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Helix Systems

11/7/2013
A selection of 1000 Genomes exomic alignment files are currently available in /fdb/1000genomes/ftp. It appears that there is a continuing interest in having the data available locally, based on recent file usage.

Interest has been expressed in also maintaining a local copy of RNASeq data (BAM alignment files and FASTQ read files) generated using samples from the 1000 Genomes project. Details about the data can be found at

http://www.1000genomes.org/faq/there-any-gene-expression-data-available-1000-genomes-project-samples

Because storage space is not unlimited, we'd like to know whether other users would find this data useful.

* Have you used any of the data from these experiments? Are any of these files already in your /data areas? * Do you plan on using any of these files in the future? If so, when? * Which of the projects are of most importance to your work?

Thanks again for your input! Helix Systems Staff




11/20/2013

There will be a general downtime for the NIH Biowulf Cluster on Saturday December 14 from approximately 7 am to 6 pm.

The cluster will be unavailable during this time. The Biowulf login node will remain available, but many data directories will be unavailable.

If you are planning on submitting long-running jobs without checkpointing or large swarms, please keep this date in mind as all running and queued jobs will be deleted from the system.

Additional details will be included in a reminder e-mail several days before the scheduled downtime.

Please send questions or comments to staff@biowulf.nih.gov.




11/20/2013

On Saturday December 14, the NIH Helix and Biowulf systems staff will be performing storage system maintenance from 7 am until approximately 6 pm.

The Helix system and most of its services, including email, will remain available for the duration of the maintenance window though a significant number of user data directories will be unavailable. Helixdrive will not be available during this maintenance window.

The Biowulf cluster is also scheduled to be down during this maintenance window, but the Biowulf login node will remain available. Details about Biowulf availability during this downtime are addressed in a separate message that has been sent to Biowulf users.

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

Helix Systems Staff




12/10/2013

A reminder that this Saturday December 14, the NIH Helix and Biowulf systems staff will be performing storage system maintenance from 7 am until approximately 6 pm.

The Helix system and most of its services, including email, will remain available for the duration of the maintenance window though a significant number of user data directories will be unavailable. Helixdrive will not be available during this maintenance window.

The Biowulf cluster is also scheduled to be down during this maintenance window, but the Biowulf login node will remain available. Details about Biowulf availability during this downtime are addressed in a separate message that has been sent to Biowulf users.

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

Helix Systems Staff




12/12/2013

The Biowulf Cluster will be unavailable from 7 am until approximately 6 pm on Saturday Dec 14. All batch jobs, both running and queued will be deleted at that time.

The login node will remain available, however many /data directories (those on /gs2 and /gs3) will be inaccessible.

Email will be sent to Biowulf Users when the cluster is again accepting jobs.

The original announcement follows. ---------------- From: Mark Patkus Subject: NIH Helix and Biowulf Systems Downtime, Saturday December 14, 2013 Date: November 20, 2013 1:58:16 PM EST To: HELIX-USERS@LIST.NIH.GOV

On Saturday December 14, the NIH Helix and Biowulf systems staff will be performing storage system maintenance from 7 am until approximately 6 pm.

The Helix system and most of its services, including email, will remain available for the duration of the maintenance window though a significant number of user data directories will be unavailable. Helixdrive will not be available during this maintenance window.

The Biowulf cluster is also scheduled to be down during this maintenance window, but the Biowulf login node will remain available. Details about Biowulf availability during this downtime are addressed in a separate message that has been sent to Biowulf users.

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

Helix Systems Staff




12/14/2013

Maintenance completed. The cluster is now accepting batch jobs. Please report problems to staff@biowulf.nih.gov




12/16/2013

The Helix/Biowulf staff will present a series of classes in Jan 2014. 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/class_details.aspx?cId=NIHCIT-SS880 Date & Time: Wed, 15 Jan, 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/class_details.aspx?cId=NIHCIT-SS890 Date & Time: Wed, 22 Jan, 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/class_details.aspx?cId=NIHCIT-SS610 Date & Time: Wed, 29 Jan, 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.




12/18/2013

Sean Davis (NCI), a very knowledgeable Biowulf user, will be teaching a = class of particular interest to users who are managing genomics = pipelines or workflows:

Workflows with Make & Snakemake on Helix & Biowulf

Description: Scientific data analysis often involves workflows composed = of multiple discrete steps, sometimes with complicated dependencies = between steps. Tools that manage these workflows can increase = reproducibility of research and productivity while decreasing code = complexity. The command-line Linux/Unix 'make' package is often used to = create complicated workflows. Snakemake is a relatively new Python-based = mini-language and execution environment for make-like workflows. This = 2-hr class will introduce make and snakemake for workflow management, = and will contain a hands-on session.

Date: 20 Feb 2014 Time: 10 am - noon

The class is free but registration is required: http://training.cit.nih.gov/class_details.aspx?cId=3DNIHCIT-SS891

Please let us know if you have problems registering for the class.=20




1/3/2014

On Thursday January 9, 2014 at 10:00 PM through January 10, 1:00 AM, engineers will be making the physical network connections to the new Building 12 Data Center Core Router infrastructure. This upgrade will provide a more robust network backbone infrastructure and increase network capacity from 10 gigabytes to 80 gigabytes within the NIH Data Center.

The NIH Helix and Biowulf systems (including Helix, Biowulf, Sciware, Helixweb and Helixdrive) should not be affected for the duration of the maintenance window.

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

Helix Systems Staff




2/5/2014

The Global Optimization toolbox is a trial installation on helix and biowulf, available until February 27, 2014. The toolbox provides methods that search for global solutions to problems that contain multiple maxima or minima. It includes global search, multistart, pattern search, genetic algorithm, and simulated annealing solvers. It's only available for Matlab R2013a on helix and biowulf.

We will consider purchasing this product if there is sufficient interest from the Matlab user community. More information on getting started can be found at: http://www.mathworks.com/help/gads/index.html


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This page last reviewed: December 14, 2010