* Added tests for sequential read/write.

* Tests revealed that the sequential read/write wasn't
  really working. Now fixed!
* Removed mpi-h5py as a dependency. Now any h5py will do.
* Removed HDF5 as a config package.
* Removed H5PY self-build option.
* Added info on compiling mpi-h5py in `COMPILE.md`.
* Added barrier to end of read/writes for safety.

COMPILE.md

@@ -15,7 +15,7 @@ Dependencies
   * PETSc 
   * numpy
   * swig
-  * h5py-mpi
+  * h5py
 
 
 Getting the code
@@ -48,3 +48,18 @@ You will first need to make the project directory available to import within pyt
 ```
 (note that if you are not using the bash shell, the required command will be different.)
 
+h5py-mpi
+--------
+Underworld now supports non-mpi versions of `h5py`. Note however that for large parallel simulations,
+saving data to disk may become a bottleneck, and collective IO via MPI-enabled `h5py` is recommended.
+To install `h5py` with MPI enabled, you will first required a parallel enabled version of `libhdf5`. 
+The following command may be useful for installed MPI-enabled `h5py`:
+
+```bash
+    $ CC=mpicc HDF5_MPI="ON" HDF5_DIR=/path/to/your/hdf5/install/ pip install --no-binary=h5py h5py
+```
+
+or alternatively you might use `CC=h5pcc` (if available). Please check the `h5py` site for more information.
+Underworld will automatically perform `save()`/`load()` operations collectively if MPI-enabled `hdf5` is 
+available. 
+

docs/test/mesh_aux.py

@@ -1,31 +1,73 @@
 '''
-This script contains auxiliary mesh related tests. 
+This script contains auxiliary mesh related tests.
+
+We test saving and loading of mesh and mesh variable objects.
+We also tests creation/load/save of non-partitioned mesh and
+variables. I'll leave this in for now, but I'm not sure if
+load/save of non-partitioned mesh is useful or even a good
+idea. Effectively, in parallel, we're saying that each process
+has its own distinct mesh object, but then we're saving it to
+a single global file. Sequentially this is fine (and each proc
+*could* specify its own filename), but collectively this doesn't
+make sense as we use COMM_WORLD but the mesh only is aware of
+COMM_SELF. Note that the test passes, but I've disabled it in
+any case as it doesn't make sense.
 '''
 import underworld as uw
 import numpy as np
 
+def meshtest(res, partitioned):
+    mesh = uw.mesh.FeMesh_Cartesian(elementRes=(res,res),partitioned=partitioned)
 
+    resp1 = res + 1
+    if not partitioned:
+        if (len(mesh.data) != (resp1*resp1)):
+            raise RuntimeError("A non-partitioned mesh should report identical vertex count "\
+                               "independent of processor count.")
+    # test save/load of mesh
+    with mesh.deform_mesh():
+        mesh.data[:] *= 2.
 
-# Simple test to check non-parallel decomposed meshing is working.
-# Note that we are only really testing this parameter when we
-# run this test in parallel.
-mesh1 = uw.mesh.FeMesh_Cartesian(elementRes=(4,4),partitioned=False)
-
-if len(mesh1.data) != 25:
-    raise RuntimeError("A non-partitioned mesh should report identical vertex count \
-                        independent of processor count.")
-
-mesh2 = uw.mesh.FeMesh_Cartesian(elementRes=(10,10),partitioned=True)
-var   = uw.mesh.MeshVariable( mesh2, nodeDofCount=2 )
-var2   = uw.mesh.MeshVariable( mesh2, nodeDofCount=2 )
-
-for ind, coord in enumerate(mesh2.data):
-    var.data[ind] = [coord[1]+5., coord[0]*-2.]
+    cpy = mesh.data.copy()
+    mesh.save('temp.h5')
+    mesh.reset()
+    if np.allclose(mesh.data, cpy):
+        raise RuntimeError("These arrays should be different.")
+    mesh.load('temp.h5')
+    if not np.allclose(mesh.data, cpy):
+        raise RuntimeError("These arrays should be identical.")
 
-var.save('temp.h5')
-var2.load('temp.h5')
+    # test save/load of meshvariable
+    var = uw.mesh.MeshVariable( mesh, nodeDofCount=2 )
+    for ind, coord in enumerate(mesh.data):
+        var.data[ind] = [coord[1]+5., coord[0]*-2.]
 
-checkpoint_pass = np.allclose(var.data, var2.data)
+    var.syncronise()
+    cpy = var.data.copy()
+    var.save('temp2.h5')
+    var.data[:] = 0.
+    if np.allclose(var.data, cpy):
+        raise RuntimeError("These arrays should be different.")
+    var.load('temp2.h5')
+    if not np.allclose(var.data, cpy):
+        if uw.mpi.rank==0:
+            print("VAR")
+            print(var.data[:])
+            print("CPY")
+            print(cpy)
+        raise RuntimeError("These arrays should be identical.")
