Rocks Clusters

NBCR Releases APBS Roll for Rocks 5.3

Administrator — Thu, 04 Feb 2010 10:28:00 +0000

The National Biomedical Computation Resource at University of California, San Diego is pleased to announce the availability of APBS Roll package for Rocks clusters version 5.3 for i386 and x86_64 architectures.

APBS (Adaptive Poisson-Boltzmann Solver) is a scalable Poisson-Boltzmann equation solver used to study electrostatic properties of small to nanoscale biomolecular systems. The APBS Roll simplifies APBS deployment and integration on Rocks clusters. More information about APBS can be found at SourceForge or at the NBCR web site.

This APBS Roll contains the latest APBS version 1.2.1b and PDB2PQR package version 1.5.

The APBS Roll can be downloaded from the APBS download site and the Roll documentation including installation and usage information is available here.

Questions or comments may be directed to Robert Konecny < rok@ucsd.edu>.

PVFS2 Roll for Rocks v5.3 is Released

Administrator — Mon, 04 Jan 2010 11:47:28 +0000

The PVFS2 Roll for i386 and x86_64 architectures is released for Rocks 5.3 (Rolled Tacos).

This roll contains executables and configuration utilities to deploy a PVFS2 file system on a Rocks cluster.

The roll includes PVFS2 v2.8.1.

ISO images for the PVFS2 Roll can be found on the Downloads page.

Installation and configuration instructions can be found here.

Rocks v5.3 is released for Linux on the i386 and x86_64 CPU architectures and for Solaris on the x86_64 architecture

Administrator — Thu, 17 Dec 2009 15:38:18 +0000

Rocks v5.3 (Rolled Tacos) is released for Linux on the i386 and x86_64 CPU architectures and Solaris for the x86_64 architecture.

Downloads

ISO images for Linux on the i386 and x86_64 architectures can be found here.

ISO images for the Solaris on the x86_64 architecture can be found here.

Release Notes

Release notes can be found here.

Sun and UCSD Release the Sun Studio Roll for Rocks 5.2

Administrator — Thu, 12 Nov 2009 17:11:51 +0000

Sun Microsystems and the Rocks Clusters group at UCSD are pleased to announce the release of the Sun Studio 12 update 1 Roll for Rocks 5.2.

The roll is available for download from the Sun Download Center.

The roll contains Sun Studio 12 update 1 compiler suite with C, C++ and Fortran compilers, Math libraries, and performance analysis tools with MPI support.

It is currently being made available for both Linux and Solaris Platforms.

Service Pack Roll v5.2.2 for Rocks v5.2 is Released

Administrator — Wed, 12 Aug 2009 11:31:43 +0000

The Service Pack Roll v5.2.2 for i386 and x86_64 architectures is released.

This roll includes the following fixes.

ISO images for the Service Pack Roll can be found on the Downloads page.

Installation instructions can be found here.

Service Pack Roll v5.2.1 for Rocks v5.2 is Released

Administrator — Mon, 20 Jul 2009 10:14:08 +0000

The Service Pack Roll v5.2.1 for i386 and x86_64 architectures is released.

This roll includes the following fixes.

ISO images for the Service Pack Roll can be found on the Downloads page.

Installation instructions can be found here.

University of Tromso Releases the Torque Roll for Rocks 5.2

Administrator — Sat, 11 Jul 2009 09:55:27 +0000

Roy Dragseth of the University of Tromso announces:

The torque roll for Rocks 5.2.0 is now ready for download. Get the bits at

ftp://ftp.uit.no/pub/linux/rocks/torque-roll/5.2.0

The changes are minimal from version 5.1.0. The only difference is the
neccessary changes needed to accomodate the new infrastructure in Rocks 5.2.

Most important software included:

Torque v2.3.6
Maui v3.2.6p21

The source code of the roll can be accessed from a public mercurial
repository: http://devsrc.cc.uit.no/hg/torque/

The Rocks way of installing the roll is as usual to reinstall your frontend
and compute nodes, but you can also use the chain of commands to install a new
roll on an existing frontend (with or without a previous version of the roll):

# rocks add roll /path/to/torque/roll.iso
# rocks enable roll torque
# rocks create distro
# rocks run roll torque | sh
# reboot

After the the frontend comes back up you should do the following to populate
the node list

# rocks sync config

then kickstart all your nodes

# tentakel /boot/kickstart/cluster-kickstart

After the nodes are reinstalled they should automatically pop up in the
queueing system.

Rocks v5.2 is released for Linux on the i386 and x86_64 CPU architectures and for Solaris on the x86_64 architecture

Administrator — Wed, 24 Jun 2009 13:54:58 +0000

Rocks v5.2 is released for Linux on the i386 and x86_64 CPU architectures and Solaris for the x86_64 architecture.

Downloads

ISO images for Linux on the i386 and x86_64 architectures can be found here.

ISO images for the Solaris on the x86_64 architecture can be found here.

New Features

Solaris support for client nodes

With the new JumpStart Roll, one can now install and configure a Linux-based Rocks frontend to “JumpStart” Solaris-based back-end machines.

Attributes

Can assign “attributes” to nodes at four levels: global, appliance type, OS (e.g., Linux or SunOS), and host. An attribute can be accessed in an XML node as an entity. For example, if you assign the attribute “foo” with the value “123″ to compute-0-0 (i.e., with the command, “rocks set host attr foo 123″), then in an XML node file, you can access the value of the attribute foo with “&foo;”.

