[CIG-ALL] CIG News - April 2008

[Sue Kientz]

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          CIG News:  April 2008
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Also available at
http://geodynamics.org/cig/proposalsndocs/newsdocs/newsletter-apr08

CIG Software Releases

     * PyLith 1.1 - PyLith is a finite element code for the solution  
of visco-elastic/plastic deformation that was designed for  
lithospheric modeling problems. This release includes new features  
such as Neumann (traction) boundary conditions, absorbing boundary  
conditions, Dirichlet boundary conditions with displacement and/or  
velocity values, a generalized Maxwell viscoelastic bulk constitutive  
model, and output of fault and material information (state variables  
and diagnostic information). Also provided are a number of  
consistency checks to trap and report errors in the input parameters.  
See
http://geodynamics.org/cig/software/packages/short/pylith/
for source code, binaries, and manual.

     * SPECFEM3D_GLOBE 4.0.1 - SPECFEM3D_GLOBE simulates global and  
regional (continental-scale) seismic wave propagation. The 4.0  
release includes a new doubling brick, making the mesh more accurate  
(in particular in the upper and mid-mantle) and perfectly load- 
balanced on a parallel computer; scaling all the way up to the  
petascale; very large number of CPUs can be used; most 1D Earth  
models are available; both 3D model S20RTS and model S362ANI  
accommodated. The package is now available under the GNU General  
Public License. The 4.0.1 bug fix corrected the 3D mantle model  
S362ANI which was improperly integrated with crustal model Crust2.0. See
http://geodynamics.org/cig/software/packages/seismo/specfem3d-globe/
for source code and manual.

Software Bug Fixes

     * CitcomS 3.0.2 - CitcomS is a finite element code designed to  
solve thermal convection problems relevant to Earth's mantle. This  
release fixes two minor bugs (one in HDF5 output which caused a  
compilation error and another in normalizing the tracer coordinate)  
and restores a feature from a previous version. This version also  
greatly reduces the number of tracers per element that is required  
for thermo-chemical convection. See
http://geodynamics.org/cig/software/packages/mc/citcoms/
or source code and manual. You can also run this latest version of  
CitcomS on the TeraGrid; see
http://geodynamics.org/cig/software/csa/

     * Gale 1.2.2 - Gale is a 2D/3D code that solves problems related  
to orogenesis, rifting, and subduction with coupling to surface  
erosion models. This latest release is now extensively benchmarked,  
and includes parallel VTK output and a rough implementation of  
friction. Several bugs are also fixed. Gale is a joint effort between  
CIG, Victorian Partnership for Advanced Computing (VPAC), and Monash  
University. See
http://geodynamics.org/cig/software/packages/long/gale/
for binaries, source code, and manual.

     * SPECFEM3D 1.4.3 - SPECFEM3D_BASIN, renamed simply SPECFEM3D,  
is now available under the GNU General Public License. The latest  
version adds the Moho boundary kernel computation option for kernel  
simulations and allows kernel computations with attenation on. Also  
offered is the possibility of replacing Hauksson's background model  
by Lin's most recent southern California tomographic model. See
http://geodynamics.org/cig/software/packages/seismo/specfem3d/
for source code and manual.

Software Additions to CIG Website

     * SEISMIC_CPML - SEISMIC_CPML is a set of six Fortran90 programs  
that solve the 2D or 3D isotropic or anisotropic elastic wave  
equation using a finite-difference method with Convolutional  
Perfectly Matched Layer (C-PML) conditions, developed by Dimitri  
Komatitsch and Roland Martin from University of Pau, France. See
http://geodynamics.org/cig/software/packages/seismo/seismic_cpml/
for source code and link to documentation.

     * SPECFEM2D - SPECFEM2D simulates seismic wave propagation in  
two-dimensional anisotropic viscoelastic or coupled viscoelastic- 
acoustic media. See
http://geodynamics.org/cig/software/packages/seismo/specfem2d/
for source code and readme.

     * SPECFEM1D - SPECFEM1D is a small code that allows users to  
learn how a spectral-element program is written. See
http://geodynamics.org/cig/software/packages/seismo/specfem1d/
for source code, which contains self-explanatory comments.

MAG Portal Available

Use the MAG Portal to Avoid Compiling, Queue Jobs. The MAG Portal  
allows users to run the geodynamo code MAG without compiling it  
locally. MAG is a serial version of a rotating spherical convection/ 
magneto-convection/dynamo code that solves the non-dimensional  
Boussinesq equations for time-dependent thermal convection in a  
rotating spherical shell filled with an electrically conducting  
fluid. The portal allows you to create and submit a MAG job to a  
selected TeraGrid site, monitor its progress and, when complete,  
download a tar-ball with the job results to further analyze locally  
or visualize with IDL software. You can also queue up a long serial  
run rather than tie up your local machine. See
https://dynamo.geodynamics.org/magwebportal/
(click "Continue" if prompted).

