Supercomputer

Note for users

This page explains basic rules for Supercomputer users.

Please agree to our terms of use, which should be followed throughout your usage

Please agree to our terms of use, which should be followed throughout your usage. When using Supercomputer, users must agree to our terms of use. Please follow these terms throughout your usage. Below is a summary of the terms:

  • Not to deviate from the purpose of use.
  • In order to use our service over one fiscal year, you need to renew your registration.
  • When publishing an article which benefits from our service, please acknowledge that you used Super Computer to complete it.
  • When terminating your account (and end of every fiscal year if you continue using our service), we request a list of your accomplishments using Super Computer.
  • To manage your account effectively and ensure that other persons do not use our service from your account.
  • To pay our service charges.
  • If these rules are not followed, your Super Computer account will be terminated.

This is a summary of our terms of use; please be sure to read the whole document. .

Checking your @hgc.jp email account

Your Supercomputer account comes with HGC email service (username@hgc.jp) All communication from the support desk will be made through this email service. Please check your account regularly, as we will send you important contents such as maintenance information and urgent communication regarding ongoing calculation jobs. You may consider forwarding these emails to an email account which you frequently use. Please refer to Using E-mail to learn more about hgc.jp email settings.

Analysis and Storage of Data in Research that is Governed by Institutional Research Ethics Board

For all research such as involving human data that are subject to institutional ethical review, the details of data analysis and use of the storage (as part of the Shirokane3 computing systems at HGC) must also be approved by the same review committee. Please confer with your institutional Research Ethics Board for details.

About installing and using the software

You can be confident for users to install software on their own in the home directory of Shirokane3.

Please observe strictly the terms of the license of the software you want to use. In the case of license fees, etc., charge occurs, please do the negotiations and payments under the responsibility of the user.
At that time, there was a supercomputer system related information that can not be found in supercomputer Wiki and Web site of HGC, please contact Supercomputing services.

Application for Software Installation are accepted only install free software.

Please note that some software have limited use license. Especially, please note that the person who uses private.

Academic work using Supercomputer

When publishing work using resources from Supercomputer, please clearly state that you benefited from Supercomputer at Human Genome Center in the main body or acknowledgement in your writing. Below are some examples, which can be altered to suit your context.

English

  • a. The super-computing resource was provided by Human Genome Center (the Univ. of Tokyo).
  • b. The super-computing resource was provided by Human Genome Center, the Institute of Medical Science, the University of Tokyo.
  • c. The super-computing resource was provided by Human Genome Center (the Univ. of Tokyo)[1].
  • d. The super-computing resource was provided by Human Genome Center, the Institute of Medical Science, the University of Tokyo[1].
  • e. The super-computing resource was provided by Human Genome Center, the Univ. of Tokyo (http://sc.hgc.jp/shirokane.html).
  • f. The super-computing resource was provided by Human Genome Center, the Institute of Medical Science, the University of Tokyo (http://sc.hgc.jp/shirokane.html).
  • [1] http://sc.hgc.jp/shirokane.html

Japansese

  • a. 本研究は、東京大学ヒトゲノム解析センター・スーパーコンピュータを利用しました。
  • b. 本研究は、東京大学医科学研究所ヒトゲノム解析センターのスーパーコンピュータを利用しました。
  • c. 本研究は、東京大学ヒトゲノム解析センター・スーパーコンピュータを利用しました [1]。
  • d. 本研究は、東京大学医科学研究所ヒトゲノム解析センターのスーパーコンピュータを利用しました [1]。
  • e. 本研究は、東京大学ヒトゲノム解析センター・スーパーコンピュータを利用しました(http://sc.hgc.jp/shirokane.html)。
  • f. 本研究は、東京大学医科学研究所ヒトゲノム解析センターのスーパーコンピュータを利用しました(http://sc.hgc.jp/shirokane.html)。
  • [1] http://sc.hgc.jp/shirokane.html

Disk quota limitation

Supercomputer system at Human Genome Center uses disk quota limitation to control the disk space and file number for users. Disk quota is calculated for to each group, not individual.

The limitation depends on which package you use. Please refer to the chart on Application Procedure for Initial Registration.

You can use the following command to check the disk usage of each user: [username@slogin1 ~]$ lfs quota -u [username] /home/[username] or [username@sc090 ~]$ lfsq

While the lfs quota command can be prompted on login node, this is not the case for the lfsq. Use qlogin to prompt the lfsq command.

If you attempt to files surpassing your limit, the following message will appear: [username@sc090 ~]$ touch testfile
touch: cannot touch `testfile': Disk quota exceeded

You can raise the limit of disk quota by applying for additional disk space. The application form can be downloaded from the Applications page.

Note for login node

Login node (slogin.hgc.jp) is the user front of Supercomputer system. Please do not conduct calculation jobs on this node; when it is overloaded, it may cause delay of work or disruption of login process for other users.

When conducting a calculation job on the Supercomputer system, a batch job system (UGE: Univa Grid Engine) is used. As you command a calculation job on UGE, the system automatically works on each task from compute node. To conduct a conversational program, please use intr.q on UGE. This is also useful for testing a calculation job.

There are several login nodes; when connecting to SSH, you will be automatically allocated one of them.

Backup

Notes on the backup procedure for the super computer system.
To restore from the backup, please contact .
Backup target Frequency of copy Description
User's home directory: /home/xxxxx/backup/ Once or twice a month Please create "backup" directory in your home directory on your own. We perform differential backups of the user's home directory. The date which data can be restored back to differs for each user. Please contact the System Administrator of the Supercomputer System. Please contact the System Administrator of the Supercomputer System.

Backup copy of the other is not doing. Please get yourself back up.

User home directory except for the above is not to make a backup copy.
MySQL and PostgreSQL data are not backuped.
Web servers are not backuped.
Mail data are not backuped.


Please use the contact details below for any questions regarding the backup.

  • TEL: 03-5449-5620
  • E-Mail:
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