Final (hopefully) changes for release!

* changed dockerfile volume to map to somewhere more useful (/workspace/user_data)
* for models, just use LU where single proc operation, otherwise use default
* update glucifer viewer to use port 9999 (to avoid it being the default port kitematic latches onto)
* updates for xdmf swarm variable output

docs/development/docker/underworld2_untested/Dockerfile

@@ -36,10 +36,10 @@ RUN git clone --branch "master" --single-branch https://github.com/underworldcod
 # expose notebook port
 EXPOSE 8888
 # expose glucifer port
-EXPOSE 8080
+EXPOSE 9999
 
 # setup space for working in
-VOLUME /workspace
+VOLUME /workspace/user_data
 WORKDIR /workspace
 
 # launch notebook

docs/examples/1_07_SlabSubduction.ipynb

@@ -356,9 +356,7 @@
    "source": [
     "# use \"lu\" direct solve if running in serial\n",
     "if(uw.nProcs()==1):\n",
-    "    solver.set_inner_method(\"lu\")\n",
-    "else: # use \"mumps\" parallel method\n",
-    "    solver.set_inner_method(\"mumps\")\n"
+    "    solver.set_inner_method(\"lu\")"
    ]
   },
   {
@@ -638,7 +636,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "version": "2.7.10"
   }
  },
  "nbformat": 4,

docs/examples/2_08_ShearBandsSimpleShear.ipynb

@@ -484,16 +484,10 @@
     "\n",
     "solver = uw.systems.Solver( stokesPIC )\n",
     "\n",
-    "# \"mumps\" instead of \"lu\" in parallel\n",
-    "#  but needs to be installed in your petsc \n",
-    "#  beforehand. See petsc docs for details.\n",
-    "\n",
     "# assuming that it is installed if you are running in parallel\n",
     "# use \"lu\" direct solve if running in serial\n",
     "if(uw.nProcs()==1):\n",
     "    solver.set_inner_method(\"lu\")\n",
-    "else: # use \"mumps\" parallel method\n",
-    "    solver.set_inner_method(\"mumps\")\n",
     "\n",
     "solver.set_penalty(1.0e6)\n",
     "solver.options.scr.ksp_rtol = 1.0e-3\n",
@@ -877,7 +871,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "version": "2.7.10"
   }
  },
  "nbformat": 4,

docs/examples/2_09_ShearBandsPureShear.ipynb

@@ -618,14 +618,9 @@
     "solver = uw.systems.Solver( stokesPIC )\n",
     "\n",
     "## Initial solve (drop the non-linearity the very first solve only)\n",
-    "## Replace \"lu\" with \"mumps\" for parallel if you have it.\n",
-    "\n",
-    "# assuming that it is installed if you are running in parallel\n",
     "# use \"lu\" direct solve if running in serial\n",
     "if(uw.nProcs()==1):\n",
     "    solver.set_inner_method(\"lu\")\n",
-    "else: # use \"mumps\" parallel method\n",
-    "    solver.set_inner_method(\"mumps\")\n",
     "\n",
     "solver.set_penalty(1.0e6)\n",
     "solver.options.scr.ksp_rtol = 1.0e-3\n",
@@ -1133,7 +1128,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.6"
+   "version": "2.7.10"
   }
  },
  "nbformat": 4,

glucifer/_glucifer.py

@@ -641,7 +641,7 @@ def image(self):
         from IPython.display import Image,HTML
         if not self._viewerProc:
             return
-        url = "http://localhost:8080/image=0"
+        url = "http://localhost:9999/image=0"
         response = urllib2.urlopen(url).read()
         image_data = "data:image/png;base64,%s" % b64encode(response)
         return HTML("<img src='%s'>" % image_data)
@@ -659,11 +659,11 @@ def open_viewer(self, args=[], background=True):
 
         if haveLavaVu and uw.rank() == 0:
             #Open viewer with local web server for interactive/iterative use
-            args = [self.db._lvbin, "-" + str(self.db.step), "-L", "-p8080", "-q90", fname] + args
+            args = [self.db._lvbin, "-" + str(self.db.step), "-L", "-p9999", "-q90", fname] + args
             if background:
                 self._viewerProc = subprocess.Popen(args, stdout=PIPE, stdin=PIPE, stderr=STDOUT)
                 from IPython.display import HTML
-                return HTML('''<a href='#' onclick='window.open("http://" + location.hostname + ":8080");'>Open Viewer Interface</a>''')
+                return HTML('''<a href='#' onclick='window.open("http://" + location.hostname + ":9999");'>Open Viewer Interface</a>''')
             else:
                 lavavu.execute(args)
 
@@ -680,7 +680,7 @@ def run_script(self):
         """ Run the saved script on an open viewer instance
         """
         self.open_viewer()
-        url = "http://localhost:8080/command=" + urllib2.quote(';'.join(self._script))
+        url = "http://localhost:9999/command=" + urllib2.quote(';'.join(self._script))
         response = urllib2.urlopen(url).read()
         #print response
 
@@ -695,7 +695,7 @@ def send_command(self, cmd, retry=True):
         """
         if haveLavaVu and uw.rank() == 0:
             self.open_viewer()
-            url = "http://localhost:8080/command=" + urllib2.quote(cmd)
+            url = "http://localhost:9999/command=" + urllib2.quote(cmd)
             try:
                 #print url
                 response = urllib2.urlopen(url).read()

underworld/utils/_utils.py

@@ -178,11 +178,11 @@ class SavedFileData(object):
     pyobj: object
         python object saved data relates to.
     filename: str
-        filename for saved data.
+        filename for saved data, full path
     '''
     def __init__(self, pyobj, filename):
         self.pyobj = pyobj
-        self.filename = filename
+        self.filename = os.path.abspath(filename)
 
 
 ### Code for XDMF output ###