 
-if( not checkpoint_pass ):
-  raise RuntimeError("Error in a checkpoint test")
+if __name__ == '__main__':
+    import underworld as uw
+    uw.utils._io.PATTERN=1 # sequential
+    meshtest(16,True)
+    meshtest(8, True)  # second run to make sure we're deleting datasets where different sizes
+    meshtest(16,False)
+    uw.utils._io.PATTERN=2 # collective
+    meshtest(16,True)
+    meshtest(8, True)
+    # meshtest(16,False)  # this isn't a good idea, so we shouldn't do it.
+    if uw.mpi.rank==0:
+        import os
+        os.remove('temp.h5')
+        os.remove('temp2.h5')

docs/test/swarm_aux.py

@@ -47,7 +47,6 @@ def swarm_save_load(swarmtype):
     clone_svar1.load("saved_swarm_variable1.h5")
     if np.allclose(clone_swarm.particleCoordinates.data,clone_svar1.data) != True:
         raise RuntimeError("Loaded swarm variable1 does not appear to contain the correct data.")
-
     clone_svar2 = clone_swarm.add_variable("int",1)
     clone_svar2.load("saved_swarm_variable2.h5")
 
@@ -59,5 +58,10 @@ def swarm_save_load(swarmtype):
 
 
 if __name__ == '__main__':
+    import underworld as uw
+    uw.utils._io.PATTERN=1 # sequential
+    swarm_save_load('global')
+    swarm_save_load('passivetracer')
+    uw.utils._io.PATTERN=2 # collective
     swarm_save_load('global')
     swarm_save_load('passivetracer')

libUnderworld/SConfigure

@@ -62,7 +62,6 @@ env.AddMethod( UWExit )
 
 env.UsePackage(packages.libm)
 env.UsePackage(packages.libXML2)
-env.UsePackage(packages.HDF5)
 env.UsePackage(packages.Mpi4pyPk)
 env.UsePackage(packages.H5py)
 env.UsePackage(packages.Python)
@@ -173,7 +172,6 @@ if not (GetOption('help') or GetOption('clean')):
     env.ConfigurePackage(packages.libm, required=False)
     env.ConfigurePackage(packages.libXML2)
     env.ConfigurePackage(packages.MPI)
-    env.ConfigurePackage(packages.HDF5, required=False)
     env.ConfigurePackage(packages.Python, required=True)
     env.ConfigurePackage(packages.PETSc)
     env.ConfigurePackage(packages.NumpyPk, required=True)

libUnderworld/config/packages/H5py.py

@@ -1,94 +1,23 @@
 import os, sys
 from config import Package
-from .MPI import MPI
-from .HDF5 import HDF5
 import subprocess
 from SCons.Script.Main import AddOption
 
 class H5py(Package):
 
-    _buildh5py = False
-    _h5pysrc   = os.path.abspath('./h5py_ext')
-    _h5pyp     = os.path.abspath('../h5py')
-
     def setup_dependencies(self):
-        self.MPI = self.add_dependency(MPI, required=True)
-        self.hdf5 = self.add_dependency(HDF5, required=False)
-
-    def _buildh5py(self, cc):
-        print("\nAttempting to build private h5py version at {} using cc={}. This may take a few minutes.".format(self._h5pyp,cc))
-        os.chdir(self._h5pysrc)
-        with open('h5py_build.out','w') as outfile:
-            with open('h5py_build.err','w') as errfile:
-                command = "python setup.py configure -rm --hdf5 " + self.hdf5.location[0]
-                self._logfile.write("\n\nh5py configuration command:\n")
-                self._logfile.write(self.launcher+command)
-                subp = subprocess.Popen((self.launcher+command).split(), stdout=outfile, stderr=errfile)
-                subp.wait()
-                if subp.wait() != 0:
-                    self._logfile.write("\nFailed configuring h5py :(\nPlease check 'h5py_build.out' and 'h5py_build.err' in libUnderworld/h5py_ext\n")
-                    raise RuntimeError
-                subp = subprocess.Popen(self.launcher+'python setup.py clean', shell=True, stdout=outfile, stderr=errfile)
-                subp.wait()
-                if subp.wait() != 0:
-                    self._logfile.write("\nFailed cleaning h5py :(\nPlease check 'h5py_build.out' and 'h5py_build.err' in libUnderworld/h5py_ext\n")
-                    raise RuntimeError
-
-                # The following doesn't work on raijin, one only requires 'setup.py build'
-                # but as we use a system h5py it isn't critical JG May2017
-                cmd = 'python setup.py build_ext --include-dirs=' 
-                # use all header paths the config has thus far added.
-                # we really just need the path to mpi.h
-                for header_path in self.env["CPPPATH"]:
-                    cmd += header_path +':'
-                cmd2 = ' --build-lib ' + os.path.dirname(self._h5pyp)
-                cmd += cmd2
-
-                self._logfile.write("\nh5py build command:\n")
-                self._logfile.write('CC='+cc+' '+self.launcher+' '+cmd )
-                subp = subprocess.Popen( 'CC='+cc+' '+self.launcher+' '+cmd, shell=True, stdout=outfile, stderr=errfile)
-                subp.wait()
-                if subp.wait() != 0:
-                    self._logfile.write("\nFailed building h5py :(\nPlease check 'h5py_build.out' and 'h5py_build.err' in libUnderworld/h5py_ext\n")
-                    raise RuntimeError
-                # need to run this now to make it importable
-                self._logfile.write("\nh5py install command:\n")
-                self._logfile.write(self.launcher+'python setup.py build' + cmd2)
-                subp = subprocess.Popen(self.launcher+'python setup.py build' + cmd2, shell=True, stdout=outfile, stderr=errfile)
-                subp.wait()
-                if subp.wait() != 0:
-                    self._logfile.write("\nFailed installing h5py :(\nPlease check 'h5py_build.out' and 'h5py_build.err' in libUnderworld/h5py_ext\n")
-                    raise RuntimeError
-        os.chdir(self._h5pysrc+'/..')
