adapt smpi tuto to use pajengr (+ dockerfile)

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
    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.
 
 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
 
 
    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
 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
 .. 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
 
 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
 
 
 .. code-block:: R
 

+   library(pajengr)

    library(ggplot2)
 
    # Read the data
    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))
    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
 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 && \    
     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');"