[CIG-SHORT] pylith-1.8.0

Tue Dec 19 15:04:29 PST 2017

Hi Brad,

This is really helpful; I see that spatialdata and pylith modules are installed with SWIG 2.0.4. However, the version 2.0.2 were installed by the pylith-1.8.0 installer. I will manually install the 2.0.4 and update if it was the issue. 

Thanks again for your time.

Best,
Ehsan

> On Dec 19, 2017, at 5:46 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> 
> Ehsan,
> 
> This error shows up when spatialdata and PyLith Python modules are not built with the same SWIG. If you are using the pylith-1.8.0 tarball via the installer, then you need to use the spatialdata version that was provided when PyLith version 1.8.0 was released (this should be the version number in the installer Makefile.am).
> 
> Alternatively, you need to install SWIG (version 3.0.2 or EARLIER) and rebuild the Python bindings files for spatialdata and PyLith. To do this, you need to remove the .py and _wrap.cxx files in modulesrc/*. Running make with SWIG installed will automatically regenerate these files.
> 
> Regards,
> Brad
> 
> 
> On 12/19/17 11:19 AM, Ehsan Haghighat wrote:
>> Hi Brad, Matt,
>> 
>> Thanks for your support. I managed to compiled it eventually with ‘make && make install’. However, now I get the error bellow while running it. I do not get this error when I do the same in 2.1.0. Any idea what may cause these? The error says type error, but I have no changes there really. I should mention that our add-on include some material models and some code that reads external pressure history for coupled simulations. We do not make any fundamental changes to pylith and how the projects are organized.
>> 
>> Thanks,
>> Ehsan
>> 
>> 
>> 
>>    self._configure()
>>  File "/home/ehsanhaghighat/tools/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc/DirichletBC.py", line 125, in _configure
>>    TimeDependentPoints._configure(self)
>>  File "/home/ehsanhaghighat/tools/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc/TimeDependentPoints.py", line 79, in _configure
>>    TimeDependent._configure(self)
>>  File "/home/ehsanhaghighat/tools/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc/TimeDependent.py", line 111, in _configure
>>    ModuleTimeDependent.dbInitial(self, self.inventory.dbInitial)
>>  File "/home/ehsanhaghighat/tools/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc/bc.py", line 205, in dbInitial
>>    def dbInitial(self, *args): return _bc.TimeDependent_dbInitial(self, *args)
>> TypeError: in method 'TimeDependent_dbInitial', argument 2 of type 'spatialdata::spatialdb::SpatialDB *const'
>> 
>> 
>> 
>> 
>> 
>> 
>>> On Dec 18, 2017, at 12:13 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>>> 
>>> Ehsan,
>>> 
>>> This is an odd error. I think it suggests that something went wrong during the build and/or install. If you ran into errors building and restarted with different settings, you may need to wipe the build and target directories clean and start fresh.
>>> 
>>> Regards,
>>> Brad
>>> 
>>> 
>>> On 12/16/17 8:43 PM, Ehsan Haghighat wrote:
>>>> Hello Brad,
>>>> 
>>>> I was able to compile the 1.8.0 libraries following your suggestions (most of the repositories need to be changed). I can share the Makefile with you if you want to update the 1.8.0 then others can still install it if needed.
>>>> 
>>>> However, after adding my libraries, I get following errors that I cannot figure them out. Can you help here? Anything you can think of? Really appreciated. The make works fine, but when I want to install it (make install), I get following error.
>>>> 
>>>> Best,
>>>> Ehsan
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -----------------
>>>> libtool: install: /usr/bin/install -c .libs/_bcmodule.soT /nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc/_bcmodule.so
>>>> libtool: install: /usr/bin/install -c .libs/_bcmodule.lai /nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc/_bcmodule.la
>>>> libtool: finish: PATH="/nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/bin:/nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/bin:/nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/bin:/nobackup1/ehsanhaghighat/dev/GRS-2.1.0/pylith/bin:/nobackup1/ehsanhaghighat/.software/os6/grs-2.1.0/bin:/home/ehsanhaghighat/tools/GPRS-Only/GPRS08/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/sbin:/usr/sbin:/sbin" ldconfig -n /nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc
>>>> ----------------------------------------------------------------------
>>>> Libraries have been installed in:
>>>>  /nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc
>>>> 
>>>> If you ever happen to want to link against installed libraries
>>>> in a given directory, LIBDIR, you must either use libtool, and
>>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>>> flag during linking and do at least one of the following:
>>>>  - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>>    during execution
>>>>  - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>>    during linking
>>>>  - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>>  - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>> 
>>>> See any operating system documentation about shared libraries for
>>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>>> ----------------------------------------------------------------------
>>>> test -z "/nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc" || /bin/mkdir -p "/nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc"
>>>> /usr/bin/install -c -m 644 ../../../pylith-1.8.0/modulesrc/bc/bc.py '/nobackup1/ehsanhaghighat/dev/GRS-1.8.0/pylith/lib/python2.7/site-packages/pylith/bc'
>>>> /bin/sh: line 16: ../../../pylith-1.8.0/./aux-config/py-compile: Permission denied
>>>> make[3]: *** [install-subpkgpyexecPYTHON] Error 126
>>>> make[3]: Leaving directory `/nobackup1b/users/ehsanhaghighat/dev/GRS-1.8.0/build/pylith/pylith-build/modulesrc/bc'
>>>> make[2]: *** [install-am] Error 2
>>>> make[2]: Leaving directory `/nobackup1b/users/ehsanhaghighat/dev/GRS-1.8.0/build/pylith/pylith-build/modulesrc/bc'
>>>> make[1]: *** [install-recursive] Error 1
>>>> make[1]: Leaving directory `/nobackup1b/users/ehsanhaghighat/dev/GRS-1.8.0/build/pylith/pylith-build/modulesrc'
>>>> make: *** [install-recursive] Error 1
>>>> 
>>>> -----------------------
>>>> 
>>>>> On Dec 15, 2017, at 5:18 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>>>>> 
>>>>> On 12/15/2017 01:53 PM, Ehsan Haghighat wrote:
>>>>>> You mentioned earlier about compiling the 1.8.0 that I should download manually the packages; where should I download the from? And how can I do that? (Because of if the link in Makefile is not working, it should not be accessible externally either. Am I missing something)
>>>>> 
>>>>> You should be able to find most of the dependencies here:
>>>>> http://geoweb.cse.ucdavis.edu/~buildbot/deps
>>>>> 
>>>>> If they are not there, then you may need to get them from the individual sites. For example, Python comes from python.org.
>>>>> 
>>>>> Regards,
>>>>> Brad
>>>>> _______________________________________________
>>>>> CIG-SHORT mailing list
>>>>> CIG-SHORT at geodynamics.org
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>>>> 
>>> 
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> 
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