[CIG-SHORT] Installation of subversion pylith

Brad Aagaard baagaard at usgs.gov
Thu Mar 11 09:18:35 PST 2010


Your errors suggest an inconsistency between spatialdata and PyLith
related to the C++/Python interface. For compatibility of the C++/Python
code, if you build either PyLith or spatialdata from the repository (and
SWIG generates the interface b/t C++ and Python), then the other must
also be built from the repository. This means you need to build
spatialdata from the repository (and configure it with the --enable-swig
option like you did for PyLith). I apologize for not including this
information in the installation instructions.

Ikuo Cho wrote:
> Brad,
> I was able to install pylith repository version following your advise.
> Now I wonder if the parameters for pylith developing version changed extensively from those for the released version.
> Actually, I tried to run the examples in the directory pylith/examples/3d/hex8, but failed.
> The attached file "typescript" is an example of the messages output from
> pylith when I tried to run pylith by typing:
> pylith savageprescott.cfg.
> I wanted to make sure if these messages mean extensive changes in the
> parameters for pylith (and my instllation was succesful).
> Ikuo Cho
> On Fri, 05 Mar 2010 08:23:48 -0800
> Brad Aagaard <baagaard at usgs.gov> wrote:
>> Ikuo-
>> If you build from the repository (applies to both spatialdata and 
>> pylith), you need to configure with the --enable-swig flag. You will 
>> also need to have a recent version of swig installed (I think 1.3.33 or 
>> later, configure will check this). The source tarball contains the swig 
>> generated files (*_wrap.cxx) , but the repository does not.
>> Brad
>> On 3/4/10 10:04 PM, Ikuo Cho wrote:
>>> Charles,
>>>> If I'm understanding your question correctly,
>>> You understand my question correctly. Thank you for your suggestion.
>>>> or you can check out the version from the subversion repository.
>>> I checked out the latest version of pylith and petsc from the subversion
>>> repository (March 4, 2010). I tried to install them, only to fail at a
>>> later stage:
>>> *******************************************************************
>>> Making install in bc
>>> make[2]: Entering directory `/work6/cho/pylith.srccompiled/Shoyu.1.4.2.dev20100304/pylith/modulesrc/bc'
>>> make[2]: *** No rule to make target `bc_wrap.cxx', needed by `bc_wrap.lo'.  Stop.
>>> make[2]: Leaving directory `/work6/cho/pylith.srccompiled/Shoyu.1.4.2.dev20100304/pylith/modulesrc/bc'
>>> make[1]: *** [install-recursive] Error 1
>>> make[1]: Leaving directory `/work6/cho/pylith.srccompiled/Shoyu.1.4.2.dev20100304/pylith/modulesrc'
>>> make: *** [install-recursive] Error 1
>>> *******************************************************************
>>> Is it a problem that I use automake 1.9.2, autoreconf 2.61 and
>>> libtoolize 1.5.6? (those recommended were automake 1.9.6 and libtoolize
>>> 1.5.22.) Attached files are make.log and config.log that were created
>>> when I tried to install pylith. I would be happy if you tell me what was
>>> wrong. All the installations other than pylith were finished
>>> correctly including petsc-dev, which was also checked out from the
>>> repositry by hg clone.
>>> By the way, I was able to compile the pylith 1.4.2 from the source code that
>>> was downloadable from the web site
>>> http://www.geodynamics.org/cig/software/packages/short/pylith.
>>> Actually, I confirmed that it runs correctly in terms of an example
>>> problem (dislocation.cfg). I took the same procedure and same sets of
>>> environmental variables when I tried to install the current version
>>> under development.
>>> Ikuo Cho
>>> On Fri, 26 Feb 2010 07:26:00 +1300
>>> Charles Williams<willic3 at gmail.com>  wrote:
>>>> Dear Ikuo Cho,
>>>> If I'm understanding your question correctly, you will not be able to do what you are planning with the current released version of PyLith (1.4.2).  In that version, it is not possible to spatially vary the power-law parameters.  The reason is what you have already noticed -- the power-law-coefficient units are dependent on the power-law-exponent.  This is a problem in most power-law implementations, and this has been fixed (but not extensively tested) in the version of the code we're working on now.  We have changed the specification so that power-law materials now require 3 parameters -- a reference stress, a reference strain rate, and the power-law exponent.  This makes the units constant, and you can therefore have spatial variations in these parameters.
>>>> Right now, you have two options to solve your problem.  You can either define a separate material for each set of parameters using the current version of the code, or you can check out the version from the subversion repository.  The documentation in the repository has been updated to reflect the changes in the power-law implementation, but we have not yet put in documentation for the example problem.  I think it will be at least a month or two before our next release, so those are your only options for now.
>>>> I hope this has answered your question.  Good luck with your modeling, and please e-mail back with any questions you might have.
>>>> Cheers,
>>>> Charles
>>>> On 25/02/2010, at 10:44 PM, Ikuo Cho wrote:
>>>>> Dear Pylith Developers:
>>>>> I have a question on a description of the parameter
>>>>> power-law-coefficient in a spatial database: Does the dimension corresponding to the power-law-coefficient have a
>>>>> meaning? I'm asking this because I want to solve a problem of spatially variable power-law exponents.
>>>>> More concretely, is the following description correct or not?
>>>>> 0. 0. 0. 2500. 3000. 5500 1.e-37 3.0
>>>>> 0. 0. 20. 2500. 3000. 5500 1.e-37 2.0
>>>>> with
>>>>> value-names = density vs vp power-law-coefficient power-law-exponent
>>>>> value-units= kg/m**3 m/s m/s Pa**(-3.0)/s None
>>>>> when the flow law is given as
>>>>> (strain rate) = At (stress)**3.0, where At=1.e-37 [Pa**(-3.0)/s], at
>>>>> (x,y,z)=(0,0,0)
>>>>> and
>>>>> (strain rate) = At (stress)**2.0, where At=1.e-37 [Pa**(-2.0)/s], at
>>>>> (x,y,z)=(0,0,20).
>>>>> Ikuo Cho
>>>>> ----------------------------------------------------------
>>>>> Geological Survey of Japan,
>>>>> National Institute of Advanced Industrial Science and Technology
>>>>> Tsukuba Central 7, Tsukuba 305-8567 Japan
>>>>> Tel +81-29-861-3891, Fax +81-29-861-3682
>>>>> ----------------------------------------------------------
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>> Charles A. Williams
>>>> Scientist
>>>> GNS Science
>>>> 1 Fairway Drive, Avalon
>>>> PO Box 30368
>>>> Lower Hutt  5040
>>>> New Zealand
>>>> ph (office): 0064-4570-4566
>>>> fax (office): 0064-4570-4600
>>>> C.Williams at gns.cri.nz
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> 長 郁夫 (Ikuo Cho)
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