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. |
To start the simulation, you need to have these types of files:
A model file in EML format.
(optionally) shared object files (.so in Linux operating system), if you are using special classes of object in the model file which is not provided by the system by default.
(optionally) a script file (E-Cell Session Script, or ESS) to automate the simulation session.
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
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.