Merge branch 'petsc'

# Conflicts:
#	.travis.yml
#	docs/source/index.rst

Author: pancetta

.travis.yml

@@ -1,4 +1,4 @@
-sudo: required
+sudo: false
 dist: trusty
 
 language: python
@@ -16,15 +16,19 @@ before_install:
   - conda update --yes conda
 
 install:
-  - conda install --yes python=${TRAVIS_PYTHON_VERSION} numpy future scipy matplotlib nose pep8 coverage mpi4py sympy dill numba
-  - conda install --yes python=${TRAVIS_PYTHON_VERSION} sphinx=1.6.3
-  - pip install --user coloredlogs
-  - if [[ $PYTHON_VERSION == 3 ]]; then pip install --user travis-sphinx; fi
+  - conda install --yes -c conda-forge petsc4py mpi4py
+  - conda install --yes python=${TRAVIS_PYTHON_VERSION} pip numpy future scipy matplotlib nose pep8 coverage sympy dill numba sphinx
+  - conda list
+  - pip install coloredlogs
+  - pip install travis-sphinx
   - sudo apt-get install -y texlive-latex-recommended texlive-fonts-recommended texlive-latex-extra dvipng
 
 script:
   - "./docs/update_apidocs.sh"
-  - nosetests --with-coverage --cover-erase --cover-inclusive --cover-package=pySDC/core,pySDC/implementations,pySDC/helpers,pySDC/tutorial --cover-html --cover-html-dir=doc/build/test_coverage pySDC/tests
+  - which nosetests
+#  - export MPICH_NO_LOCAL=1
+  - export PYTHONPATH=$PYTHONPATH:../../..
+  - nosetests -v --with-coverage --cover-erase --cover-inclusive --cover-package=pySDC/core,pySDC/implementations,pySDC/helpers,pySDC/tutorial,pySDC/projects --cover-html --cover-html-dir=doc/build/test_coverage pySDC/tests
   - if [[ $PYTHON_VERSION == 3 ]]; then travis-sphinx build; fi
 
 after_success:
@@ -39,4 +43,14 @@ deploy:
       secure: id5Pg/GL/YdXFmbi5h4xLmmyv/0L8lj9Rlr7lFJBrHrmkHIlu78NgO+LnQsGvhSrZqdDvZwRzFFCKRLiDugp07rzfwM41ROPrcgwnSRuqnzG2sUecNulNGHHoqej/z8nG5Ss8k2+viMqpOjhhZoY3LR0D1nFxRzu3HtHs0MKpRc=
     on:
       tags: true
+      condition: $TRAVIS_PYTHON_VERSION = "2.7"
+  - provider: pypi
+    edge:
+      branch: jc-pypi
+    user: pancetta
+    password:
+      secure: id5Pg/GL/YdXFmbi5h4xLmmyv/0L8lj9Rlr7lFJBrHrmkHIlu78NgO+LnQsGvhSrZqdDvZwRzFFCKRLiDugp07rzfwM41ROPrcgwnSRuqnzG2sUecNulNGHHoqej/z8nG5Ss8k2+viMqpOjhhZoY3LR0D1nFxRzu3HtHs0MKpRc=
+    server: https://test.pypi.org/legacy/
+    on:
+      tags: false
       condition: $TRAVIS_PYTHON_VERSION = "2.7"

docs/source/index.rst

@@ -96,6 +96,7 @@ Projects
    projects/asymp_conv.rst
    projects/matrixPFASST.rst
    projects/Hamiltonian.rst
+   projects/SDC_showdown.rst
 
 
 Tests

docs/source/projects/SDC_showdown.rst

@@ -0,0 +1 @@
+.. include:: /../../pySDC/projects/SDC_showdown/README.rst

docs/source/projects/doc_SDC_showdown.rst

@@ -0,0 +1,18 @@
+Full code: `pySDC/projects/SDC_showdown/SDC_timing_Fisher.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/projects/SDC_showdown/SDC_timing_Fisher.py>`_
+
+.. literalinclude:: ../../../pySDC/projects/SDC_showdown/SDC_timing_Fisher.py
+
+Results:
+
+.. image:: ../../../data/timings_SDC_variants_Fisher.png
+   :scale: 100 %
+
+
+Full code: `pySDC/projects/SDC_showdown/SDC_timing_GrayScott.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/projects/SDC_showdown/SDC_timing_GrayScott.py>`_
+
+.. literalinclude:: ../../../pySDC/projects/SDC_showdown/SDC_timing_GrayScott.py
+
+Results:
+
+.. image:: ../../../data/timings_SDC_variants_GrayScott.png
+   :scale: 100 %

