Chapter 2. Getting Started

By reading this chapter, you can get information about the following items.

What types of files are needed to run the simulator.
How to prepare the files needed to run the simulator.
How to run the simulation with E-Cell Simulation Environment.

2.1. Preparing Simulation

To start the simulation, you need to have these types of files:

2.1.1. Converting EM to EML

Simulation models for E-Cell is often written in EM format. To convert EM (.em) files to EML (.eml) files, type the following command.

ecell3-em2eml filename.em

2.1.2. Compiling C++ Dynamic Modules

If may have your own classes (Dynamic Modules, or DM) defined for the simulation model in form of C++ source code files. Those files must be compiled before using.

Use ecell3-dmc command as the DM compiler.

ecell3-dmc [options] filename.cpp [compiler options]

The arguments given before the file name ([command options] are interpreted as options to the ecell3-dmc command itself.

The arguments after the file name are passed to a backend compiler (such as g++) as-is. The backend compiler used is the same as that used to build the system itself.

To inspect what the command actually does inside, enable verbose mode by specifying -v option.

To get a full list of available ecell3-dmc options, invoke the command with -h option, and without the input file. Here is the help message gotten by ecedll3-dmc -h.


Compile dynamic modules for E-Cell Simulation Environment Versin 3.

Usage:
        ecell3-dmc [ ecell3-dmc options ] sourcefile [ compiler options ]
        ecell3-dmc -h|--help

ecell3-dmc options:
        --no-stdinclude          Don't set standard include file path.
        --no-stdlibdir           Don't set standard include file path.
        --ldflags=[ldflags]      Specify options to the linker.
        --cxxflags=[cxxflags]    Override the default compiler options.
        --dmcompile=[path]       Specify dmcompile path.
        -v or --verbose          Be verbose.
        -h or --help             Print this message.