20 posts tagged with "News"

• The URL for the NIG supercomputer account application form => Registration
• The URL for application instructions => Account Application and Change of Application Details

initial screen

The first screen after login

• The NIG supercomputer account Application has been made more simple.
• SSH public key registration is now available on the account application form.
  • In the previous two-step procedure, users received an account registration certificate about one week after applying for new use, and then had to register their SSH public key after logging in by themselves.
  • From now on, however, SSH public key registration can be done when you fill out the account application form.
• Renewal at the end of the year has beem made more simple.
  • It is no longer necessary to manually enter all the items one by one, and the article information can be obtained and automatically entered by simply entering the PubMedID.

Note​

• Please login from gw2.ddbj.nig.ac.jp immediately after setting up your public key etc.
  • We are currently in the process of migrating to a account application system. Therefore, public key registrations to the new gateway gw2.ddbj.nig.ac.jp will be reflected immediately, but it will take about one day for the settings to be reflected in the old gateway gw.ddbj.nig.ac.jp. The system will be modified at the next scheduled maintenance in December so that the old gateway will also reflect the setting immediately.
• The sc2.ddbj.nig.ac.jp server has been closed.

Added pages on the home page about package managers spack and nix that can be used with user privileges.

The following package managers can be used only with user permission. They facilitate the construction of development and analysis environments.

• Guix (✨Updated May 19)
• spack (✨Updated May 19)
• Environmental Modules (April 13)

Thank you very much for using the NIG supercomputer.

Due to the computing resources of CPU and Disk are current very tight, we suspend the NIG supercomputer account application for the following users.

• Application for using large-scale for the general analysis division
• Account Application of personal genome analysis division users

The following applications will be accepted as before.

• For current already large-scale users for the general analysis division and the personal genome analysis division users, we will continue to accept additions of resources to chang the usage plan table as before.
• Regular creating an account of the general analysis division will also be accepted as before. In this case, the disk memory will be limited to the default setting of 1TB.
• For using of the service for workshops, etc.

Thank you for your understanding that we may not be able to meet your request in such cases.

The timing for resuming the account application will be decided by checking the availability of computer resources. The availability forecast for each 4 month period will be posted on the website as needed. When you plan to use it, refer to the outlook for availability and submit your usage plan table in advance. However, note that availability is not guaranteed and we may not be able to meet your request.

For the NGS analysis pipeline, the tool called Portablepipeline has been developed by Professor Kazutoshi Yoshitake of the Laboratory of Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, Graduate school of Agricultural and Life Sciences, The Univresity of Tokyo.

「PortablePipeline is software that allows Windows and Mac users to perform NGS analysis in a GUI on a local or remote server or supercomputer.」（Referenced from the Laboratory of Aquatic Molecular Biology and Biotechnology）

• PortablePipeline introduction（「Advanced Guides Overview」>「Latest topic」)

Grie Engine page

Revised description. Added slides presented at Data Scientist Training Session of Informatics In Biology, Medicine and Pharmacology(IIBMP) 2021 conference.

The basic fee for DDBJ Group Cloud has been reduced from 15 million yen to 3.5 million yen.

• DDBJ Group Cloud
• NIG supercomputer acceptable use policy

The DDBJ Group Cloud is a service for sharing data that requires access restrictions, including personal genome data, within a research group.

Depending on the scale such as the number of users, you can use DDBJ Group Cloud as a calculation platform for the NBDC group shared database, or the DDBJ group cloud alone.

Overview​

For congestion control and hardware redundancy A new gateway node gwa2.ddbj.nig.ac.jp will be installed and opened to the public in the personal genome analysis division.

Work Schedule​

Thursday, March 17, 2022, around 13:00

• Publication work has been completed and is now available.

Scope of Impact​

• There will be no system shutdowns or other impacts associated with this work.
• The existing personal genome analysis compartment gateway gwa.ddbj.nig.ac.jp will be available as before.
• The new gateway gwa2.ddbj.nig.ac.jp will be used in the same way as the existing gwa.ddbj.nig.ac.jp.
• The server name displayed at the prompt when logging in will be changed.
  • The existing gateway will be changed from gwa to gwA1.
  • For the added new gateway: gwA2 will be displayed.

Overview​

For congestion control and hardware redundancy A new gateway node gw2.ddbj.nig.ac.jp will be installed and opened to the public in the personal genome analysis division.

Work Schedule​

Thursday, March 17, 2022, around 13:00

• Publication work has been completed and is now available.

Scope of Impact​

• There will be no system shutdowns or other impacts associated with this work.
• The existing personal genome analysis compartment gateway gw.ddbj.nig.ac.jp will be available as before.
• The new gateway gw2.ddbj.nig.ac.jp will be used in the same way as the existing gw.ddbj.nig.ac.jp.
• The server name displayed at the prompt when logging in will be changed.
  • The existing gateway will be changed from gw to gwB1.
  • For the added new gateway: gwB2 will be displayed.

Dear Users of the NIG Supercomputer System

At 11:00(24h) Thursday, May 13, 2021, we will change the setting of some services of the general analysis plot Grid Engine.

The purpose of this change is to increase the turnover rate of short.q jobs because it is becoming difficult to running user jobs due to the congestion of the NIG supercomputer.

We did the same configuration work the other day, but since the previous configuration did not behave as intended, we will redo the configuration work. For jobs submitted before the date and time of the change, the values before the setting change will be applied.

The details of the setting change are as follows.

• Change the configuration of the NIG supercomputer short.q
  • Target queue: short.q
  • Maximum execution time limit: Previously 3 days will be changed to 1 hour.

May 12, 2021

Supercomputer System Management Team, DDBJ Center, National Institute of Genetics