Add the download and compiling of GYSELAX

GYSELAX/README.md

@@ -4,19 +4,18 @@ Description:
 Presentation
 ------------
 
-This template is just here to show the way that we should present the README for a given application. 
+YALES2BIO is a red blood flow solver. It is used for the analysis of medical devices in contact with blood such as flow diverters, Ventricular Assist Devices, extra corporal circulation, artificial heart and valves, cytometers among others. Optimizing such devices requires dealing with both macroscopic (pressure loss, residence time, wall shear stress, turbulence) and microscopic (blood cells deformation and interaction with other cells or solid boundaries) features.
 
-Here I describe that this template is not performing any scientific simulation, and uses no specific library.
 
 Technical information:
 ----------------------
 
-* website : http://this.url.doesnot.work 
-* Scientific domain : none 
-* Language : C/C++/Fortran/Python
+* website : https://imag.umontpellier.fr/~yales2bio/index.html 
+* Scientific domain : haemodynamics 
+* Language : Fortran
 * Parallelism : MPI + OpenMP
-* GPU acceleration : Yes (CUDA) 
-* Scalability : high
+* GPU acceleration : No  
+* Scalability : good
 * Vectorization: poor
 
 
@@ -28,9 +27,8 @@ Here we describe the different phases from the download to the validation of the
 Download:
 ---------
 
-Information (if needed) about how to get the sources.
+The sources are available in a tarball and correspond to a stable release. To un-tar this release, run  
 
-For instance:
 ```
 ./download.sh
 ```
@@ -38,9 +36,12 @@ For instance:
 Compile:
 --------
 
-Information (if needed) about how to compile the application. 
+To compile the code, several librairies are needed:  
+* hdf5 in sequential (works with the 1.8.17 version)
+* parmetis
+* scotch
 
-For instance:
+Then, a Makefile.in is needed. For IRENE, OCCIGEN and JEAN-ZAY platforms, this file is already made. For another platform one has to write it. An example can be found in... 
 
 Compile the code using:
 ```

GYSELAX/compile.sh

+####################################
+# TEST THE ENVIRONMENT
+####################################
+echo "################################"
+
+####################################
+# GO TO GYSELAX DIRECTORY
+####################################
+cd $GYSELA_PATH
+
+####################################
+# COMPILING
+####################################
+echo "COMPILING: it can take several minutes"
+./scripts/gysmake 1>01.make.out 2>01.make.err
+echo "COMPILING: end"
+
+####################################
+# TEST THE COMPILATION
+####################################
+echo "CHECKING THE COMPILATION:"
+if test -f "$GYSELA_PATH/wk/gysela.exe"; then
+   echo ">> Compilation: SUCCESSFUL"
+else
+   echo ">> Compilation: FAILED"
+   echo ">> Please look at the $GYSELA_PATH/01.make.out "
+   echo ">> and $GYSELA_PATH/01.make.err files"
+   exit
+fi
+echo "################################"

GYSELAX/download.sh

-git clone https://gitlab.maisondelasimulation.fr/gysela-developpers/gysela.git
+####################################
+# CLONE THE GYSELAX REPO
+####################################
+git clone https://gitlab.maisondelasimulation.fr/gysela-developpers/gysela.git 1>/dev/null 2>/dev/null
+
+####################################
+# TEST THE DOWNLOAD
+####################################
+echo "##########################"
+echo "CHECKING THE DOWNLOAD:"
+if [ "$(ls -A ./gysela/src/ 2>/dev/null)" ]; then
+     echo ">> main directory is not empty - DOWNLOAD SUCCESSFUL"
+else
+     echo ">> main directory is empty - DONWLOAD FAILED"
+     exit
+fi 
+echo "##########################"

GYSELAX/machines/occigen-bdw/env_bench

@@ -2,4 +2,5 @@ module purge
 module load intel/17.0 openmpi/intel/2.0.1 mkl/17.0 hdf5-seq/1.8.17 cmake python/2.7.13
 
 export ARCH=occigen2
-source $HOME/cines_git/abs/GYSELAX/gysela/scripts/lib/setup_path.sh
+pwd
+source ./gysela/scripts/lib/setup_path.sh