Helix Systems

The Helix/Biowulf staff will present a series of classes in Oct/Nov 2012. Classes are free but registration is required. You can register by clicking the link for each class. Helix/Biowulf users will have priority enrollment, and new users are highly encouraged to attend.

Introduction to Linux: http://training.cit.nih.gov/?SS880 Date & Time: Tuesday, Oct 30, 2012. 9 am - 4 pm. Location: Bldg 12A, Rm B51. This class is intended as a starting point for individuals new to Linux and UNIX. The class will center on basic UNIX/Linux concepts: logging in, navigating the file system, commands for interacting with files, running and viewing processes, checking disk space and other common tasks. The class will also cover the use of some services specific to Helix/Biowulf usage.

Bash Shell Scripting for Helix and Biowulf: http://training.cit.nih.gov/?SS890 Date & Time: Wednesday, Nov 7, 2012. 10 am - 4 pm. Location: Bldg 12A, Rm B51. The default shell on many Linux systems is bash. Bash shell scripting provides a method for automating common tasks on Linux systems (such as Helix and Biowulf), including transferring and parsing files, creating qsub and swarm scripts, pipelining tasks, and monitoring jobs. This class will give a hands-on tutorial on how to create and use bash shell scripts in a Linux environment.

NIH Biowulf Cluster: Scientific Computing: http://training.cit.nih.gov/?SS610 Date & Time: Wednesday, Nov 8, 2012. 9 am - 4 pm Location: Bldg 12A, Rm B51 Morning: Introduction to the Biowulf Linux cluster, cluster concepts, accounts, logging in, storage options, interactive vs. batch jobs, how to set up and submit a simple batch job, batch queues, available software, and job monitoring. Afternoon: Hardware and network configuration, types of nodes, selection of nodes using properties, system software, parallel programs, programming tools.




8/27/2012

Important Reminder to Helix and Biowulf Users: Tomorrow morning, Tuesday, August 28th at 7:00 AM, the password you use to log into Helix (including Helix mail) and Biowulf will change. You will use your NIH Active Directory (AD) account password when logging into Helix and/or Biowulf rather than the old separately maintained passwords.

Action required: To avoid service interruptions, please be sure that you know your NIH AD account password if you do not regularly use it. This is the same password that you would use to access NIH-managed workstations and other NIH password-authenticated services.

For more information: See the Q&A on migration to NIH AD authentication at http://helix.nih.gov/migration_qa.html.

Reference: For additional details, see Important Changes in Helix/Biowulf Login Procedures (March 14, 2012).

Questions? The Helix/Biowulf staff is ready to help you during this migration to NIH AD authentication. Please contact the NIH IT Service Desk if you need assistance.

    http://itservicedesk.nih.gov
    301-496-4357 (local)
    866-319-4357 (toll free)
    301-496-8294 (TTY)

Thank you.
NIH Helix Systems Staff

9/13/2012

The default system installed version of perl has been changed from non-threaded v5.12.1 to threads-enabled v5.12.1. For the majority of perl users, this change will not affect anything. There is a chance that users who maintain their own repository of perl modules and libraries but use the default system perl will have incompatibility problems.

For those who want to know more about using threaded perl, please see

http://perldoc.perl.org/5.12.1/perlthrtut.html

The NIH Helix Staff


9/21/2012

Effective immediately, running R sessions on the Biowulf login node will no longer be permitted.

Over the past few months users running R jobs have exhausted memory on the login node causing performance problems and system-hangs, and so will no longer be allowed.

R jobs can be submitted to the batch system (http://biowulf.nih.gov/apps/R.html) or run by allocating interactive nodes (http://biowulf.nih.gov/user_guide.html#interactive).




10/15/2012

On Tuesday October 23, the NIH Helix and Biowulf systems staff will be performing storage system maintenance from 6 pm until approximately 10 pm.

For Helix users, all services, including email, will be unavailable from 6 pm until approximately 8 pm. By 8 pm it is anticipated that Helix and its email will become available though anonymous ftp will remain inaccessible to users for the remainder of the maintenance period.

The Biowulf cluster and login node are also scheduled to be down during this maintenance window. Details about their availability during this downtime will be addressed in a separate message being sent to Biowulf users.

If you have any questions, please contact the Helix Systems staff at staff@helix.nih.gov.

Helix Systems Staff




10/19/2012

This is a follow-up message to the one sent to Helix users on Oct 15.

The Biowulf cluster will be shut down for file system maintenance the afternoon and evening of Tuesday October 23.

The batch system will be shut down at 3 pm and all running and queued jobs deleted from the system. No further batch jobs will be accepted after 3 pm.

The login node will remain available until 6 pm.

We hope to have the cluster available around 10-11pm and email will be sent to Biowulf users at that time.




10/23/2012

Please report any problems to staff@biowulf.nih.gov.




10/23/2012

Please report any problems to staff.


12/5/2012

This email is for Biowulf users who have their /data directories on the /gs2 filesystem. If you use the "gpfs" property for your 'qsub' or 'swarm' jobs, this means you.

Biowulf staff will have to take the gs2 filesystem OFFLINE to repair filesystem damage incurred last week.

This means that when the filesystem is taken offline, any jobs currently accessing that filesystem will be terminated, and that jobs submitted requiring that filesystem will be rejected.

The software vendor informs us that it will take anywhere between 8 and 48 hours to repair the filesystem.

Jobs accessing or submitting to the /gs2 filesystem will be terminated starting TODAY at 10 am. Email will be sent to biowulf users when /gs2 is again available.

We apologize for this disruption to your work, but delaying this repair could have serious consequences for the integrity of data on /gs2.




11/28/2012

The Helix/Biowulf staff will present a series of classes in Jan 2013 Classes are free but registration is required. Helix/Biowulf users will have priority enrollment, and new users are highly encouraged to attend.

Introduction to Linux ---------------------- http://training.cit.nih.gov/?SS880 Date & Time: Wed, Jan 9, 9 am - 4 pm Location: Bldg 12A, Rm B51. This class is intended as a starting point for individuals new to Linux and UNIX. The class will center on basic UNIX/Linux concepts: logging in, navigating the file system, commands for interacting with files, running and viewing processes, checking disk space and other common tasks. The class will also cover the use of some services specific to Helix/Biowulf usage.

Bash Shell Scripting for Helix and Biowulf ------------------------------------------ http://training.cit.nih.gov/?SS890 Date & Time: Wed, Jan 16, 10 am - 4 pm Location: Bldg 12A, Rm B51. The default shell on many Linux systems is bash. Bash shell scripting provides a method for automating common tasks on Linux systems (such as Helix and Biowulf), including transferring and parsing files, creating qsub and swarm scripts, pipelining tasks, and monitoring jobs. This class will give a hands-on tutorial on how to create and use bash shell scripts in a Linux environment.

NIH Biowulf Cluster: Scientific Computing ----------------------------------------- http://training.cit.nih.gov/?SS610 Date & Time: Wed, Jan 23, 9 am - 4 pm Location: Bldg 12A, Rm B51 Morning: Introduction to the Biowulf Linux cluster, cluster concepts, accounts, logging in, storage options, interactive vs. batch jobs, how to set up and submit a simple batch job, batch queues, available software, and job monitoring. Afternoon: Hardware and network configuration, types of nodes, selection of nodes using properties, system software, parallel programs, programming tools.