[CIG-SHORT] Error on running .cfg files
Mahesh Singh Dhar (msdhar)
msdhar at memphis.edu
Fri Feb 17 12:46:02 PST 2012
Brad,
PYTHONPATH IS
PYTHONPATH=/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-packages
So it's in the correct path. and I am using Mac OS X version 10.6.8.
-mahesh
________________________________________
From: Brad Aagaard [baagaard at usgs.gov]
Sent: Friday, February 17, 2012 2:32 PM
To: Mahesh Singh Dhar (msdhar)
Cc: cig-short at geodynamics.org; olboyd at usgs.gov
Subject: Re: [CIG-SHORT] Error on running .cfg files
Mahesh,
After you run "source setup.sh" make sure your PYTHONPATH is
DIR_WHERE_PYLITH_IS_INSTALLED/lib/python2.6/site-packages
If starting up the python provided with the PyLith binary fails as you
indicate, only a few things can be wrong. Either your environment is not
setup properly or the binary is not compatible with your system. There
are lots of people using this binary on Darwin 10.6 systems, so the
binary is almost certainly fine. Just to make sure your system is
compatible, what version of OS X are you using (Click on the Apple icon
in the upper left and "About This Mac"?
Regards,
Brad
On 02/17/2012 12:12 PM, Mahesh Singh Dhar (msdhar) wrote:
> Hi Brad,
>
> My system administrator changed tcsh to bash. now it's good with $SHELL
> -----------------------------
> bash-3.2$ echo $0
> /bin/bash
> bash-3.2$ echo $SHELL
> /bin/bash
> ---------------------------------
>
> With this also same error message appeared.
>
> Then using "which" command as you indicated in your previous email, appeared as
>
>
> ---------------------------------------------------
> bash-3.2$ source setup.sh
> Ready to run PyLith.
> bash-3.2$ which python
> /gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/python
> bash-3.2$ python
> 'import site' failed; use -v for traceback ---------- this is an extra line than yours--------
> Python 2.6.6 (r266:84292, Jun 18 2011, 09:44:38)
> [GCC 4.6.0] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>> ^D
> bash-3.2$ which nemesis
> /gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/nemesis
> bash-3.2$ nemesis
> 'import site' failed; use -v for traceback -------------- ---------- this is an extra line than yours--------
> Python 2.6.6 (r266:84292, Jun 18 2011, 09:44:38)
> [GCC 4.6.0] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
>>>>>
> bash-3.2$ which pylith
> /gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/pylith
> bash-3.2$ pylith
> 'import site' failed; use -v for traceback --------------------- ------------ ---------- this is an extra line than yours--------
> Traceback (most recent call last):
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/pylith", line 28, in<module>
> import os.path, sys, site
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-packages/site.py", line 73, in<module>
> __boot()
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-packages/site.py", line 33, in __boot
> imp.load_module('site',stream,path,descr)
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py", line 525, in<module>
> main()
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py", line 508, in main
> known_paths = addsitepackages(known_paths)
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py", line 288, in addsitepackages
> addsitedir(sitedir, known_paths)
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py", line 185, in addsitedir
> addpackage(sitedir, name, known_paths)
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py", line 159, in addpackage
> if not dircase in known_paths and os.path.exists(dir):
> File "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/genericpath.py", line 18, in exists
> st = os.stat(path)
> TypeError: stat() argument 1 must be encoded string without NULL bytes, not str
> bash-3.2$
>
>
>
> --------------------------------------------------------------------------------------------------------
>
> I think now the environment problem is solved. Does the line ('import site' failed; use -v for traceback) indicating any source of error? or is there still environment problem?
> note: pylith-1.6.2-darwin-10.6.8 is a folder which contains setup.sh file.
