Home.md

 # Introduction
 
-Nemo modelfactors is a wrapper made to simplify the process of obtaining basic performance metrics from NEMO using the BSCTOOLS set.
+Nemo modelfactors is a wrapper made to simplify and automatize the process of obtaining basic performance metrics from NEMO using the BSCTOOLS set.
 
-The script does all the required modifications to the NEMO configuration and arch files in order to be able to obtain traces from a NEMO execution with extrae, afterwards, the traces are processed and finally the performance metrics are generated using the basicanalysis tool.  
+# Installation
 
-The script was developed using NEMO 4.2 and it is not tested in other versions. For this reason is highly recommended to have installed that NEMO version.
+This script relies on the following tools:
 
-# Parameters
+* *Extrae (4.0.0 or above)*
+* *Paraver*
+* *Dimemas (5.4.2-devel)*
+* *Basicanalysis*
+
+*They can be downloaded at https://tools.bsc.es/downloads* and need to be installed, loaded and available through the PATH environment variable.
+
+Here the list of the modules that need to be loaded before the script execution.
+
+* Perl interpreter.
+* Fortran compiler (ifort, gfortran, pgfortran, ftn, …),
+* Message Passing Interface (MPI) implementation (e.g. OpenMPI or MPICH).
+* Network Common Data Form (NetCDF) library with its underlying Hierarchical Data Form (HDF).
+
+# Usage
+
+* Clone this repository wherever you please.
+* Inside the cloned repository use `git submodule update --init` to load the submodules.
+* ***Edit the file perf_metrics.config and replace the parameters values with the suited information.***
+* ***MINIMUM CHANGES perf_metrics.config:***
+  * Nemo_path, change the value to the path were NEMO is installed in your machine.
+  * Nemo_input_data, change the value to the path were the input data for the configuration is downloaded.
+  * Compilation_arch, replace the value with the name of the arch file that you use to compile NEMO.
+  * Modules, change the value to suit the name of the modules you need to load.
+  * Jobs_scheduler, replace the value with the name of the scheduler installed in your machine (currently supports slurm, lsf and torque)
+* Execute perf_metrics.bash
+
+```
+./perf_metrics.bash
+```
+
+* If the script executes without problems the data will be by default ready inside ../Output/Metrics folder. The Output dir path can be changed using a parameter.
+
+## Parameters
 
 Nemo modelfactors requires parameters in order to work properly, those are added by modifying the perf_metrics.config file.
 
@@ -36,7 +69,7 @@ Nemo modelfactors requires parameters in order to work properly, those are added
 * Compilation_sub (string): Add or remove sub-components.
 * Modules (string): List of modules loaded.
 
-# Output
+## Output
 
 Nemo modelfactors generates a Output folder during execution.The location of this folder can be modified in perf_metrics.config, this allows having the main script in a low capacity file system while the heavy data is stored somewhere else.
 
@@ -46,7 +79,7 @@ It contains:
 - **Run_Nemo:** Is where the NEMO execution will be produced, contains all the input data, the executable and the output files of NEMO.
 - **Metrics:** Folder where the performance metrics data produced is stored, more information in the next section.
 
-# Data generated
+## Data generated
 
 All the data generated can be found inside the Metrics folder.