Skip to content
Snippets Groups Projects
Commit 21a2b5ac authored by midou's avatar midou
Browse files

Create YALES2BIO directory + update the download file and occigen environment

parent b676d810
No related branches found
No related tags found
No related merge requests found
Showing
with 113 additions and 0 deletions
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.
git clone git@gitlab.coria-cfd.fr:yales2bio-devel/yales2bio-devel.git
source machines/occigen-bdw/env_bench
cd $YALES2_HOME
git checkout 8de0e3c11c0d701d93bdaa2e034cd496e0ed60b2
module purge
module load intel/18.1
module load intelmpi/2018.1.163
module load hdf5-seq/1.8.17
module load parmetis/4.0.3-real64
module load scotch/6.0.4
module load python #/3.6.3
export YALES2_HOME=$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'
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/)
This diff is collapsed.
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment