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Helix Systems

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




9/17/2014

The Biowulf cluster will be unavailable Saturday September 20 for network and storage system maintenance, beginning at 7:30 am. The cluster and the Biowulf login node (biowulf.nih.gov) will remain unavailable until approximately 6 pm. Email will be sent to users when the system is again available.

All jobs will be deleted from the batch queue.

The original announcement follows (note that the login node will _not_ remain available during the downtime). -------------- Date: 27 August 2014 08:08:40 Subject: DOWNTIME Scheduled for NIH Biowulf Cluster, Sep 20 From: steven fellini (sfellini@NIH.GOV)

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.




9/20/2014

The Biowulf cluster is now available. Please report any problems to staff@biowulf.nih.gov




9/23/2014

On Monday, Oct 6 the default umask, which determines file and directory permissions for Helix and Biowulf users, will change from 022 to 027.

The current umask of 022 allows read/write access for the owner and read-only access for both the group members and everyone else. The new umask of 027 will allow read/write access for the owner and read-only access for group members, but no access for others. Access on existing files and directories will be unaffected.

For the vast majority of users, particularly those who haven't knowingly worked with umask settings up to now, this change will not impact your work. If others have specific concerns, please contact staff@helix.nih.gov

For more information about umasks and file/directory permissions, please see

helix.nih.gov/Documentation/permissions.html

Helix Systems Staff




11/5/2014

The Parallel Computing Toolbox for Matlab is available as a trial installation on the Helix systems. This toolbox lets you solve computationally and data-intensive problems using multicore processors, GPUs and computer clusters. For instructions on how to use the toolbox on the NIH Biowulf cluster, see

http://biowulf.nih.gov/apps/matlabdce.html

The toolbox is available on helix/biowulf until November 14, 2014 (this will probably be extended). We are considering purchasing this product if there is sufficient interest from our user community. There will be a Webex/Conference call with a 1.5 hour overview of the Parallel Computing toolbox.

------------------------------------- Meeting Information ------------------------------------ Topic: Parallel Computing with MATLAB Date: Thursday, November 6, 2014 Time: 1:00 pm, Eastern Daylight Time (New York, GMT-04:00) Meeting Number: 592 633 643 Meeting Password: (This meeting does not require a password.)

To Join the audio, please call 866-872-4258 Conf code # 590 420 6802

------------------------------------------------------- To join the online meeting (Now from mobile devices!) ------------------------------------------------------- 1. Go to https://mathworks.webex.com/mathworks/j.php?ED=314126497&UID=0&RT=MiMxMQ%3D%3D 2. If requested, enter your name and email address. 3. If a password is required, enter the meeting password: (This meeting does not require a password.) 4. Click "Join".




11/24/2014

ACEMD is a a high performance molecular dynamics code for biomolecular systems designed specifically for NVIDIA GPUs. Simple and fast, ACEMD uses very similar commands and input files of NAMD and output files as NAMD or Gromacs. Some NIH users have reported excellent simulation performance with ACEMD.

ACEMD is a commercial product, and we currently have 2 test licenses (for 2 GPU nodes) available on Helix. Information about running ACEMD on Biowulf is available at http://biowulf.nih.gov/apps/acemd.html

We are considering the purchase of some ACEMD licenses for the Biowulf GPU nodes if there is sufficient interest from the Biowulf user community. Please let us know whether you would be interested in continuing to use ACEMD on Biowulf.

Susan.


12/2/2014

The Helix/Biowulf staff will present a series of classes in January/February 2015. All 3 classes will be hands-on, including the Biowulf class.

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: Mon, Jan 26, 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, Jan 27, 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.

NIH Biowulf Cluster: Scientific Computing ----------------------------------------- Date & Time: Thu, Feb 19, 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.

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




12/10/2014

In order to improve fair user access to the modest number of Infiniband- connected nodes on the Biowulf Cluster, effective immediately, a 240 hour walltime limit will be placed on jobs allocating nodes with the "ib" resource. Jobs running for longer than 240 hours will be automatically terminated by the batch system.

Jobs having run for more than 240 hours as of Thursday morning will be deleted at that time; they can be restarted from checkpoint files.

Users who wish to run simulations for longer than 240 hours may wish to use a "job chaining" strategy which is explained in the following web pages:

For GROMACS, http://biowulf.nih.gov/apps/gromacs.html#chain For NAMD, http://biowulf.nih.gov/apps/namd.html#chain For AMBER, http://biowulf.nih.gov/apps/amber.html#chain For CHARMM, http://biowulf.nih.gov/apps/charmm/#daisy

Please send questions and comments to staff@biowulf.nih.gov In particular, if you have better ways to set up chaining jobs than described above, please let us know.




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This page last reviewed: December 14, 2010