5. Running TM5

A typical way to run TM5 is to take following steps:

1. Go to the TM5 directory (not necessary):

   cd TM5/cy2

2. Copy a template rcfile and give it a suitable name:

   cp rc/tm5.rc tm5-test.rc

   Modify it using your favorite editor. The contents of the template rcfile should be self explainable, if not, take a more inteligent look at it.
3. Start TM5 using:

   run-tm5 tm5-test.rc

   For exact synopsis, use:

   run-tm5 --help

The following steps are taken (might be switched off by settings in the rcfile).

Preprocessing the rcfile

The run scripts preprocesses the rcfile and gives it a unique name including the process id number, for example:

jb.12345.rc

In future, the 'run-tm5' script should be able to submit jobs to a queue (on ECMWF machines) or the background (workstatins), writing similar files for the submitted job and output:

jb.12345.jb
jb.12345.out
jb.12345.err

Preprocessing an rcfile includes evaluation of environment variables. For more info, use:

base/bin/go_pprc --help

Configuration of a source code

A TM5 source code is created in subdirectories of the run directory (specified in the rcfile):

<rundir>/src/
<rundir>/bin/

First, the sources in 'base/' are copied. This is a working copy with default grid and dummy chemistry.

The files from the base version are then optionally overwritten by project specific versions from 'proj/' directories. See section 3.3.

A 'Makefile' is created by the 'configure' script. The created makefile contains the correct compiler flags for the platform you are working on and for the optimization level specified in the rcfile.

Job file creation

A job file is created from the template 'run-tm5.jb'. By default the job file is run in the foregroud. If the run is started with 'run-tm5 -q', the job is submitted to a queue system or, if no queue available, to the background.

Compile

The source is compiled in '<rundir>/src/'.

Since object files might consume a lot of disk space, it might be a good idea to have the '<rundir>' on a scratch partion.

Run

The executable is copied to the run directory and executed.