@ def install(self, spec, prefix):
         with working_dir(join_path(self.stage.source_path, 'src')):
             make('install')
 
+        # make sure the executable finds and uses the Spack-provided
+        # libraries, otherwise the executable may or may not run depending
+        # on what is installed on the host
+        patchelf = which('patchelf')
+        rpath = ':'.join(
+            self.spec[dep].libs.directories[0]
+            for dep in ['libx11', 'libxi', 'libxinerama', 'gl'])
+        patchelf('--set-rpath', rpath,
+                 join_path(self.prefix, 'lib64', 'vmd_LINUXAMD64'))
+
     def setup_run_environment(self, env):
         env.set('PLUGINDIR', self.spec.prefix.lib64.plugins)