Update INSTALL.org to match upstream chameleon merge(C++ header type)

INSTALL.org

+# -*- mode: org -*-
+# -*- coding: utf-8 -*-
+
+#+TITLE: Fabulous installation procedure (Plafrim2)
+
 * INSTALLATION on PLAFRIM2 with chameleon
 ** With SPACK
 *** Install SPACK
 
     If you dont have spack, download it:
-    #+begin_src sh
+    #+begin_src bash
     cd ${HOME}
     git clone https://github.com/solverstack/spack.git
     #+end_src
 
+    Set SPACK_ROOT variable to the directory where spack is installed:
+    #+begin_src bash :session *INSTALLFABULOUS* :tangle install-fabulous.sh
+    #!/bin/bash
+    export SPACK_ROOT=/home/tmijieux/spack
+    #+end_src
+
     Load spack to into your terminal environment:
-    #+begin_src sh :tangle load_spack.sh
-    PWD=$(pwd)
-    WORKDIR=${WORKDIR:-${PWD}}
-    export SPACK_ROOT=${SPACK_ROOT:-${WORKDIR}}
+    #+begin_src bash :session *INSTALLFABULOUS* :tangle install-fabulous.sh
     source ${SPACK_ROOT}/share/spack/setup-env.sh
     export MODULEPATH=$SPACK_ROOT/share/spack/modules/linux-x86_64:$MODULEPATH
     spack compiler find
@@ -20,68 +28,30 @@
 
 *** Install Fabulous
     On plafrim, you need to load the required modules:
-    #+begin_src sh :tangle plafrim_module.sh
+    #+begin_src bash :session *INSTALLFABULOUS* :tangle install-fabulous.sh
     module purge
     module load compiler/gcc/6.1.0
     module load build/cmake/3.2.1
     module load intel/mkl/64/11.2/2016.0.0
     #+end_src
 
-    Fabulous is a c++ application that use Chameleon kernel whose API are written in C.
-    More specifically Chameleon API use C literal complex types that does not exist in C++.
-    The good point is that C complex type 'float _Complex' and 'double _Complex'
-    are 'binary compatible' (they have the same memory layout and constraints) with
-    c++ std::complex<float> and std::complex<double>.
-    Hence it is possible to replace C complex type with C++ complex types in Chameleon header
-    depending on the langage of the targeted application.
-    (For instance, this is done in LAPACKE header, see 'lapacke_config.h')
-    This is (currently) not handled in the main branch of Chameleon, so we need to clone
-    a fork of the main chameleon release which can do that.
-    (you can expect that it will be included in the main release in the future)
-
-    #+begin_src sh :tangle install_with_chameleon.sh
-    #!/bin/bash
-    PWD=$(pwd)
-    WORKDIR=${WORKDIR:-${PWD}}
-    cd ${WORKDIR}
-    source plafrim_module.sh
-    source load_spack.sh
-    git clone https://gitlab.inria.fr/tmijieux/chameleon.git --branch complex_type_header
-    cd chameleon
-    git submodule init && git submodule update
-    cd ..
-    #+end_src
-
     Set shell variables for spack to find the dependencies
-    #+begin_src sh :tangle install_with_chameleon.sh
+    #+begin_src bash :session *INSTALLFABULOUS* :tangle install-fabulous.sh
     export CMAKE_DIR=/cm/shared/dev/apps/build/cmake/3.2.1
-    export CHAMELEON_DIR=${WORKDIR}/chameleon
     #+end_src
 
     Check the specification with:
-    #+begin_src sh :tangle install_with_chameleon.sh
-    SPEC="fabulous@develop+chameleon%gcc@6.1.0 ^chameleon@src ^mkl@exist ^cmake@exist"
+    #+begin_src bash :session *INSTALLFABULOUS* :tangle install-fabulous.sh
+    SPEC="fabulous@develop+chameleon%gcc@6.1.0 ^chameleon@master ^mkl@exist ^cmake@exist"
     spack spec ${SPEC}
     #+end_src
 
-    If you use the tangled script, this prompt you so you can check the spec
-    safely before installing:
-    #+begin_src sh :tangle install_with_chameleon.sh
-    echo CMAKE_DIR=${CMAKE_DIR}
-    echo CHAMELEON_DIR=${CHAMELEON_DIR}
-    read -p "Is this ok? [Y/n] " -n 1 -r
-    echo
-    if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-        exit 1
-    fi
-    #+end_src
-
     On plafrim, spack may have troubles fetching the required dependencies
     on the internet. If you encounter this issue, you can create a spack
     mirror on your machine and sent it to plafrim:
-    #+begin_src sh
+    #+begin_src bash
     #local machine:
-    spack mirror create -d chameleon_mirror -D -o fabulous
+    spack mirror create -d fabulous_mirror -D -o fabulous@develop+chameleon^chameleon@master
     # mirror store dependencies as compressed archives already
     # so it is not very useful to add anymore compression at this stage:
     tar cf fabulous_mirror.tar fabulous_mirror/
@@ -92,21 +62,20 @@
     #+end_src
 
