= General hints for using the NEC SX-Aurora TSUBASA A300-8 system at IMUK =

The system is part of the [https://www.luis.uni-hannover.de/scientific_computing.html LUIS-cluster at LUH].

You need a user-account for the cluster-system to access the NEC-system. The login procesure is as follows:

 1. Login to the LUIS cluster-system from a workstation at IMUK:
{{{ssh -X <your LUIS username>@login.luis.uni-hannover.de}}}

 2. From the LUIS system, you need to start an interactive job on the NEC-machine:
{{{qsub -I -l nodes=1:ppn=1,mem=20gb -W x=PARTITION:muk}}}

By default, the interactive job sessions runs for 24h. Your $HOME-filesystem of the LUIS cluster is mounted on the NEC-System. For storing large output files, use the NEC-local filesystem {{{/scratch/<your LUIS username>}}}



On the NEC-machine only specific software to compile and run PALM is available (NEC Fortran compiler, NetCDF-, 

Furthermore, edit file {{{$HOME/.bash_profile}}} and add the following lines:
{{{
# User specific environment and startup programs

PALM_BIN=$HOME/palm/current_version/trunk/SCRIPTS
export PALM_BIN

PATH=$PALM_BIN:$PATH
export PATH

LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/netcdf/4.1.1/lib
export LD_LIBRARY_PATH
}}}

== tatara-system [http://www2.cc.kyushu-u.ac.jp/scp/system/general/CX/how_to_use] ==

The system is supported starting from revision r1097. You can find a configuration file adjusted for this system in the svn-repository under [source:/palm/trunk/SCRIPTS/.mrun.config.tatara /palm/trunk/SCRIPTS/.mrun.config.tatara]. Just copy this file to your working directory
{{{
cd ~/palm/current_version
cp trunk/SCRIPTS/.mrun.config.tatara .mrun.config
}}}
Don't forget to edit the file in order to replace the string {{{<replace by your tatara username>}}} with your respective username.

For the rest of the installation procedure just follow the instructions given on the [wiki:doc/install installation page].

== hayaka-system [http://www2.cc.kyushu-u.ac.jp/scp/system/general/FX10/how_to_use] ==

This system is supported starting from r1103 The configuration file adjusted for this system can be found under [source:/palm/trunk/SCRIPTS/.mrun.config.hayaka /palm/trunk/SCRIPTS/.mrun.config.hayaka]. Copy this file to your working directory
{{{
cd ~/palm/current_version
cp trunk/SCRIPTS/.mrun.config.hayaka .mrun.config
}}}
Don't forget to edit the file in order to replace the string {{{<replace by your hayaka username>}}} with your respective username.

=== Restrictions on hayaka ===

The hayaka login node only provides a cross compiler ({{{frtpx}}}) for the compute nodes. Therefore, the utility programs like {{{interpret_config}}} and {{{check_parameter_files}}} can be compiled, but they cannot be run. This requires to set appropriate {{{mrun}}} options
{{{
mrun ... -z -S ...
}}}
in order to switch off the parameter check ({{{-z}}}) and to interpret the configuration file directly from the script ({{{-S}}}).

For compiling some parts of the PALM code, the Fujitsu compiler (frtpx) requires more memory than given by default. Please increase the maximum virtual memory size by command
{{{
ulimit -v 8097152
}}}
For convenience, you should add this command to the file {{{$HOME/.bash_profile}}}.

No automatic restarts are possible on the hayaka system. You have to submit restart runs manually after the previous job has finished. In the job protocol file (see {{{~/job_queue}}}) of the previous run information is given about which '''mrun''' options are to be used for the restart.