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====== PyLith Hints, Tips, and Tricks ======

==== cig-short email archive ====

To search the cig-short email archive, do a Google search with
<code>
site:http://www.geodynamics.org/pipermail/cig-short/ MY_SEARCH_STRING
</code>

==== Installation ====

// Issues related to installing PyLith //

=== OS X binary ===
== Errors on starting PyLith ==
  * Error:

  'import site' failed; use -v for traceback
  --LOTS OF OUTPUT--
  TypeError: stat() argument 1 must be encoded string without NULL bytes, not str

We have seen this error on Darwin system running OS X 10.5 and
later. Files downloaded from the web are marked with an extra
attribute that can prevent python from starting up properly. The
best solution in these cases is to download PyLith using command
line tools:

  mkdir pylith
  cd pylith
  curl -O http://www.geodynamics.org/cig/software/pylith/pylith-1.6.2-darwin-10.6.8.tgz
  tar -zxf pylith-1.6.2-darwin-10.6.8.tgz

=== Windows binary ===

== Error on starting PyLith ==
  * Error:

  ImportError: numpy.core.multiarray failed to import
  Traceback (most recent call last):
    File "/usr/bin/pylith", line 37, in <module>
      from pylith.apps.PyLithApp import PyLithApp
   File "/usr/lib/python2.6/site-packages/pylith/apps/PyLithApp.py", line 26, in <module>
      class PyLithApp(PetscApplication):
    File "/usr/lib/python2.6/site-packages/pylith/apps/PyLithApp.py", line 33, in PyLithApp
      class Inventory(PetscApplication.Inventory):
    File "/usr/lib/python2.6/site-packages/pylith/apps/PyLithApp.py", line 51, in Inventory
      from pylith.topology.MeshImporter import MeshImporter
    File "/usr/lib/python2.6/site-packages/pylith/topology/MeshImporter.py", line 28, in <module>
      class MeshImporter(MeshGenerator):
    File "/usr/lib/python2.6/site-packages/pylith/topology/MeshImporter.py", line 37, in MeshImporter
      class Inventory(MeshGenerator.Inventory):
    File "/usr/lib/python2.6/site-packages/pylith/topology/MeshImporter.py", line 58, in Inventory
      from pylith.meshio.MeshIOAscii import MeshIOAscii
    File "/usr/lib/python2.6/site-packages/pylith/meshio/MeshIOAscii.py", line 26, in <module>
      from MeshIOObj import MeshIOObj
    File "/usr/lib/python2.6/site-packages/pylith/meshio/MeshIOObj.py", line 26, in <module>
      from meshio import MeshIO as ModuleMeshIO
    File "/usr/lib/python2.6/site-packages/pylith/meshio/meshio.py", line 25, in <module>
      _meshio = swig_import_helper()
    File "/usr/lib/python2.6/site-packages/pylith/meshio/meshio.py", line 21, in swig_import_helper
      _mod = imp.load_module('_meshio', fp, pathname, description)
  ImportError: numpy.core.multiarray failed to import

This error arises from having another version of Python
installed that interferes with the Python included with
PyLith. The solution is to set your environment variables so
that the shell doesn't see the existing Python when you run
PyLith.

  * Double click on the PyLith icon to get the cygwin terminal window for Pylith.
  * Run "env >& env.log" and examine the env.log file for environment variables related to Python.
  * Remove all environment variables related to Python and set the PATH variable to the absolute minimum. For example:

  unset PYTHON
  unset PYTHON26
  unset PYTHON27
  unset PYTHONPATH
  PATH=/usr/bin:/bin:/lib:/lib/lapack

  * You should now be able to use PyLith.
In general, you will need to perform steps 1 and 3 (but not
2) every time you run PyLith. To add these commands to the
PyLith startup script, add the commands to the bottom of the
pylithrc file included in the PyLith distribution. Usually
this file is in Program Files (x86)/PyLith. This shell
script is run every time PyLith starts up.

=== PyLith installer utility ===
See the INSTALL file included with the PyLith installer utility
for directions and example configuration
parameters. Troubleshooting tips are also included at the end of
the INSTALL file.

  * gcc 4.7
    * We have encountered segmentation faults building netcdf with gcc 4.7 on OS X 10.8 (Mountain Lion). Running "make check" in nctest generates a segmentation fault.
  * clang
    * We have encountered problems building PETSc w/Sieve support using clang due to C/C++ issues.

