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 APP.

Preparing Simulation

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 (ECELL Session Script, or ESS) to automate the simulation session.

Converting EM to EML

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

ecell3-em2eml filename.em

You can obtain the full description of the command line options giving -h option to ecell3-em2eml.

ecell3-eml2em -- convert eml to em

        ecell3-eml2em [-h] [-f] [-o outfile] infile

        -h or --help    :  Print this message.
        -f or --force   :  Force overwrite even if outfile already exists.
        -o or --outfile=:  Specify output file name.  '-' means stdout.

Compiling C++ Dynamic Modules

You might have some Dynamic Modules (or DM in short) specifically made for the simulation model in the form of C++ source code. If that is the case, those files have to be compiled and linked to form shared module files (usually suffixed by .so on Unix-like platforms, .dylib on Mac OS X or .dll on Windows) before running the simulation. You will also need to set ECELL3_DM_PATH environment variable to the appropriate value to use the DMs (discussed below).

To compile and like DMs, ecell3-dmc command is provided for convenience.

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 shown by issuing 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.

Starting APP

You can start APP either in scripting mode and GUI mode.

GUI mode

To start APP in GUI mode, type the following command.


This will invoke an instance of the simulator with Osogo Session Manager attached as a GUI frontend.

Scripting mode

To start APP in scripting mode, type the following command:

where filename.ess is the name of the Python script file you want to execute.

If filename.ess is omitted, the interpreter starts up in interactive mode.

See chapter 5 for the scripting feature.

DM search path and ECELL3_DM_PATH environment variable

If your model makes use of non-standard DMs that you had to build using ecell3-dmc, then you need to specify the directory where the DMs are placed in ECELL3_DM_PATH environment variable. ECELL3_DM_PATH can have multiple directory names separated by either : (colon) on Unix-like platform or ; (semicolon) on Windows.

The following is an example of setting ECELL3_DM_PATH before launching ecell3-session-monitor:

Note that up to E-Cell SE 3.1.105, the current working directory was implicitly treated as if it was included in ECELL3_DM_PATH. This quirk is removed since 3.1.106.