General hints for users of machines at the Kyushu University computing center

​http://www2.cc.kyushu-u.ac.jp

The default shell at Kyushu University seems to be the tcsh. You should switch to bash-shell using the chsh command:

chsh -s /bin/bash

You will be prompted for your LDAP password.

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 /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 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 /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.