command-line arguments (if any -- roundtrip does not expect any arguments).
Feel free to tweak the content of the XML platform file and the
-prorgam to see the effect on the simulated execution time. Note that
-the simulation accounts for realistic network protocol effects and MPI
-implementation effects. As a result, you may see "unexpected behavior"
-like in the real world (e.g., sending a message 1 byte larger may lead
-to significant higher execution time).
-
-
+program to see the effect on the simulated execution time. It may be
+easier to compare the executions with the extra option
+``--cfg=smpi/display_timing:yes``. Note that the simulation accounts
+for realistic network protocol effects and MPI implementation
+effects. As a result, you may see "unexpected behavior" like in the
+real world (e.g., sending a message 1 byte larger may lead to
+significant higher execution time).
+
+Lab 1: Visualizing LU
+---------------------
+
+We will now simulate a larger application: the LU benchmark of the NAS
+suite. The version provided in the code template was modified to
+compile with SMPI instead of the regular MPI. Compare the difference
+between the original ``config/make.def.template`` and the
+``config/make.def`` that was adapted to SMPI. We use ``smpiff`` and
+``smpicc`` as compilers, and don't pass any additional library.
+
+Now compile and execute the LU benchmark, class S (i.e., for `small
+data size
+<https://www.nas.nasa.gov/publications/npb_problem_sizes.html>`_) with
+4 nodes.
+
+.. code-block:: shell
+
+ $ make lu NPROCS=4 CLASS=S
+ (compilation logs)
+ $ smpirun -np 4 -platform ../cluster_backbone.xml bin/lu.S.4
+ (execution logs)
+
+To get a better understanding of what is going on, activate the
+vizualization tracing, and convert the produced trace for later
+use:
+
+.. code-block:: shell
+
+ smpirun -np 4 -platform ../cluster_backbone.xml -trace --cfg=tracing/filename:lu.S.4.trace bin/lu.S.4
+ pj_dump --ignore-incomplete-links lu.S.4.trace | grep State > lu.S.4.state.csv
+
+You can then produce a Gantt Chart with the following R chunk. You can
+either copy/paste it in a R session, or `turn it into a Rscript executable
+<https://swcarpentry.github.io/r-novice-inflammation/05-cmdline/>`_ to
+run it again and again.
+
+.. code-block:: R
+
+ library(ggplot2)
+
+ # Read the data
+ df_state = read.csv("lu.S.4.state.csv", header=F, strip.white=T)
+ names(df_state) = c("Type", "Rank", "Container", "Start", "End", "Duration", "Level", "State");
+ df_state = df_state[!(names(df_state) %in% c("Type","Container","Level"))]
+ df_state$Rank = as.numeric(gsub("rank-","",df_state$Rank))
+
+ # Draw the Gantt Chart
+ gc = ggplot(data=df_state) + geom_rect(aes(xmin=Start, xmax=End, ymin=Rank, ymax=Rank+1,fill=State))
+
+ # Produce the output
+ plot(gc)
+ dev.off()
+
+This produces a file called ``Rplots.pdf`` with the following
+content. You can find more visualization examples `online
+<http://simgrid.gforge.inria.fr/contrib/R_visualization.html>`_.
+
+.. image:: /tuto_smpi/img/lu.S.4.png
+ :align: center
+
+Lab 2: Tracing and Replay of LU
+-------------------------------
+
+Now compile and execute the LU benchmark, class A, with 32 nodes.
+
+.. code-block:: shell
+
+ $ make lu NPROCS=32 CLASS=A
+
+This takes several minutes to to simulate, because all code from all
+processes has to be really executed, and everything is serialized.
+
+SMPI provides several methods to speed things up. One of them is to
+capture a time independent trace of the running application, and
+replay it on a different platform with the same amount of nodes. The
+replay is much faster than live simulation, as the computations are
+skipped (the application must be network-dependent for this to work).
+
+You can even generate the trace during as live simulation, as follows:
+
+.. code-block:: shell
+
+ $ smpirun -trace-ti --cfg=tracing/filename:LU.A.32 -np 32 -platform ../cluster_backbone.xml bin/lu.A.32
+
+The produced trace is composed of a file ``LU.A.32`` and a folder
+``LU.A.32_files``. To replay this with SMPI, you need to first compile
+the provided ``smpi_replay.cpp`` file, that comes from
+`simgrid/examples/smpi/replay
+<https://framagit.org/simgrid/simgrid/tree/master/examples/smpi/replay>`_.
+
+.. code-block:: shell
+
+ $ smpicxx ../replay.cpp -O3 -o ../smpi_replay
+
+Afterward, you can replay your trace in SMPI as follows:
+
+ $ smpirun -np 32 -platform ../cluster_torus.xml -ext smpi_replay ../smpi_replay LU.A.32
+
+All the outputs are gone, as the application is not really simulated
+here. Its trace is simply replayed. But if you visualize the live
+simulation and the replay, you will see that the behavior is
+unchanged. The simulation does not run much faster on this very
+example, but this becomes very interesting when your application
+is computationally hungry.
+
+.. todo:: smpi_replay should be installed by SimGrid, and smpirun interface could be simplified here.
+
+Lab 3: Execution Sampling on EP
+-------------------------------
+
+The second method to speed up simulations is to sample the computation
+parts in the code. This means that the person doing the simulation
+needs to know the application and identify parts that are compute
+intensive and take time, while being regular enough not to ruin
+simulation accuracy. Furthermore there should not be any MPI calls
+inside such parts of the code.
+
+Use the EP benchmark, class B, 16 processes.
+
+.. todo:: write this section, and the following ones.
+
+Further Readings
+----------------
+
+You may also be interested in the `SMPI reference article
+<https://hal.inria.fr/hal-01415484>`_ or these `introductory slides
+<http://simgrid.org/tutorials/simgrid-smpi-101.pdf>`_. The `SMPI
+reference documentation <SMPI_doc>`_ covers much more content than
+this short tutorial.
+
+Finally, we regularly use SimGrid in our teachings on MPI. This way,
+our student can experiment with platforms that they do not have access
+to, and the associated visualisation tools helps them to understand
+their work. The whole material is available online, in a separate
+project: the `SMPI CourseWare <https://simgrid.github.io/SMPI_CourseWare/>`_.
+
.. LocalWords: SimGrid
