{{{
#!access
#allow(DOWNLOADS_VIEW)
= idefix user documentation =
\\
== System overview ==
{{{#!table align=left style="border: none; text-align:left"
   {{{#!tr 
      {{{#!td style="border: none; width:40%"
   {{{#!table
|| hostname ||idefix ||
|| CPU architecture ||Intel Xeon Haswell || 
|| CPU model ||E7-4850 v4 ||
|| # CPU ||4 ||
|| Processor cores / CPU ||16 ||
|| Threads / CPU ||32 ||
|| Total processor cores ||64 ||
|| CPU clock ||2.1GHz ||
|| CPU peak ||2150 GFlop/s ||
|| L1d/L1i/L2/L3 cache ||32K/32K/256K/40960K ||
|| RAM ||265GB DDR4 ||
|| Harddisk ||1.6 TB SSD PCIe3 (/work) ||
||          ||0.5 TB SSD SATA (/) ||
||          ||2.0 TB SAS 7.2K (/data) ||
   }}}
      }}}
      {{{#!td align=left style="border: none; vertical-align:top; width: 60%"
         [[Image(idefix.png, 60%, left, border=0, color=black)]]
      }}}
   }}}
}}}


== Access and user environment ==
'''idefix''' can be accessed via:
{{{
ssh -X replace_by_your_idefix_username@idefix.muk.uni-hannover.de  or
ssh -X replace_by_your_idefix_username@130.75.105.239
}}}

Create an ssh key on your local PC, and copy it to idefix using the command:\\\\
{{{
ssh-copy-id -i replace_by_your_local_path_to/.ssh/id_dsa.pub replace_by_your_idefix_username@130.75.105.239
}}}

Add this user login script file [attachment:.myprofile .myprofile] to your $HOME directory on '''idefix'''. The file contains the following lines:
{{{
#Required software modules for running PALM
module load intel-compiler/2017.1.132
module load mvapich2/2.2/intel
module load fftw/3.3.6-pl1/mvapich2-intel
module load hdf5-parallel/1.10.0-patch1/intel
module load netcdf4_hdf5parallel/4411c_443f/intel

#To use the PALM scripts, the PATH variable has to be extended and the environment variable PALM_BIN has to be set
export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH
export PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS

#Increase stack size to unlimited, otherwise large runs may abort
ulimit -s unlimited
}}}
You may have to login again in order to activate these settings.


\\
== Installation of PALM ==
To download and install the latest PALM version, follow the first steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Packageinstallation advanced installation procedure] as described on the PALM website. The [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/automatic automatic installer] will be available soon. Following steps also need to be carried out and are slightly different to those described on the PALM website. With the automatic installer, the following steps will be carried out automatically.

(1) Copy '''idefix'''-specific palmbuild/palmrun configuration file (available from r2523) to your working directory:
{{{
cp $HOME/palm/current_version/trunk/SCRIPTS/.palm.config.idefix $HOME/palm/current_version/.
}}}
Besides many other things, this file contains typical installation parameters like compiler name, compiler options, etc. In this file, enter your '''idefix''' user name at locations ''<replace_by_your_IDEFIX_username>''.\\\\
'''Warning: When editing the configuration file, please NEVER use the TAB key. Otherwise, very confusing errors may occur when palmrun is executing.'''\\\\

(2) Compilation of utilities and source code:
After modifying the configuration file, helper programs and PALM code are compiled by executing
{{{
  palmbuild -h idefix
}}}

(3) Installation verification: 
Follow the steps of the [https://palm.muk.uni-hannover.de/trac/wiki/doc/install/advanced#Installationverification verification procedure] as described on the PALM website.\\
To start an interactive PALM run, create a {{{palmrun}}} command (formerly {{{mrun}}}):
{{{
  palmrun -d <run_identifier> -h idefix -a "d3# ts# ..." -X <total number of cores to be used (max. 64)> -T <number of cores/node (=X, since idefix has only one node)> -m <memory per node>
}}}
The graphical user interface [https://palm.muk.uni-hannover.de/trac/wiki/doc/app/palmrungui palmrungui] (formerly mrungui) can be used to create a palmrun command line for starting a selected PALM simulation.

== Batch system ==
The Portable Batch System (PBS, version PBSPro14) is available on '''idefix'''. In the configuration file {{{.palm.config.idefix}}}, the necessary settings for using the PBS are already included.

== File systems and data management ==

== Software ==
(1) Compiler, MPI, NetCDF, ...
* Intel Fortran
* mvapich2
* fftw
* netcdf4
* hdf5-parallel \\\\

(2) Data processing and visualization
* ncl
* nco/cdo
* ncview
* udunits \\\\

}}}