----

==== Meshing ====

// Issues related to generating a mesh to use as input for PyLith. //

=== Best Practices ===

  * Always check the quality of your mesh BEFORE running a PyLith simulation. The ideal aspect ratio is 1.0.
    * CUBIT: Aspect ratios should be less than about 4.0 in quasi-static simulations and less than about 2.0 in dynamic simulations. Use the "Quality" command to show a summary of the element quality. See the "Mesh Quality Assessment" section of the CUBIT manual for more information about the various quality checks. We find the aspect ratio and condition number checks the most useful. We generally use condition number smoothing to improve the mesh quality.
    * LaGriT: Aspect ratios should be greater than about 0.2 in quasi-static simulations and greater than about 0.4 in dynamic simulations. Use the command "quality" to show a summary of the element quality.
  * Always check your nodesets/psets to make sure they match the desired boundaries, etc. Nodesets/pets for Dirichlet boundary conditions cannot overlap if they set the same components (i.e., x-component, y-component, z-component), but they can overlap if they set difference components.

=== CUBIT ===

  * Nonplanar fault geometry
See ''examples/2d/subduction'' and Sessions III and IV of the 2011 Crustal Deformation Modeling tutorial.
  * Varying discretization size with distance from the fault
See ''examples/2d/subduction'' and ''examples/meshing/cubit_cellsize''.
    
=== LaGriT ===

  * Identifying faults using surface meshes
Using surface meshes to identify the fault surface is a development feature
that is fragile and untested. ** Use with extreme caution. **
Identifying faults using psets is a much more thoroughly
tested feature.

----

==== General ====

// General issues related to running PyLith //

=== Nondimensionalization ===

It is ** VERY IMPORTANT ** to make sure that the scales used in
the nondimensionalization are appropriate for your
problem. PyLith can solve problems across an extremely wide
range of spatial and temporal scales if the appropriate scales
are used in the nondimensionalization.

Due to roundoff errors and convergence tolerances in the
iterative solvers, PyLith relies on reasonable scales in the
solution in constructing the friction criterion and
preconditioning the system. Failure to set appropriate scales in
the nondimensionalization will cause the solution to be garbage.

  * Quasi-static problems

  Default values:
    relaxation_time = 1.0*year
    length_scale = 1.0*km
    pressure_scale = 3.0e+10*Pa
  Recommended values:
    relaxation_time = TIME_STEP
    length_scale = DISCRETIZATION_SIZE or DISPLACEMENT_MAGNITUDE
    pressure_scale = SHEAR_MODULUS

  * Dynamic problems

  Default values:
    shear_wave_speed = 3.0*km/s
    density = 3000.0*kg/m**3
    wave_period = 1.0*s

  Recommended values:
    shear_wave_speed = MINIMUM_SHEAR_WAVE_SPEED
    density = DENSITY
    wave_period = MINIMUM_WAVE_PERIOD

=== Fault output ===
    
Slip and traction vectors are output in the fault coordinate
system (along strike, up-dip, and opening). The direction of the
slip vector corresponds to the direction of motion on the
"negative" side of the fault, which is defined by the origin of
the fault normal vector. To convert to the global coordinate
system, request that the fault orientation be included in the
fault output via:

  vertex_info_fields = [strike_dir,dip_dir,normal_dir]

With this information it is easy to rotate the slip or traction vector
from the fault coordinate system to the global coordinate system. This
is usually done in a Python script with HDF5 output or within ParaView
using the calculator. The expression for the slip in global
coordinates is:

  (slip_X*strike_dir_X+slip_Y*dip_dir_X)*iHat+(slip_X*strike_dir_Y+slip_Y*dip_dir_Y)*jHat+(slip_X*strike_dir_Z+slip_Y*dip_dir_Z)*kHat

=== Spontaneous (Dynamic) Rupture in Quasistatic Simulations ===

Use of the FaultCohesiveDyn object for spontaneous (dynamic) rupture in quasistatic simulations requires careful selection of solver parameters. See [[software:pylith:cdm2013|Session V]] of the 2013 Crustal Deformation Modeling tutorial for a detailed discussion.

----
==== Errors running PyLith ====

// Errors when running PyLith //

=== Spatialdata ===

  * Error:

  RuntimeError: Error occurred while reading spatial database file 'FILENAME'.
  I/O error while reading SimpleDB data.

Make sure the ''num-locs'' values in the header matches
the number of lines of data and that the last line of data
includes an end-of-line character.

