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GillespieHT

WARNING : SOFTWARE IN BETA, UNDER DEVELOPMENT

Gillespie Algo High Throughput MPI application

https://github.com/EricPascolo/GillespieHT/

This software take in input a Biological linear system of reaction described to json file. If you use MPI you can compute more system in parallel because this is High Throughput application.

COMPILATION

Requirements: Compiler C (icc preferred), Intel MKL library, MPI Software Stack

The software is compiled through Makefile.

In make file you must change the flag -DVECTOR_SIZE=$YOUR_SIZE, where $YOUR_SIZE is the size with which the arrays are aligned. The another flag you must change depending to your architecture is MKL flags: -DMKL_ILP64.

For found correct MKL flags, you can use Intel® Math Kernel Library Link Line Advisor: https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor

USE application

You can launch application using:

mpirun -np $NCORE ./GillespieHT $DIR_INPUT $DIR_OUTPUT where:

  • $NCORE : numer of pes(1 master, NCORE -1 slave)
  • $DIR_INPUT : directory that contains jSON file that described input system
  • $DIR_OUTPUT : directory that will contain output file

Serial run is allow, in this case master node compute the algorithm. You can launch application in serial mode using:

./GillespieHT $DIR_INPUT $DIR_OUTPUT

jSON Input

#####Description

Il JSON che descrive il sistema deve avere le seguenti caratteristiche:

  • nameSystem (String): system name (output file is named as this)
  • simultationTime (int) : max simulation time
  • species (jSON array) : array of chemical species
    • name (String) : name of specie;
    • idx (int) : index unique corresponding specie in simulation ;
  • reaction (jSON array) : array of reaction in the system
    • K (double) : K costant of reaction
    • reagents (JSON array) : reagents array
      • idx (int) : index of species
      • stechio(int) : stechiometrics index
    • products (JSON array) : reagents array
      • idx (int) : index of species
      • stechio(int) : stechiometrics index
  • status (jSON array) : number of initial quantities per species, the order is the same of species jSON array.

ATTENTION : all stechiometrics idex must be positive.

#####Example of jSON input:

{
    "nameSystem": "prova1", 
    "simultationTime":1000,
    "species" :[
	  {"name":"Na","idx":0}, {"name":"Cl","idx":1},{"name":"NaCl","idx":2},
	  {"name":"CH4","idx":3},{"name":"O2","idx":4},{"name":"CO2","idx":5},
	  {"name":"H2O","idx":6},{"name":"F","idx":7},{"name":"NaF","idx":8}
    
    ],
    
    
    "status" :[{"num":0},{"num":1},{"num":3},{"num":4},{"num":5},{"num":6},{"num":7},{"num":8},{"num":9}],
    
    "reaction": [

      {  
 	"K" :       8,
        "reagents": [
	  {"idx":0,"stechio":1},{"idx":1,"stechio":1}   
	 ], 
        "products": [
	  {"idx":2,"stechio":1}   
	 ]
       },
	
	{ 
 	"K" :       10,
        "reagents": [
	  {"idx":3,"stechio":1},{"idx":4,"stechio":1}   
	 ], 
        "products": [
	  {"idx":5,"stechio":1},{"idx":6,"stechio":1}    
	 ]
       },
       
       { 
 	"K" :      12,
        "reagents": [
	  {"idx":0,"stechio":1},{"idx":7,"stechio":1}   
	 ], 
        "products": [
	  {"idx":8,"stechio":1}    
	 ]
       }
     ]
}

NOTE: In the example the reactions are not balanced and K is random, is not mistake, is only example.

OUTPUT

#####MASTER OUTPUT

The ouput of master process give information about the progress of the simulation and its parameter. The example is reported below.

GILLESPIE HT v 1.0                                                                                                                                                     
Gillespie algo high throughput software                                                                                                                                
https://github.com/EricPascolo/GillespieHT                                                                                                                                
Created by Eric Pascolo                                                                                                                                                
                                                                                                                                                                       
        Parallel Run with 3 slave
        Threads/Task : 4
        Input directory : ../test/                                                                                                                                     
        Output directory : ../testOut//                                                                                                                                
        Number of file: 7                                                                                                                                              
                                                                                                                                                                       
BEGIN Simulation at 10:23:09 2014:09:25                                                                                                                                
                                                                                                                                                                       
                                                                                                                                                                       
        LIST FILE                                                                                                                                                      
        ---------                                                                                                                                                      
            0          prova5.json                                                                                                                                     
            1          prova4.json                                                                                                                                     
            2          prova2.json                                                                                                                                     
            3          prova6.json                                                                                                                                     
            4          prova3.json                                                                                                                                     
            5          prova7.json                                                                                                                                     
            6          prova1.json                                                                                                                                     
        ---------                                                                                                                                                      
                                                                                                                                                                       
SLAVE     2      BEGIN:           10:23:09 2014:09:25  -> file     1                                                                                                   
SLAVE     3      BEGIN:           10:23:09 2014:09:25  -> file     2                                                                                                   
SLAVE     1      BEGIN:           10:23:09 2014:09:25  -> file     0
SLAVE     2        END:           10:23:09 2014:09:25  -> file     1
SLAVE     2      BEGIN:           10:23:09 2014:09:25  -> file     3
SLAVE     3        END:           10:23:09 2014:09:25  -> file     2
SLAVE     3      BEGIN:           10:23:09 2014:09:25  -> file     4
SLAVE     1        END:           10:23:09 2014:09:25  -> file     0
SLAVE     1      BEGIN:           10:23:09 2014:09:25  -> file     5
SLAVE     2        END:           10:23:09 2014:09:25  -> file     3
SLAVE     2      BEGIN:           10:23:09 2014:09:25  -> file     6
SLAVE     3        END:           10:23:09 2014:09:25  -> file     4
SLAVE     1        END:           10:23:09 2014:09:25  -> file     5
SLAVE     2        END:           10:23:09 2014:09:25  -> file     6
SLAVE     2   SHUTDOWN:           10:23:09 2014:09:25 
SLAVE     1   SHUTDOWN:           10:23:09 2014:09:25
SLAVE     3   SHUTDOWN:           10:23:09 2014:09:25

END Simulation at 10:23:09 2014:09:25

#####SLAVE OUTPUT All slave write an output file in $DIR_OUTPUT named as nameSystem. For each time step, slave print two line:

STATUS ARRAY
TIME   NUM_REACTION    K_SUM

EXTERNAL LIBS

Thanks to cJSON (http://sourceforge.net/projects/cjson/)

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