Attributes also enable “conditionals”. Using the example above, a “post” section can be optionally executed based on the value of an attribute. For example, if a post section is defined as:

The above post section will only be executed if the attribute “foo” is set to “123″ for the installing host.

Enhancements

OS: Based on CentOS release 5/update 3 and all updates as of June 22, 2009.
Base: Anaconda installer updated to v11.1.2.168.
Base: Isolated MySQL for the Rocks database under /opt/rocks.
Base: Fix for software RAID partitioning.
Base: Increase timeout for package downloads when on slow networks (e.g., 100 or 10 Mbit).
Base: Converted all ‘dbreports’ to the Rocks command line.
Base: Configure ‘MTU’ for networks through the Rocks command line.
Base: Configure network routes through the Rocks command line.
Base: Configure host aliases through the Rocks command line.
Base: Added ‘/var/log/authpriv’ to log rotate list.
Base: Added ‘iburst’ flag to NTP configuration on frontend.
Base: Added version and release info to vmlinuz and initrd.img to enable cross-kickstarting via PXE and making it easier to host different Rocks VMs on a physical system.
Base: Added a YUM configuration file to each node that points to the distribution on the frontend.
Bio: Updated biopython to v1.50.
Bio: Updated clustalw to v2.0.11.
Bio: Updated fasta to v35.4.7.
Bio: Updated fftw to v3.2.1.
Bio: Updated elph archive in glimmer to v1.0.1.
Bio: Updated gromacs to v4.0.1.
Bio: Updated perl-Data-Stag to v0.11.
Bio: Updated perl-Digest-MD5 to v2.38.
Bio: Updated perl-File-Temp to v0.21.
Bio: Updated perl-GD to v2.41.
Bio: Updated perl-GD-SVG to v0.33.
Bio: Updated perl-Graph to v0.91.
Bio: Updated perl-HTML-Parser to v3.60.
Bio: Updated perl-HTML-Tagset to v3.20.
Bio: Updated perl-PathTools to v3.30.
Bio: Updated perl-SOAP-Lite to v0.710.08.
Bio: Updated perl-SVG to v2.49.
Bio: Updated perl-SVG-Graph to v0.02.
Bio: Updated perl-Scalar-List-Utils to v1.21.
Bio: Updated perl-Storable to v2.20.
Bio: Updated perl-Text-Iconv to v1.7.
Bio: Updated perl-URI to v1.38.
Bio: Updated perl-XML-Parser to v2.36.
Bio: Updated perl-XML-Twig to v3.32.
Bio: Updated perl-XML-Writer to v0.606.
Bio: Updated perl-bioperl to v1.6.0.
Bio: Updated perl-libnet to v1.22.
Bio: Updated perl-libwww-perl to v5.826.
Bio: Updated phylip to v3.68.
Bio: Updated reportlab to v2.3.
Bio: Updated t_coffee to v7.81.
Ganglia: Updated to v3.1.2.
HPC: Updated OpenMPI to v1.3.2.
HPC: Updated MPICH2 to v1.0.8p1.
HPC: Updated stream to v5.9.
Java: Updated java to v1.6.0_13.
Java: Updated jdk to v6 update 13.
Java: Updated antlr to v3.1.
Java: Updated jboss to v5.0.1.GA.
Java: Updated jogl to v1.1.1.
SGE: Updated to v6.2 update 1.
Viz: Support for single, dual and quad display nodes.
Viz: Chromium support for 32-bit and 64-bit applications.
Viz: Added CUDA driver. Users can optionally run CUDA programs on the tiled-display nodes.
Viz: User updatable nVidia driver. Makes it easy for users to refresh the nVidia driver without having to wait for an updated Viz Roll.
Xen: Using libvirt instead of ‘xm’ command line programs to start/stop VMs.
Xen: Fix to ensure all routes are active after Xen is started.
Xen: Allow VM disk to be backed by a physical disk partition.
Xen: Fix ‘rocks set host vm’ command to allow users to resize a VM’s disk.
Xen: Use threading in the ‘rocks add cluster’ command to decrease the time to add a virtual cluster.

Rocks v5.2 Beta is Released for x86_64

Administrator — Fri, 08 May 2009 12:13:09 +0000

Rocks v5.2 Beta is released for x86_64 CPU architecture.

Downloads

Rocks-A-Palooza IV Registration is Open

Administrator — Wed, 25 Feb 2009 22:02:04 +0000

May 13, 14 2009
Rocks-A-Palooza IV (Rocks All Hands Meeting)
Atkinson Hall (CalIT2), UCSD
La Jolla, CA

Rocks-a-Palooza IV will be held at Atkinson Hall on the campus of UCSD in La Jolla on May 13th and 14th 2009.

There will be one main session focused on Rocks internals. Participants will leave with an understanding on how to tune Rocks to fit their specific requirements.

In addition, there will be a poster session where Rocks community members can share their creativity and cleverness.

The preliminary agenda can be found here.

Attendance is free for participants from non-profit organizations.

Since this meeting is supported by the NSF, attendees from for-profit entities can attend, but they must become sponsors of the event. The minimum sponsorship is $1,000 which includes two passes to the event. Additional passes cost $500 each.

We encourage all to attend to learn the latest in Rocks and to meet users and developers from the Rocks community.

Registration is limited to 100 and registration will be closed on May 1st (to allow us to accurately budget for meals, snacks and other costs).

To register or to enter a poster, send your request to:

rap@rocksclusters.org