docs/source/tutorial/doc_step_7_C.rst

@@ -0,0 +1,12 @@
+Full code: `pySDC/tutorial/step_7/C_pySDC_with_PETSc.py <https://github.com/Parallel-in-Time/pySDC/blob/master/pySDC/tutorial/step_7/C_pySDC_with_PETSc.py>`_
+
+Results:
+
+1 processor in time, 1 processor in space
+.. literalinclude:: ../../../step_7_C_out_1x1.txt
+
+1 processor in time, 2 processors in space
+.. literalinclude:: ../../../step_7_C_out_1x2.txt
+
+2 processor in time, 2 processors in space
+.. literalinclude:: ../../../step_7_C_out_2x2.txt

pySDC/helpers/plot_helper.py

@@ -65,3 +65,4 @@ def savefig(filename, save_pdf=True, save_pgf=True, save_png=True):
         plt.savefig('{}.pdf'.format(filename), rasterized=True, bbox_inches='tight')
     if save_png:
         plt.savefig('{}.png'.format(filename), rasterized=True, bbox_inches='tight')
+    plt.close()

pySDC/implementations/controller_classes/allinclusive_classic_MPI.py

@@ -152,35 +152,6 @@ def restart_block(self, size, time, u0):
             lvl.status.time = time
             lvl.status.sweep = 1
 
-    @staticmethod
-    def recv(target, source, tag, comm):
-        """
-        Receive function
-
-        Args:
-            target: process/level which will receive the values
-            source: process/level which initiated the send
-            tag: identifier to check if this message is really for me
-            comm: communicator
-        """
-        # do a blocking receive and re-compute f(u0)
-        target.u[0] = comm.recv(source=source, tag=tag)
-        target.f[0] = target.prob.eval_f(target.u[0], target.time)
-
-    @staticmethod
-    def send(source, target, tag, comm):
-        """
-        Send function
-
-        Args:
-            source: process/level which has the new values
-            target: process/level which will receive the values
-            tag: identifier for this message
-            comm: communicator
-        """
-        # do a blocking send
-        comm.send(source.uend, dest=target, tag=tag)
-
     def predictor(self, comm):
         """
         Predictor function, extracted from the stepwise implementation (will be also used by matrix sweppers)
@@ -199,7 +170,7 @@ def predictor(self, comm):
                 self.logger.debug('recv data predict: process %s, stage %s, time, %s, source %s, tag %s, phase %s' %
                                   (self.S.status.slot, self.S.status.stage, self.S.time, self.S.prev,
                                    self.S.status.iter, p))
-                self.recv(target=self.S.levels[-1], source=self.S.prev, tag=self.S.status.iter, comm=comm)
+                self.S.levels[-1].u[0].recv(source=self.S.prev, tag=self.S.status.iter, comm=comm)
 
             # do the sweep with new values
             self.S.levels[-1].sweep.update_nodes()
@@ -209,7 +180,7 @@ def predictor(self, comm):
                 self.logger.debug('send data predict: process %s, stage %s, time, %s, target %s, tag %s, phase %s' %
                                   (self.S.status.slot, self.S.status.stage, self.S.time, self.S.next,
                                    self.S.status.iter, p))
-                self.send(source=self.S.levels[-1], target=self.S.next, tag=self.S.status.iter, comm=comm)
+                self.S.levels[-1].uend.send(dest=self.S.next, tag=self.S.status.iter, comm=comm)
 
         # interpolate back to finest level
         for l in range(len(self.S.levels) - 1, 0, -1):
@@ -320,7 +291,7 @@ def pfasst(self, comm, num_procs):
                 self.logger.debug('isend data: process %s, stage %s, time %s, target %s, tag %s, iter %s' %
                                   (self.S.status.slot, self.S.status.stage, self.S.time, self.S.next,
                                    0, self.S.status.iter))
-                self.req_send.append(comm.isend(self.S.levels[0].uend, dest=self.S.next, tag=0))
+                self.req_send.append(self.S.levels[0].uend.isend(dest=self.S.next, tag=0, comm=comm))
 
