I recommend you to use TSUBAME for computationally demanding tasks.
If you want to use TSUBAME, please send your student ID to Murata.
Then you will receive an invitation to group "tga-crest-deep-mu".
The following sites will be helpful for you.
TSUBAME計算サービス (TSUBAME site in Japanese)
http://www.t3.gsic.titech.ac.jp/
TSUBAME Computing Services (TSUBAME site in English)
http://www.t3.gsic.titech.ac.jp/en
User's Guide in English and Japanese
http://www.t3.gsic.titech.ac.jp/en/manuals
tutorials (UNIX, GPU programming, parallel programming...)