----

==== Running on a Cluster ====

// Issues related to running PyLith on a cluster or other parallel computer. //


=== OpenMPI and Infiniband ===

  * Segmentation faults when using OpenMPI with Infiniband

  PETSC ERROR: ------------------------------------------------------------------------
  PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
  PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
  PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[14]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
  PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
  PETSC ERROR: to get more information on the crash.
  PETSC ERROR: --------------------- Error Message ------------------------------------
  PETSC ERROR: Signal received!
  PETSC ERROR: ------------------------------------------------------------------------
  PETSC ERROR: Petsc Development HG revision: 78eda070d9530a3e6c403cf54d9873c76e711d49  HG Date: Wed Oct 24 00:04:09 2012 -0400
  PETSC ERROR: See docs/changes/index.html for recent updates.
  PETSC ERROR: See docs/faq.html for hints about trouble shooting.
  PETSC ERROR: See docs/index.html for manual pages.
  PETSC ERROR: ------------------------------------------------------------------------
  PETSC ERROR: /home/brad/pylith-1.8.0/bin/mpinemesis on a arch-linu named des-compute11.des by brad Tue Nov 13 10:44:06 2012
  PETSC ERROR: Libraries linked from /home/brad/pylith-1.8.0/lib
  PETSC ERROR: Configure run at Wed Nov  7 16:42:26 2012
  PETSC ERROR: Configure options --prefix=/home/brad/pylith-1.8.0 --with-c2html=0 --with-x=0 --with-clanguage=C++ --with-mpicompilers=1 --with-debugging=0 --with-shared-libraries=1 --with-sieve=1 --download-boost=1 --download-chaco=1 --download-ml=1 --download-f-blas-lapack=1 --with-hdf5=1 --with-hdf5-include=/home/brad/pylith-1.8.0/include --with-hdf5-lib=/home/brad/pylith-1.8.0/lib/libhdf5.dylib --LIBS=-lz CPPFLAGS="-I/home/brad/pylith-1.8.0/include " LDFLAGS="-L/home/brad/pylith-1.8.0/lib " CFLAGS="-g -O2" CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS="-g -O2" PETSC_DIR=/home/brad/build/pylith_installer/petsc-dev
  PETSC ERROR: ------------------------------------------------------------------------
  PETSC ERROR: User provided function() line 0 in unknown directory unknown file

This appears to be associated with how OpenMPI interprets calls to fork() when PyLith starts up. Set your environment (these can also be set on the command line like other OpenMPI parameters) to turn off Infiniband support for fork so that a normal fork call is made:

  export OMPI_MCA_mpi_warn_on_fork=0
  export OMPI_MCA_btl_openib_want_fork_support=0

  * Turn on processor and memory affinity by using the ''--bind-to-core'' command line argument for mpirun.
	
=== Submitting to batch systems ===

== PBS/Torque ==
  * pylithapp.cfg:

  [pylithapp]
  scheduler = pbs
  
  [pylithapp.pbs]
  shell = /bin/bash
  qsub-options = -V -m bea -M johndoe@university.edu
  
  [pylithapp.launcher]
  command = mpirun -np ${nodes} -machinefile ${PBS_NODEFILE}

Command line arguments:

  −−nodes=NUMPROCS --scheduler.ppn=N --job.name=NAME --job.stdout=LOG_FILE
  
  # NPROCS = total number of processes
  # N = number of processes per compute node
  # NAME = name of job in queue
  # LOG_FILE = name of file where stdout will be written

== Sun Grid Engine ==
  * pylithapp.cfg:

  [pylithapp]
  scheduler = sge
  
  [pylithapp.pbs]
  shell = /bin/bash
  pe-name = orte
  qsub-options = -V -m bea -M johndoe@university.edu -j y
  
  [pylithapp.launcher]
  command = mpirun -np ${nodes}
  # Use the options below if not using the OpenMPI ORTE Parallel Environment
  #command = mpirun -np ${nodes}-machinefile ${PE_HOSTFILE} -n ${NSLOTS}

Command line arguments:

  −−nodes=NPROCS --job.name=NAME --job.stdout=LOG_FILE
  
  # NPROCS = total number of processes
  # NAME = name of job in queue
  # LOG_FILE = name of file where stdout will be written

=== HDF5 and parallel I/O ===

The PyLith HDF5 data writers (DataWriterHDF5Mesh, etc) use HDF5 parallel I/O to write files in parallel. As noted in the PyLith manual, this is not nearly as robust as the HDF5Ext data writers (DataWriterHDF5ExtMesh, etc) that write raw binary files using MPI I/O accompanied by an HDF5 metadata file written. If you experience errors when running on multiple compute nodes where jobs mysteriously get hung up with or without HDF5 error messages, switching from the DataWriterHDF5 data writers to the DataWriterHDF5Ext data writers may fix the problem (if HDF5 parallel I/O is the source of the problem). This will produce one raw binary file per HDF5 dataset, so it means lots more files that must be kept together.


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