             # update stage
             self.S.status.stage = 'IT_CHECK'
@@ -349,7 +320,7 @@ def pfasst(self, comm, num_procs):
                     self.logger.debug('isend data: process %s, stage %s, time %s, target %s, tag %s, iter %s' %
                                       (self.S.status.slot, self.S.status.stage, self.S.time, self.S.next,
                                        l, self.S.status.iter))
-                    self.req_send.append(comm.isend(self.S.levels[l].uend, dest=self.S.next, tag=l))
+                    self.req_send.append(self.S.levels[l].uend.isend(dest=self.S.next, tag=l, comm=comm))
 
                 # transfer further up the hierarchy
                 self.S.transfer(source=self.S.levels[l], target=self.S.levels[l + 1])
@@ -364,7 +335,7 @@ def pfasst(self, comm, num_procs):
                 self.logger.debug('recv data: process %s, stage %s, time %s, source %s, tag %s, iter %s' %
                                   (self.S.status.slot, self.S.status.stage, self.S.time, self.S.prev,
                                    len(self.S.levels) - 1, self.S.status.iter))
-                self.recv(target=self.S.levels[-1], source=self.S.prev, tag=len(self.S.levels) - 1, comm=comm)
+                self.S.levels[-1].u[0].recv(source=self.S.prev, tag=len(self.S.levels) - 1, comm=comm)
 
             # update stage
             self.S.status.stage = 'IT_COARSE'
@@ -386,7 +357,7 @@ def pfasst(self, comm, num_procs):
                 self.logger.debug('isend data: process %s, stage %s, time %s, target %s, tag %s, iter %s' %
                                   (self.S.status.slot, self.S.status.stage, self.S.time, self.S.next,
                                    len(self.S.levels) - 1, self.S.status.iter))
-                self.send(source=self.S.levels[-1], target=self.S.next, tag=len(self.S.levels) - 1, comm=comm)
+                self.S.levels[-1].uend.send(dest=self.S.next, tag=len(self.S.levels) - 1, comm=comm)
 
             # update stage
             self.S.status.stage = 'IT_DOWN'
@@ -402,7 +373,7 @@ def pfasst(self, comm, num_procs):
                     self.logger.debug('recv data: process %s, stage %s, time %s, source %s, tag %s, iter %s' %
                                       (self.S.status.slot, self.S.status.stage, self.S.time, self.S.prev,
                                        l - 1, self.S.status.iter))
-                    self.recv(target=self.S.levels[l - 1], source=self.S.prev, tag=l - 1, comm=comm)
+                    self.S.levels[l - 1].u[0].recv(source=self.S.prev, tag=l - 1, comm=comm)
 
                 # prolong values
                 self.S.transfer(source=self.S.levels[l], target=self.S.levels[l - 1])

pySDC/implementations/controller_classes/allinclusive_classic_nonMPI.py

@@ -1,6 +1,7 @@
 import itertools
 import copy as cp
 import numpy as np
+import dill
 
 from pySDC.core.Controller import controller
 from pySDC.core import Step as stepclass
@@ -27,10 +28,17 @@ def __init__(self, num_procs, controller_params, description):
 
         self.logger.warning('classic controller is about to become deprecated, use multigrid controller instead')
 
-        self.MS = []
-        # simply append step after step and generate the hierarchies
-        for p in range(num_procs):
-            self.MS.append(stepclass.step(description))
+        self.MS = [stepclass.step(description)]
+
+        # try to initialize via dill.copy (much faster for many time-steps)
+        try:
+            for p in range(num_procs - 1):
+                self.MS.append(dill.copy(self.MS[0]))
+        # if this fails (e.g. due to un-picklable data in the steps), initialize seperately
+        except dill.PicklingError and TypeError:
+            self.logger.warning('Need to initialize steps separately due to pickling error')
+            for p in range(num_procs - 1):
+                self.MS.append(stepclass.step(description))
 
         assert not (len(self.MS) > 1 and len(self.MS[0].levels) == 1), "ERROR: classic cannot do MSSDC"