Helix Systems

Environment Modules are a convenient way for users to dynamically set paths, library paths, and other required environment variables for an application. Instead of typing shell-dependent commands, for example, a user could now type:

module load ThisApp

to set up all environment variables for the program ThisApp, and:

module unload ThisApp

to unset all those environment variables.

Almost all the scientific applications, libraries, and interpreters such as Perl, Python and Java on Helix & Biowulf now use modules. Details are on the application webpages.

If you are not familiar with the use of modules, please see http://helix.nih.gov/Applications/modules.html for an introduction.

Please contact staff@helix.nih.gov with any questions.


6/17/2013

There will be a general downtime for the NIH Biowulf Cluster during the morning and afternoon of Saturday July 20th.

Both the cluster and the login node will be unavailable during this time.

If you are planning on submitting long-running jobs without checkpointing or large swarms, please keep this date in mind as all 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.




3/27/2013

The Helix Systems staff maintains a small collection of 1000 genomes data (vcf files) in /fdb/1000genomes/. We are considering maintaining a copy of the BAM files (alignments) from 1000 Genomes.

These files are very large (currently 132 TB total, and growing), and since disk space is always in short supply, we need to seriously consider their value to the Helix/Biowulf user community before downloading them.

* Have you ever used the 1000 Genomes BAM files? * Do you currently have a copy of any of the 1000 Genomes data on your Helix/Biowulf account? * Do you plan to use the 1000 Genomes BAM files? If so, when?

Thanks for your input! Helix Systems Staff.




4/17/2013

For NIH Helix & Biowulf users who have Linux or Mac systems in their labs, there is a new file transfer program available for the Helix Systems.

'bbcp' is a high-performance version of scp which can provide significantly increased file transfer performance over scp. You can use 'bbcp' on Biowulf or Helix to transfer files to your local Linux or Mac system; you can also download a version of 'bbcp' for your local system and use it there.

For details on using 'bbcp' on Biowulf see the section entitled "Commandline File Transfer: Macs & Unix/Linux: bbcp" at http://helix.nih.gov/Documentation/transfer.html




3/12/2013

The Helix/Biowulf staff will present a series of classes in April 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/class_details.aspx?cId=NIHCIT-SS880 Date & Time: Wed, Apr 10, 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, Apr 17, 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, Apr 24, 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.




3/18/2013

The Helix Systems staff is pleased to announce a utility tool that lets users monitor their usage of CPU and storage on Biowulf and Helix.

To view your usage, go to https://helixweb.nih.gov/usage/

You will need to authenticate with your NIH login username and password. This utility is only available within the NIH network.

The website also displays papers that cited Helix and Biowulf during this period. If you have additional papers that are not listed, please let us know by sending email to staff@helix.nih.gov

Helix Systems Staff.


5/21/2013

Recent publication citing Helix/Biowulf resources:

Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space

Gelio Alves and Yi-Kuo Yu DOI: 10.1021/pr301139y (2013) J. Proteome Research :


5/3/2013

Recent publication citing Helix/Biowulf resources:

Degenerate polymerase chain reaction strategy with DNA microarray for detection of multiple and various subtypes of virus during blood screening

K. Takizawa, T. Nakashima, T Mizukami et al. DOI: 10.1111/trf.12193 (2013) Transfusion :


12/27/2012

Recent publication citing Helix/Biowulf resources:

RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells

MA Alhoot, SM Wang, SD Sekaran RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells (2012) PLoS One :


1/4/2013

Recent publication citing Helix/Biowulf resources:

Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase

H. Sepasi Tehrani, A.A. Moosavi-Movahedia, H. Ghourchian, F. Ahmad, A. Kiany, M.S. Atri, Sh Ariaeenejad, K. Kavousi & A.A. Sabourya DOI:10.1080/07391102.2012.742460 (2012) J. Biomol. Struct. Dynamics :