>
>
> sincerely,
>
> mahesh
>
>
> ________________________________________
> From: Brad Aagaard [baagaard at usgs.gov]
> Sent: Friday, February 17, 2012 11:49 AM
> To: Mahesh Singh Dhar (msdhar)
> Cc: cig-short at geodynamics.org; olboyd at usgs.gov
> Subject: Re: [CIG-SHORT] Error on running .cfg files
>
> Mahesh,
>
> Because your default shell is tcsh ($SHELL == /bin/tcsh), you will need
> to startup a bash shell before running PyLith. So your typical workflow
> will be
>
> bash
> cd DIRECTORY_WHERE_PYLITH_IS_INSTALLED
> source setup.sh
> RUN_PYLITH
>
> In order to verify that your environment is setup properly after running
> setup.sh, please try this:
>
> bash
> cd DIRECTORY_WHERE_PYLITH_IS_INSTALLED
> source setup.sh
> which python
> which nemesis
> which pylith
> python [exit python shell by typing CONTROL-D]
> nemesis [exit python shell by typing CONTROL-D]
> pylith
>
> When I do this with the v1.6.2 binary I get:
>
> brad at arling$ source setup.sh
> Ready to run PyLith.
>
> brad at arling$ which python
> /tools/common/pylith-dev/releases/v1.6.2/pylith-1.6.2-linux-x86_64/bin/python
>
> brad at arling$ which nemesis
> /tools/common/pylith-dev/releases/v1.6.2/pylith-1.6.2-linux-x86_64/bin/nemesis
>
> brad at arling$ which pylith
> /tools/common/pylith-dev/releases/v1.6.2/pylith-1.6.2-linux-x86_64/bin/pylith
>
> brad at arling$ python
> Python 2.6.6 (r266:84292, Mar 8 2011, 04:12:50)
> [GCC 4.5.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
>
> brad at arling$ nemesis
> Python 2.6.6 (r266:84292, Mar 8 2011, 04:12:50)
> [GCC 4.5.2] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
>
> brad at arling$ pylith
> --- LOTS OF STUFF ---
> raise ValueError("Filename for ASCII input mesh not specified.")
> ValueError: Filename for ASCII input mesh not specified.
>
>
> If you don't get similar results when you do "which python", "which
> nemesis", or "which pylith", then your shell environment is not setup
> correctly and we can't offer much assistance. If this happens, I
> recommend switching your environment to the bash shell (ask your system
> administrator for help), which is now the default shell on most unix
> systems.
>
> Regards,
> Brad
>
>
> On 02/17/2012 09:24 AM, Mahesh Singh Dhar (msdhar) wrote:
>> Hi,
>>
>> Default shell environment in my lab is tcsh. As your suggestion I typed "bash" and followed your steps and after running " pylith axialdisp.cfg" , then again similar error appeared as previous one.
>>
>> Just for information;
>> echo $SHELL gives tcsh and
>> echo $0 gives bash
>>
>> -----------------------------------------------------------
>> ceriml09:~ msdhar$ echo $SHELL
>> /bin/tcsh
>> ceriml09:~ msdhar$ bash
>> bash-3.2$ echo $SHELL
>> /bin/tcsh
>> bash-3.2$ echo $0
>> bash
>> bash-3.2$
>> --------------------------------------------------------------
>>
>> Does it make any difference?
>>
>> and I did unset PYTHOPATH also and after running pylith same error message appeared.
>>
>> I am looking forward for your suggestion.
>>
>> sincerely,
>>
>> Mahesh Singh Dhar
>> Graduate Research Assistant
>> CERI/University of Memphis
>>
>> ________________________________________
>>
>>
>> On 2/10/12 3:34 PM, "Brad Aagaard"<baagaard at usgs.gov> wrote:
>>
>>> On 02/10/2012 01:15 PM, Mahesh S Dhar wrote:
>>>> Hi,
>>>> I installed Pylith software (using the link;
>>>> pylith-1.6.2-darwin-10.6.8.tgz) and ran set up file by source setup.sh.
