[CIG-ALL] PyLith 1.0.2
baagaard at usgs.gov
Wed Dec 5 11:25:07 PST 2007
I am pleased to announce the 1.0.2 release of PyLith, a finite element
code designed to solve quasi-static viscoelastic problems in tectonic
This is a bugfix release, which fixes several bugs discovered since
the release of version 1.0.1 in July. We encourage all users of PyLith
1.0 to switch to this latest release. We have also made some
significant performance improvements. A binary package for Intel Macs
is now available too!
You can download the source code and binaries from
Installation instructions are in the bundled README and INSTALL
files, as well as in the User Manual on the web page.
* Performance optimizations have significantly reduced runtime and
memory use relative to version 1.0.1. The default quadrature order
for tetrahedral cells is now 1, which is appropriate for the
default basis functions.
- For most crustal deformation problems, we recommend using the
Additive Schwartz preconditioner via the following PETSc
+ Command line arguments
+ pylithapp.cfg (or your other favorite .cfg file)
pc_type = asm
ksp_max_it = 100
ksp_gmres_restart = 50
ksp_rtol = 1.0e-08
- If the solve takes more than a few hundred iterations for a
large problem (use the --petsc.ksp_monitor=1 and
--petsc.ksp_view=1 to see diagnostic information for the
solver), this is an indication that something is wrong. Either
the preconditioner is inappropriate for the type of problem you
are solving (try other PETSc preconditioners) or there is an error in
the problem setup.
* Added checks to verify the compatibility of quadrature scheme for solid
and cohesive cells.
* Bug fixes
- In some cases, cohesive cells were not inserted into the
finite-element mesh properly. The cells mixed together vertices
from the different sides of the fault. A more efficient
procedure for creating cohesive cells fixed this problem.
- Cell adjacency graph was created incorrectly which resulted in
a poor quality of partitioning among processors.
- VTK output for meshes with N faults included cohesive cells
for N-1 faults. Since VTK output does not understand cohesive
cells, we now remove all cohesive cells from the VTK output.
- Using the SimpleDB in Spatialdata from Python limited
interpolation to the "linear" scheme instead of allowing use of
the "nearest" scheme. Setting the SimpleDB property to "nearest"
and "linear" now works as expected.
- The reader for Spatialdata coordinate systems information did not
correctly putback characters in the input stream, resulting in
reading errors. The putback routines were fixed.
- Fault "up" and "normal" directions remained as string arrays
when passed to the module, instead of being converted to float
* Known issues
- The VTK output contains the Lagrange vertices in the cohesive
cells. These are forces, not displacements, which can cause
confusion when visualizing the output. These will be removed
when we improve the output in version 1.1.
- Using the 32-bit linux binary on 64-bit linux systems
The error message is ""merlin.DistributionNotFound:
Cheetah". This error arises because one of the packages that
PyLith uses does not know how to determine the system
architecture at runtime. The workaround is:
(1) Go to the lib/python2.5/site-packages directory.
(2) Unzip merlin-1.3-py2.5.egg (if it is a file and not a directory).
(3) Go to the merlin directory.
(4) Edit __init__.py. Replace line 308
plat = get_platform()
plat = "linux-i686"
(5) If merlin-1.3-py2.5.egg is a file, rezip merlin. Go to the
site-packages directory and enter
"zip -r merlin-1.3-py2.5.egg merlin".
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