Merge branch 'master' of https://framagit.org/simgrid/simgrid

diff --git a/docs/source/Tutorial_MPI_Applications.rst b/docs/source/Tutorial_MPI_Applications.rst
index 4c641cc..f33253c 100644 (file)
--- a/docs/source/Tutorial_MPI_Applications.rst
+++ b/docs/source/Tutorial_MPI_Applications.rst
@@ -274,7 +274,7 @@ 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 +303,14 @@ 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 +405,6 @@ 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 +413,11 @@ 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))

diff --git a/tools/docker/Dockerfile.tuto-smpi b/tools/docker/Dockerfile.tuto-smpi
index 1dba690..77df661 100644 (file)
--- a/tools/docker/Dockerfile.tuto-smpi
+++ b/tools/docker/Dockerfile.tuto-smpi
@@ -2,7 +2,9 @@
 FROM simgrid/unstable
 
 # - Clone simgrid-template-smpi, as it is needed by the tutorial
-RUN apt update && apt install -y pajeng r-base r-cran-ggplot2 r-cran-dplyr build-essential g++ gfortran git libboost-all-dev && \
+RUN apt update && apt install -y pajeng libssl-dev r-base r-cran-ggplot2 r-cran-dplyr r-cran-devtools build-essential g++ gfortran git libboost-all-dev cmake flex bison && \
     cd /source && \
     git clone --depth=1 https://framagit.org/simgrid/simgrid-template-smpi.git simgrid-template-smpi.git && \    
-    apt autoremove -y && apt clean && apt autoclean
\ No newline at end of file
+    apt autoremove -y && apt clean && apt autoclean
+    
+RUN Rscript -e "library(devtools); install_github('schnorr/pajengr');"