= PALM Quickstart Guide =

Ideally, you have successfully installed PALM using the [wiki:doc/install/automatic automatic installer]. If so, the installer has 
* downloaded PALM from the subversion control (svn) repository into a predefined directory structure on your local computer (see Fig. 1),\\\\
* created the required palmrun [wiki:doc/app/palmrun configuration file], e.g. '''.palm.config.default''' (hidden file),\\\\
* written some environment variables to Bash configuration file {{{$HOME/.bashrc}}}
{{{
  export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH
  export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS
}}}
* pre-compiled ([wiki:doc/app/palmbuild palmbuild]) the '''UTIL'''ity programs and '''SOURCE''' code,\\\\
* run some small test simulations ('''JOBS''', see Fig. 2).\\


{{{#!table style="border: none"
   {{{#!tr
      {{{#!td  style="border: none; width:10%" \\
      }}}
      {{{#!td style="border: none;vertical-align:top"
'''Fig. 1'''\\\\
[[Image(file_tree_1.png, 50%, left)]]
      }}}
      {{{#!td  style="border: none; width:0%" \\
      }}}
      {{{#!td style="border: none;vertical-align:top"
'''Fig. 2'''\\\\
[[Image(file_tree_2.png, 50%, left)]]\\\\
      }}}
   }}}
}}}

\\
Somewhere near the end of the automatic installation process, the following lines should have appeared in your terminal:\\
{{{
PALM installation successful
...
PALM installer finished.
}}}

\\
Further, the installer has printed an example command for starting a PALM simulation, e.g.

{{{#!div style="background: #e8ffdd;  border: 3px ridge"
{{{
palmrun -r example_cbl   -a d3#      -c default       -X 4     -T 4

                |           |             |              |        |                
            run identifier  |  configuration identifier  |   tasks per node   
                     I/O control list             number of cores           
}}}
}}}

We have a [wiki:doc/app/palmrungui GUI] to create and submit the palmrun command (software requirements: QT4, python). Typing:
{{{
palmrungui
}}}
into the terminal opens the GUI:
{{{
#!table style="border:none;vertical-align:top;text-align:left;width:750px"
  {{{#!tr style="border:none;width:750px"
    {{{#!td style="border:none"
    [[Image(palmrun_gui.png, width=750px, left, nolink)]]
    }}}
  }}}
}}}
Make your selections and click '''palmrun'''. A terminal window will appear with some messages. If this doesn't work, copy and paste the command into the terminal.

== [=#create Create and run a new setup] ==
(1) Create a new directory
{{{
  cd $HOME/palm/current_version/JOBS
  mkdir -p <new_run_identifier>/INPUT
}}}
(2) Create a new parameter file {{{<new_run_identifier>_p3d}}} with your own parameter settings under
{{{
  $HOME/palm/current_version/JOBS/<new_run_identifier>/INPUT
}}}
(3) Submit palmrun command
{{{
  palmrun -r <new_run_identifier>  -a d3#  -c default -X 4 -T 4
}}}
(4) The [wiki:doc/app/palmrun#interactive terminal output] tells you if everything went fine, and if so, where to find the output files.



{{{#!comment
== How to create a new simulation set-up ==

First give your new set-up a name to be used as the run identifier, e.g. {{{neutral}}}. Create a new parameter file and set all parameters required for defining your set-up (number of grid points, grid spacing, etc.) . You may find it more convenient to use an existing parameter file and modify it, e.g. the one which has come with the automatic installation:
{{{
   cd ~/palm/current_version
   mkdir -p JOBS/neutral/INPUT
   cp JOBS/example_cbl/INPUT/example_cbl_p3d JOBS/neutral/INPUT/neutral_p3d
}}}
Edit file {{{neutral_p3d}}} and add, delete, or change parameters. Run your new set-up with
{{{
   palmrun -r neutral -c default -X4 -a "d3#"
}}}
If the run has finished successfully, results can be found in folders {{{JOBS/neutral/MONITORING}}} and {{{JOBS/neutral/OUTPUT}}}.
}}}