X-Git-Url: http://info.iut-bm.univ-fcomte.fr/pub/gitweb/simgrid.git/blobdiff_plain/bb487e9a35d93afe6715b9bdc7a2dd98fd37a6be..62d39371e58b7640d50f64baa6a29ae4b35320c1:/docs/source/Tutorial_MPI_Applications.rst

diff --git a/docs/source/Tutorial_MPI_Applications.rst b/docs/source/Tutorial_MPI_Applications.rst
index 4c641cc3cc..673d4eadb4 100644
--- a/docs/source/Tutorial_MPI_Applications.rst
+++ b/docs/source/Tutorial_MPI_Applications.rst
@@ -81,21 +81,26 @@ examples.
 Simple Example with 3 hosts
 ...........................
 
-At the most basic level, you can describe your simulated platform as a
-graph of hosts and network links. For instance:
+Imagine you want to describe a little platform with three hosts,
+interconnected as follows:
 
 .. image:: /tuto_smpi/3hosts.png
    :align: center
 
+This can be done with the following platform file, that considers the
+simulated platform as a graph of hosts and network links.
+	   
 .. literalinclude:: /tuto_smpi/3hosts.xml
    :language: xml
 
-Note the way in which hosts, links, and routes are defined in
-this XML. All hosts are defined with a speed (in Gflops), and links
-with a latency (in us) and bandwidth (in MBytes per second). Other
-units are possible and written as expected. Routes specify the list of
-links encountered from one route to another. Routes are symmetrical by
-default.
+The elements basic elements (with :ref:`pf_tag_host` and
+:ref:`pf_tag_link`) are described first, and then the routes between
+any pair of hosts are explicitely given with :ref:`pf_tag_route`. Any
+host must be given a computational speed (in flops) while links must
+be given a latency (in seconds) and a bandwidth (in bytes per
+second). Note that you can write 1Gflops instead of 1000000000flops,
+and similar. Last point: :ref:`pf_tag_route`s are symmetrical by
+default (but this can be changed).
 
 Cluster with a Crossbar
 .......................
@@ -274,7 +279,7 @@ container to enjoy the provided dependencies.
    when you log out of the container, so don't edit the other files!
 
 All needed dependencies are already installed in this container
-(SimGrid, the C/C++/Fortran compilers, make, pajeng and R). Vite being
+(SimGrid, the C/C++/Fortran compilers, make, pajeng, R and pajengr). Vite being
 only optional in this tutorial, it is not installed to reduce the
 image size.
 
@@ -303,6 +308,14 @@ Debian and Ubuntu for example, you can get them as follows:
 
    sudo apt install simgrid pajeng make gcc g++ gfortran vite
 
+For R analysis of the produced traces, you may want to install R, 
+and the `pajengr<https://github.com/schnorr/pajengr#installation/>`_ package.
+
+.. code-block:: shell
+
+   sudo apt install r-base r-cran-devtools cmake flex bison
+   Rscript -e "library(devtools); install_github('schnorr/pajengr');"
+
 To take this tutorial, you will also need the platform files from the
 previous section as well as the source code of the NAS Parallel
 Benchmarks. Just  clone `this repository
@@ -397,7 +410,6 @@ 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
@@ -406,10 +418,11 @@ run it again and again.
 
 .. code-block:: R
 
+   library(pajengr)
    library(ggplot2)
 
    # Read the data
-   df_state = read.csv("lu.S.4.state.csv", header=F, strip.white=T)
+   df_state = pajeng_read("lu.S.4.trace")
    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))