-        self._logfile.write("\nh5py build completed successfully.\n")
+        pass
 
     def _importtest(self):
-        '''
-        We run test on h5py here. Note that we first check if a custom h5py is
-        in the parent directory ie it is preferenced over system packages. 
-	Also note that we do this via subprocess to keep our own python environment 
-	clean and allow re-importing after (perhaps) we have built our own h5py.
-        '''
         # next check for mpi compat
-        self._logfile.write("\nChecking if h5py is importable and built against mpi.\n")
+        self._logfile.write("\nChecking if h5py is available.")
         self._logfile.flush()
-        proj_folder = os.path.realpath(os.path.dirname("../.."))
-
-        # try h5py in the parent directory
-        subp = subprocess.Popen(self.launcher+'python3 -c \'import sys\nsys.path.insert(0, \"{}\")\nimport h5py\nif not h5py.get_config().mpi: raise RuntimeError(\"h5py imported, but not compiled against mpi.\")\''.format(proj_folder), shell=True, stdout=self._logfile, stderr=self._logfile)
-        subp.wait()
 
+        subp = subprocess.Popen(self.launcher+'python3 -c \'import h5py\'', shell=True, stdout=self._logfile, stderr=self._logfile)
         if subp.wait() != 0:
-            self._logfile.write("\nh5py is not importable from {}, or does not appear to be built against mpi.\n".format(proj_folder))
-            # try h5py in PYTHONPATH
-            subp = subprocess.Popen(self.launcher+'python3 -c \'import h5py\nif not h5py.get_config().mpi: raise RuntimeError(\"h5py imported, but not compiled against mpi.\")\'', shell=True, stdout=self._logfile, stderr=self._logfile)
-            if subp.wait() != 0:
-                self._logfile.write("\nh5py is not importable from system, or does not appear to be built against mpi.\n")
-                self._logfile.write("\nNote that you can install parallel h5py via pip using the following command:\n \
-    CC=mpicc HDF5_MPI=\"ON\" HDF5_DIR=/path/to/your/hdf5/install/ pip install --no-binary=h5py h5py\n")
-
-                self._logfile.flush()
-                return False
+            self._logfile.write("\nh5py does not appear to be available.\n")
+            self._logfile.flush()
+            return False
 
         # if we made it this far, all is probably good
         self._logfile.write("\nh5py configuration succeeded.\n")
@@ -103,35 +32,8 @@ def check(self, conf, env):
 
         with open('config.log', 'a') as self._logfile:
             self._logfile.write("\n\nCONFIGURE H5PY\n")
-            self._logfile.write("Checking if h5py in built in uw2 already, or provided by system (in that order of preference).\n")
             if self._importtest():
                 return True
-
-            self._logfile.write("\n")
-            self._logfile.write("h5py not found. try build local version using uw2 CC.\n")
-            if not self.hdf5.result:
-                self._logfile.write("    libhdf5 not found by config. Please explicitly specify your libhdf5 install via the --hdf5-dir flags.\n")
-                return False
-
-            # let's get h5py
-            self.pull_from_git( "https://github.com/h5py/h5py", "2.7.0", self._h5pysrc, logfile=self._logfile)
-
-            try:
-                self._buildh5py(self.env['CC'])
-                if self._importtest():
-                    return True
-            except:
-                pass
-
-
-            self._logfile.write("\n")
-            self._logfile.write("h5py not found, try build local version using h5pcc.\n")
-            try:
-                self._buildh5py('h5pcc')
-                if self._importtest():
-                    return True
-            except:
-                pass
 
             return False
 

libUnderworld/config/packages/__init__.py

@@ -1,7 +1,6 @@
 from .libXML2 import libXML2
 from .MPI import MPI
 from .PETSc import PETSc
-from .HDF5 import HDF5
 from .spatialdata import spatialdata
 from .pcu import pcu
 from .Underworld import Underworld

underworld/__init__.py

@@ -158,7 +158,7 @@ def matplotlib_inline():
 if isinstance(underworld.mpi.size, int) and underworld.mpi.size > 1:
     _origexcepthook = _sys.excepthook
     def _uw_uncaught_exception_handler(exctype, value, tb):
-        print('An uncaught exception was encountered on processor {}.'.format(uw.mpi.rank))
+        print('An uncaught exception was encountered on processor {}.'.format(underworld.mpi.rank))
         # pass through to original handler
         _origexcepthook(exctype, value, tb)
         import sys