Tsubame

This document contains local support information for PALM users on the Linux Cluster Tsubame of the Tokyo Institute of Technology, Tokyo, Japan (http://www.gsic.titech.ac.jp/~ccwww). Japanese and English user manuals are available for download (http://www.gsic.titech.ac.jp/~ccwww/tebiki).

Subversion

Installation:
The following lines should be added to your ~/.profile (for ksh users - create if necessary) or ~/.bashrc (for bash users). These settings will be active from the next login.

Usage:
Since Tsubame is located behind a firewall, the usual address svn://130.75.105.45 is unreachable from Tsubame. Instead, please login to media-o and use svn://p9c.cc.titech.ac.jp:36900. This port works in both directions, i.e. for svn update as well as svn commit commands.

Batch system

The implementation of the n1ge command on Tsubame requires modifications to mrun and subjob for PALM to run on Tsubame. Since mrun must be executed on one PE only, a one-PE "submitting job" is created when the user calls mrun. At the time when this "submitting job" is actually executed, it starts the main PALM job in the foreground. However, this only works if enough resources are available at that time. Therefore PALM users on Tsubame are advised to consider the queue load of the available queues for the main job (qstat -g c) before job submission.

According to the current queue configuration (http://www.gsic.titech.ac.jp/~ccwww/tgc/q_e.html), the following mrun options are available:

Note that the default value "sla3" of the mrun option -q may not always be the best choice. For code development, debugging or short test runs the value "novice" for both options may be suitable. Production runs should use the respective production queues (see http://www.gsic.titech.ac.jp/~ccwww/tgc/q_e.html for details). In the past the queueing system on Tsubame has undergone several changes, so this information may change.

The computer center advised us that due to restrictions of the batch system the value "novice" should not be mixed with the other queues. Please specify either a combination of slan for -n and slan or RAM* for -q, or specify the combination "novice" + "novice".

The group number contains the accounting information. You must specify it using the mrun option -g. Alternatively, you may set also a default value in your .mrun.config file like this:

%group_number      12345678                                        lctit parallel


The mrun option -t contains the CPU time demand for the main job in s which will be automatically converted into min for the n1ge command. The option -m contains the memory demand for the main job in MB which will be automatically converted into GB for the n1ge command.

Finally, PALM batch jobs on Tsubame require the mrun option -b.

NetCDF

In order to use NetCDF commands like ncdump and the graphical NetCDF tools NCL, Ncview and Ferret, please add the following lines to ~/.profile (for ksh users) or ~/.bashrc (for bash users):

# NetCDF
export PATH=$PATH:~mkanda/netcdf-3.6.2/bin:~mkanda/netcdf-3.6.2/include

# NCL
export NCARG_ROOT=~mkanda/ncl
PATH=~mkanda/ncl/bin:$PATH

# Ncview
export PATH=$PATH:~mkanda/ncview/bin
export XAPPLRESDIR=~mkanda/.app-defaults

# Ferret
export FER_DIR=~mkanda/ferret
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FER_DIR/lib
export PATH=$PATH:$FER_DIR:$FER_DIR/bin
export FER_DSETS=$FER_DIR
export FER_WEB_BROWSER=firefox
export FER_EXTERNAL_FUNCTIONS="$FER_DIR/lib"
export FER_GO=". $FER_DIR/go $FER_DIR/examples $FER_DIR/contrib"
export FER_DATA="."
export FER_DESCR="."
export FER_GRIDS=". $FER_DSETS/grids"
export TMAP="$FER_DIR/fmt"
export PLOTFONTS="$FER_DIR/ppl/fonts"
export SPECTRA="$FER_DIR/ppl"         # for old ferret versions
export FER_PALETTE=". $FER_DIR/ppl"       # palette search list