AMAPstudio

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Installing/running

This page describes how to run AmapSim simulator (named gaspp in Linux world and gaspp.exe in windows world) from a command prompt window. It may be convenient to use this policy when intending to perform many automatic simulations through scripts. Nevertheless, most of the time, newprg will allow a more confortable way to run simulations.

Syntax

there are two calling syntax :

Single simulation command :

gaspp plant age [seed] [-sGeomSimplification] [-STopoSimplification [-deltaDelta]] [-g[step]] [-gl[step]] [-a[step]] [-oOutputFileName] [-cModule [-eModuleData]] [[-fsstep] -foCustomOutputFormat] [-beginx] [-posxx] [-posyx] [-poszx] 
      plant : name of the plant (if single name, .cfg file will be used for parameter file location) 
      age : age to be computed 
      seed : random number initialisation number 
      -s : GeomSimplification is the simplification level on geometrical output (from 0 to 4, default 1)
      -S : TopoSimplification is the simplification level on topological computing (from 0 to 3, defoault 0)
      -delta : birth date threshold to build simplified classes
      step : output step (only at simulation end by default)
      -o : output to a particular OutputFileName file (without extension), this MUST be a complete path/filename
      -g : output linetree format
      -gl : output opf format
      -a : output mtg format
      -n : output natFX format
      -c : dynamicaly link the module file Module to the simulation kernel
      -e : provide the current Module with ModuleData as private data configuration file
      -swap : change bytes output order (switch between little and big endian
      -fo : load a custom output format module
      -fs : custom output step
      -posx : the x world position of this plant (0 by default)
      -posy : the y world position of this plant (0 by default)
      -posz : the z world position of this plant (0 by default)
      -begin : the absolute beginning time for growth simulation (0 by default)

Multiple simultaneous simulation command

gaspp Scene
       Scene : a text file describing a scene which means that each line consists in a single command

For instance :

  gaspp "d:/myplant.fpa" 30 1

would compute (in a windows world) the plant species described in the file d:/myplant.fpa up to age 30 with random seed 1. There will be no output.

  gaspp "d:/myplant.fpa" 30 1 -s0 -g2 -o"d:/myOutput/plant"

would compute the same plant with geometrical simplification level 0 and output to an internal format every two computing steps. The output will be saved in directory d:/myOutput to files with name plant_xx_1.lig where xx is the current simulation step age.

  gaspp "d:/myplant.fpa" 30 1 -S2 -gl -o"d:/myOutput/plant"

would compute the same plant with topological simplification level 2 and output to opf format at the end of simulation in a file named d:/myOutput/plant_30_1.opf.

  gaspp "/home/me/parameterFiles/myplant.fpa" 30 1 -S2 -a -o"/home/me/myOutput/plant" -c"/usr/local/bin/light.so" -e"/home/me/data/lightparameter.txt"

would perform the same computing (in a linux world) connecting the executable plug-in file /usr/local/bin/light.so that uses its own data coming from file /home/me/data/lightparameter.txt. The output will be stored in the file /home/me/myOutput/plant_30_1.mtg

  gaspp "d:/myScene.txt"

would run a multiple simulation configured in the scene file d:/myScene.txt. A scene file is a text file where each line describes a single simulation command. It is important to anderstand that every simulations will be carried out using the same scheduler thus mimicing a simultaneous growth of some individual plants. This feature allows to think about simulating competition between growing plants. Here is an example of a scene file :

  #plant simulation
  gaspp D:\merisierv20.fpa 30 0 -gl -s0 -cd:/thevitisnew/release/light.dll -ed:/lightParameter.txt -od:/mir/opf/plant1 posx1 posy1
  gaspp D:\merisierv20.fpa 30 0 -gl -s0 -cd:/thevitisnew/release/light.dll -ed:/lightParameter.txt -od:/mir/opf/plant2 posx5 posy1
  gaspp D:\merisierv20.fpa 30 0 -gl -s0 -cd:/thevitisnew/release/light.dll -ed:/lightParameter.txt -od:/mir/opf/plant3 posx1 posy5
  gaspp D:\merisierv20.fpa 30 0 -gl -s0 -cd:/thevitisnew/release/light.dll -ed:/lightParameter.txt -od:/mir/opf/plant4 posx5 posy5

In this file, any line beginning with a '#' will be skipped. The 4 plant simulation commands will simulate 4 different plants described in the file D:\merisierv20.fpa. Each of them will be simulated up to 30 with a random seed 0; an output in opf format to file d:/mir/opf/plantx_30_0.opf; and a position on the corner of a square. The core simulator will be connected to the d:/thevitisnew/release/light.dll plug-in with light data in the file d:/lightParameter.txt (see the light plug-in for more details).

Environment variable setup

To be ready to run, your system must be aware of the software location. If the software does not run at all (file not found) or if it has strange behaviour, this may come from non-accurate environment variable setting. Here are some advice on how to check and adapt it.

Under Linux system you should check that both environment variable PATH and LD_LIBRARY_PATH are correctly set. To do so, open a shell window (Xterm, terminal) from the desktop menu bar and type the command :

  echo $PATH; echo $LD_LIBRARY_PATH

You should see something looking like :

 .:/home/me/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 .:/home/me/bin:/usr/local/lib:/usr/lib

If you don't see in both lines the path to the AmapSim installation directory, you will have to add it. To do so, have a look to this web page : http://www.cyberciti.biz/faq/set-environment-variable-linux/ Assume your AmapSim software installation directory is : /home/me/bin, after configuration, the same command should display something like :

 .:/home/me/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 .:/home/me/bin:/usr/local/lib:/usr/lib

Under Windows system you should check that environment variable PATH is correctly set. To do so, open a cmd window and type

  echo %PATH%

You should see something looking like :

  C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Common Files\SYSTEM\MSMAPI\1036

If you don't see in the line the path to the AmapSim installation directory, you will have to add it. To do so, have a look to this web page : http://www.ditainfocenter.com/eclipsehelp/index.jsp?topic=/ditaotug_top/installing/windows_settingenvvariables.html

soft/amapsim/b_installing_running/start.txt ยท Last modified: 2015/01/08 14:01 by barczi