     If everything looks good, you can proceed the installation with:
-    #+begin_src sh :tangle install_with_chameleon.sh
+    #+begin_src bash :session *INSTALLFABULOUS* :tangle install-fabulous.sh
     spack install -v ${SPEC}
     #+end_src
 
-    To perform all this with an automated script you can do
-    #+begin_src emacs-lisp
+    You can perform these actions either manually, by evaluating the code blocks
+    directly inside emacs if your org-mode support it, or by tangling this org
+    document to produce [[./install-fabulous.sh][install-fabulous.sh]] and execute it:
+
+    #+begin_src emacs-lisp :results silent
     (org-babel-tangle)
     #+end_src
-    or with the emacs command:
-    #+begin_src emacs
-    M-x org-babel-tangle
-    #+end_src
 
     then:
-    #+begin_src sh
-    chmod +x ./install_with_chameleon.sh
-    ./install_with_chameleon.sh
+    #+begin_src bash
+    chmod +x ./install-fabulous.sh
+    ./install-fabulous.sh
     #+end_src

RESULTS.org

@@ -2,10 +2,8 @@
 # -*- coding: utf-8 -*-
 
 #+TITLE: FABuLOuS numericals results
-#+STARTUP: showeverything
 
-* RESULTS
-** Get Test files
+* Get Test files
    [[file:./build/src/data/young1c.mtx][young1c.mtx]]
    [[file:./build/src/data/matrices_BEM/MatconeSpherePC_MAIN_MAIN_0][MatconeSpherePC_MAIN_MAIN_0]] (binary)
    [[file:./build/src/data/matrices_BEM/coneSpherePC_RHS_MAIN.0.res][coneSpherePC_RHS_MAIN.0.res]] (binary)
@@ -21,8 +19,8 @@
    [[file:./build/src/data/bidiagonalmatrix3.mtx][bidiagonalmatrix3.mtx]]
    [[file:./build/src/data/bidiagonalmatrix4.mtx][bidiagonalmatrix3.mtx]]
 
-*** Downloads
-#+begin_src shell :session *DOWNLOADS* :results none
+** Downloads
+#+begin_src shell :session *DOWNLOADS* :results silent
 files=(
     "ftp://math.nist.gov/pub/MatrixMarket2/Harwell-Boeing/bcsstruc2/bcsstk14.mtx.gz"
     "ftp://math.nist.gov/pub/MatrixMarket2/Harwell-Boeing/sherman/sherman4.mtx.gz"
@@ -38,10 +36,10 @@ for i in "${files[@]}"; do
 done
 #+end_src
 
-** Run Examples
+* Run Examples
    Set this variable to your work directory (where you downloaded fabulous):
-#+begin_src sh :session *TEST* :results none
-export WORKDIR=/home/tmijieux/fabulous
+#+begin_src sh :session *TEST* :results silent
+export WORKDIR=/home/tmijieux/fabulous # for example
 #+end_src
 
 To be able to run the following test cases, you must have compiled fabulous:
@@ -53,9 +51,9 @@ cmake .. # -DCHAMELEON_DIR=$(spack location -i chameleon)
 make
 #+end_src
 
-*** Impact of restart parameter
-**** run test case
-#+begin_src sh :session *TEST* :results none
+** Impact of restart parameter
+*** run test case
+#+begin_src sh :session *TEST* :results silent
 cd ${WORKDIR}/build/src/test_core/
 mkdir -p ../data/res
 sizes=(200 400 600 800 1000)
@@ -64,7 +62,7 @@ for siz in "${sizes[@]}"; do
 done
 #+end_src
 
-**** plot the graphic
+*** plot the graphic
 #+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
 library(ggplot2)
 df <- read.table("./build/src/data/res/r=200.res", header=T)
@@ -78,10 +76,9 @@ ggplot(df, aes(x=nb_mvp, y=maxRes, color=name)) +
     geom_hline(aes(yintercept=1e-4, color="threshold")) +
     scale_y_log10() + ggtitle("Memory usage influence (young1c IB IMGS-RUHE)")
 #+end_src
-
-*** Impact of incremental QR factorization
-**** run test case
-#+begin_src sh :session *TEST* :results none
+** Impact of incremental QR factorization
+*** run test case
+#+begin_src sh :session *TEST* :results silent
 cd ${WORKDIR}/build/src/test_core/
 ./testMatrixMarketChoice -t BLOCK -s CGS -m 900 -A STDDR -u -o "Basic_GELS"
 ./testMatrixMarketChoice -t BLOCK -s CGS -m 900 -A QR -u -o "QR_factorization"
@@ -96,14 +93,14 @@ ggplot(df, aes(x=global_iteration, y=least_square_time, color=name)) +
 
 #+end_src
 
-*** Influence of the Algorithm
-**** run test case
-#+begin_src sh :session *TEST* :results none
+** Influence of the Algorithm
+*** run test case
+#+begin_src sh :session *TEST* :results silent
 cd ${WORKDIR}/build/src/test_core/
 mkdir -p ../data/res
 ./testMatrixIW_DR
 #+end_src
-**** plot the graphic
+*** plot the graphic
 #+begin_src R :results output graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
 library(ggplot2)
 df <- read.table("./build/src/data/res/STD.res", header=T)