Upcoming Meetings

     *  2008 Workshop on Numerical Modeling of Crustal Deformation  
and Earthquake Faulting, June 23-27, 2008, UC Davis. The focus of  
this gathering will be on computational models addressing the seismic  
cycle across single and multiple events. The workshop blends science  
talks on case studies from particular faulting environments and on  
key rheological behavior with discussions of current obstacles to  
crustal deformation modeling. The first four days (Monday-Thursday)  
will be a mixture of science talks, discussion, and hands-on  
tutorials. The fifth day (Friday) is dedicated to informal tutorials  
and collaboration. See
http://geodynamics.org/cig/workinggroups/short/workshops/cfem-08
for links to registration and other details.

     * Workshop for Advancing Numerical Modeling of Mantle Convection  
and Lithospheric Dynamics, July 9-11, 2008, UC Davis. This workshop  
on Numerical Modeling of Mantle and Lithospheric Dynamics will build  
on the success of the 2005 Boulder workshop on Mantle Convection, but  
be broader in terms of audience than the Boulder workshop in that we  
will bring together both the mantle convection and lithospheric  
dynamics communities. Plans are to discuss scientific advances and,  
importantly, technical and scientific issues related to the  
quantitative modeling of the origin and evolution of the mantle- 
lithosphere system. Conveners: Magali I. Billen (UC Davis), Jolante  
van Wijk (LANL), Scott King (Virginia Tech), and Thorsten Becker  
(USC). See
http://geodynamics.org/cig/workinggroups/mc/workshops/litho2008
for registration form and other useful information.

CIG Receives LRAC Allocation for Science Gateway, Community Codes  
Support

In order to continue support of the Seismology Science Gateway (which  
offers a web interface to run SPECFEM3D_GLOBE and MAG) and gain  
sufficient TeraGrid allocations to perform benchmarking, training  
sessions, and nurturing new users, CIG requested an upgrade for its  
MRAC to a Large Resource Allocations Committee (LRAC) on Jan. 11, and  
was granted an additional 300,000 SUs on March 12. View the PDF  
proposal at
http://geodynamics.org/cig/proposalsndocs/documents/ 
cig_lrac_proposal_Jan08.pdf

CIG Grants Sub-Award for AMR Development

CIG granted a sub-award to Wolfgang Bangerth at Texas A&M University  
to continue developing the deal.II (which provides infrastructure  
code on which applications supporting adaptive mesh refinement can  
rapidly be built) into a library with wide applicability to  
geodynamics. Under this project, Bangerth will produce a suite of  
programs that demonstrates using this technology for geodynamics  
applications. For more details, see
http://geodynamics.org/cig/proposalsndocs/proposals/ 
TAMU_Bangerth_AMR_Jan08


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Who to contact

CIG Administration, contracts, travel, etc.:
Ariel Shoresh, (626) 395-1699
ariel at geodynamics.org

Equation solvers (PETSc) and PyLith development:
Matt Knepley, knepley at mcs.anl.gov

Gale and Magma development:
Walter Landry, (626) 395-4621
walter at geodynamics.org

Benchmarking, Cigma, and visualization:
Luis Armendariz, (626) 395-1695
luis at geodynamics.org

Build procedure and computational seismology:
Leif Strand, (626) 395-1697
leif at geodynamics.org

Citcom and Mantle convection benchmarks:
Eh Tan, (626) 395-1693,
tan2 at geodynamics.org

Website and user manuals:
Sue Kientz, (626) 395-1694
sue at geodynamics.org

Geodynamo, SVN software repository, and systems administration:
Wei Mi, (626) 395-1692
wei at geodynamics.org

Software architecture and Pyre framework:
Michael Aivazis, (626) 395-1696
aivazis at caltech.edu

Administration:
Mike Gurnis, (626) 395-1698
gurnis at caltech.edu

Science Steering Committee: contact Chairman
Brad Aagaard (USGS),
baagaard at usgs.gov

Executive Committee: contact Chairman
Marc Spiegelman (Columbia),
mspieg at lamont.ldeo.columbia.edu

-- 
Sue Kientz

Technical Writer/Web Manager
Computational Infrastructure of Geodynamics (CIG)
     http://www.geodynamics.org/
sue at geodynamics.org
ofc: (626) 395-1694
     ~Metaphors Be With You~




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