Create YALES2BIO directory + update the download file and occigen environment

YALES2BIO/README.md

+Description:
+============
+
+Presentation
+------------
+
+This template is just here to show the way that we should present the README for a given application. 
+
+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
+* Parallelism : MPI + OpenMP
+* GPU acceleration : Yes (CUDA) 
+* Scalability : high
+* Vectorization: poor
+
+
+Compilation and simulation:
+===========================
+
+Here we describe the different phases from the download to the validation of the simulation.
+
+Download:
+---------
+
+Information (if needed) about how to get the sources.
+
+For instance:
+```
+./download.sh
+```
+
+Compile:
+--------
+
+Information (if needed) about how to compile the application. 
+
+For instance:
+
+Compile the code using:
+```
+source machines/occigen-bdw/env
+./compile.sh
+```
+
+`machines/occigen-bdw/env` contains the information for compilation (module load gcc openmpi lapack hdf5 ...)
+
+Run and validate the simulation:
+--------------------------------
+
+For each test case, given in a separate folder (e.g. testcase_small), you can find three scripts:
+
+*  prepare.sh: prepare the simulation (move data to the right location, recompile some minor changes, ...)
+*  run.sh : run the application and print out the evaluated metric
+*  validate.sh: validation of the simulation on a scientific point of view
+
+For running and validating the simulation, one should be able to do:
+```
+cd testcase_XXX
+./prepare.sh
+./run.sh
+./validate.sh
+```
+And getting no error code returned.
+Those steps can also be used in a batch file for running the simulation using a job scheduler.
+
+
+
+

YALES2BIO/download.sh

+git clone git@gitlab.coria-cfd.fr:yales2bio-devel/yales2bio-devel.git
+source machines/occigen-bdw/env_bench 
+cd $YALES2_HOME
+git checkout 8de0e3c11c0d701d93bdaa2e034cd496e0ed60b2

YALES2BIO/machines/occigen-bdw/env_bench

+module purge
+module load intel/18.1
+module load intelmpi/2018.1.163
+module load hdf5-seq/1.8.17
+module load parmetis/4.0.3-real64
+module load scotch/6.0.4
+module load python #/3.6.3
+
+export YALES2_HOME=$HOME/cines_git/abs/YALES2BIO/yales2bio-devel/ # installation path
+export YALES2_HOSTTYPE=occigen  # name of the platform
+
+export METIS_IDXTYPEWIDTH=`grep IDXTYPEWIDTH $PARMETIS_DIR/include/metis.h | head -n 1 | awk -F" " '{print $3}'`
+export METIS_REALTYPEWIDTH=`grep REALTYPEWIDTH $PARMETIS_DIR/include/metis.h | head -n 1 | awk -F" " '{print $3}'`
+
+module use $YALES2_HOME/modules
+module load y2o
+#module load y2py
+
+alias y2o='module unload -f y2d && module load y2o'
+alias y2d='module unload -f y2o && module load y2d'

YALES2BIO/testcase_small/README.md

+Test case presentation
+======================
+
+The small test case of the template application is doing nothing but watching videos on Youtube all day long.
+It uses no DFT method, nor spectral method or anything else. The FFTW is widely not use for this case.
+
+
+Case profile
+------------
+
+A profiling of a small specfem3D test case performed on Occigen on 1 haswell node (64GB) is available in this folder:
+`profile_occigen-hsw.html"
+
+It has been generated using Intel APS (infos: https://software.intel.com/sites/products/snapshots/application-snapshot/)