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Helix Systems

8/4/2014
Imputing big data from GWAS

A discussion of imputation and large scale meta-analyses of GWAS data on the Biowulf cluster featuring hands on examples and experienced instruction.

Instructor: Michael Nalls (NIA) Date: Wed Sep 10 2014 Time: 9 am - noon Location: Bldg 12, Rm B51

The class is free but registration is required. Please register at http://helixweb.nih.gov/nih/classes/ A Helix & Biowulf account is required for the hands-on exercises in this class. Contact staff@helix.nih.gov if you have questions about your account.

[Michael Nalls is the Head of Statistical Genetics at the Lab. of Neurogenetics, NIA. His work focuses on creating analytic pipelines for health informatics by applying cutting edge statistical methodologies to massive datasets as a means of facilitating the investigation of neurological diseases and complex traits. Recent paper: Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease. Nalls, Pankratz, et al.Nature Genetics, doi:10.1038/ng.3043. (2014)]




8/14/2014

This morning a hardware failure on the cluster network's core switch caused several hundred nodes to go offline which in turned caused filesystem problems such as: "Stale NFS file handle"

During this time job scheduling was turned off to prevent new jobs from starting on nodes affected by the problem. Scheduling has now been turned back on.

Please check the health of your jobs, and resubmit if necessary.

Steven Fellini Biowulf staff




8/18/2014

The Helix/Biowulf staff will present two classes in October 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 ---------------------- Date & Time: Tue, Oct 7, 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 ------------------------------------------ Date & Time: Tue, Oct 21, 9 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.

Registration for both classes is available at http://helixweb.nih.gov/nih/classes/




8/27/2014

The Helix/Biowulf staff will present an all-day introduction to the Biowulf cluster in November. Biowulf users will have priority enrollment for this class, and new users are highly encouraged to attend.

The class is free but registration is required.

NIH Biowulf Cluster: Scientific Computing ----------------------------------------- Date & Time: Mon, 3 Nov 2014. 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.

Register at http://helixweb.nih.gov/nih/classes/




8/27/2014

There will be a general downtime for the NIH Biowulf Cluster on Saturday September 20 from approximately 8 am to 6 pm.

The cluster will be unavailable during this time. The Biowulf login node will remain available.

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.




8/13/2014

The Global Optimization Toolbox for Matlab is now available on the Helix systems. This 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. One license has been purchased.

NOTE to Sciware users of Matlab-8.1: You might have to rehash the toolbox cache before running the toolbox:

rehash toolboxcache

For more information on using Matlab on the systems, see

Helix: http://helix.nih.gov/Applications/matlab.html Biowulf: http://biowulf.nih.gov/apps/matlab.html Sciware: http://sciware.nih.gov/sciware_appinfo_matlab.html

For license availability, see

http://helixweb.nih.gov/nih/license_status




8/13/2014

The Helix/Biowulf staff will present two classes in October 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 ---------------------- Date & Time: Tue, Oct 7, 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 ------------------------------------------ Date & Time: Tue, Oct 21, 9 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.

Registration for both classes is available at http://helixweb.nih.gov/nih/classes/index.php




9/8/2014

The time has come for the annual Biowulf account renewals. The NIH High-Performance Working Group requires that all Biowulf users renew their accounts each year. (More information at https://helix.nih.gov/recert.html).

Later today you will receive a message asking you to fill out the account renewal form. You will need to select your PI, as before. You will have until 1 Oct 2014 to complete the form. Your PI will have the month of October to approve your renewal. If your account renewal has not been completed and approved by your PI by Nov 1, your Biowulf account will be suspended until the account renewal is complete.

Users who are PIs themselves should still complete the form, and will be instantly approved.

Users who received new Biowulf accounts in July or Aug 2014 will not need to go through this process, as their accounts have recently been approved by their PIs.

Please send email to staff.nih.gov if you have any questions.

Biowulf/Helix Systems Staff.




9/8/2014

Please fill out the Biowulf Account Renewal form at: https://helix.nih.gov/accounts/recert.php

You will need to log in with your NIH login name and password.

While filling out the Account Renewal form, you will need to select the name of your Principal Investigator (PI), as before. You will have until 1 October 2014 to complete the form. Your PI will have the month of October to certify your request. If your account renewal has not been completed and approved by your PI by Nov 1, your Biowulf account will be suspended until the account renewal is complete.

Users who are PIs themselves should still complete the form, and will be instantly approved.

Users who received new Biowulf accounts in July or Aug 2014 do not need to go through this process, as their accounts have recently been approved by their PIs.

Send email to staff@helix.nih.gov if you have any questions.

Biowulf/Helix Systems Staff.




9/11/2014

On Saturday September 20, the NIH Helix and Biowulf systems staff will be performing system maintenance from 8 am until approximately 6 pm.

The Helix system (including email) will not be available from approximately 10am-12noon. During the rest of the maintenance window, Helix and most of its services will be available, though Helixdrive and a significant number of user data directories will be unavailable throughout this period.

The Biowulf cluster is also scheduled to be down during this maintenance window. The Biowulf login node will be unavailable from approximately 10am-12noon. 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




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This page last reviewed: December 14, 2010