>>>> From tutorial file I tried to run .cfg file ( e.g. pylith
>>>> axialdisp.cfg). the error message comes as below;
>>>> ceriml09:pylith-1.6.2-darwin-10.6.8 msdhar$ source setup.sh Ready to
>>>> run PyLith.ceriml09:pylith-1.6.2-darwin-10.6.8 msdhar$ cd ssetup.sh
>>>> share/ src/ ceriml09:pylith-1.6.2-darwin-10.6.8 msdhar$ cd
>>>> src/pylith/examples/twocells/twot twotet4/ twotet4-geoproj/
>>>> twotri3/ ceriml09:pylith-1.6.2-darwin-10.6.8 msdhar$ cd
>>>> src/pylith/examples/twocells/twotri3/ceriml09:twotri3 msdhar$ pylith
>>>> axialdisp.cfg 'import site' failed; use -v for tracebackTraceback (most
>>>> recent call last): File
>>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/pylith", line
>>>> 28, in<module> import os.path, sys, site File
>>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-p
>>>> ackages/site.py", line 73, in<module> __boot() File
>>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-p
>>>> ackages/site.py", line 33, in __boot
>>>> imp.load_module('site',stream,path,descr) File
>>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.
>>> py", line 525, in<module> main() File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 508, in main known_paths = addsitepackages(known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 288, in addsitepackages addsitedir(sitedir, known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 185, in addsitedir addpackage(sitedir, name, known_paths)
>>> File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 159, in addpackage if not dircase in known_paths and
>>> os.path.exists(dir): File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/generic
>>> path.py", line 18, in exists st = os.stat(path)TypeError: stat()
>>> argument 1 must be encoded string without NULL bytes, not
>>> strceriml09:twotri3 msdhar$ pysetReady to run
>>> PyLith.ceriml09:pylith-1.6.2-darwin-10.6.8 msdhar$ pylith
>>> axialdisp.cfg'import site' failed;
>>> use -v for tracebackTraceback (most recent call last): File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/pylith", line
>>> 28, in<module> import os.path, sys, site File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-pa
>>> ckages/site.py", line 73, in<module> __boot() File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-pa
>>> ckages/site.py", line 33, in __boot
>>> imp.load_module('site',stream,path,descr) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 525, in<module> main() File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 508, in main known_paths = addsitepackages(known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 288, in addsitepackages addsitedir(sitedir, known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 185, in addsitedir a
>>> ddpackage(sitedir, name, known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 159, in addpackage if not dircase in known_paths and
>>> os.path.exists(dir): File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/generic
>>> path.py", line 18, in exists st = os.stat(path)TypeError: stat()
>>> argument 1 must be encoded string without NULL bytes, not
>>> strceriml09:pylith-1.6.2-darwin-10.6.8 msdhar$ cd
>>> src/pylith/examples/twocells/twotri3/ceriml09:twotri3 msdhar$ pylith
>>> axialdisp.cfg'import site' failed; use -v for tracebackTraceback (most
>>> recent call last): File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/bin/pylith", line
>>> 28, in<module> import os.path, sys, site File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-pa
>>> ckages/site.py", line 73, in<module> __boot() File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site-pa
>>> ckages/site.py", line 33, in __boot i
>>> mp.load_module('site',stream,path,descr) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 525, in<module> main() File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 508, in main known_paths = addsitepackages(known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 288, in addsitepackages addsitedir(sitedir, known_paths) File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 185, in addsitedir addpackage(sitedir, name, known_paths)
>>> File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/site.py
>>> ", line 159, in addpackage if not dircase in known_paths and
>>> os.path.exists(dir): File
>>> "/gaia/home/msdhar/pylith/pylith-1.6.2-darwin-10.6.8/lib/python2.6/generic
>>> path.py", line 18, in exists st = os.stat(path)TypeError: stat()
>>> argument 1 must be encoded string without NULL bytes, not
>>> strceriml09:twotri3
>>> msdhar$
>>>> How do I fix this? I am using MAC OS X Version 10.6.8.
>>>> sincerely,mahesh
>>>
>>> The error you are getting is likely caused by conflicts in your
>>> environment setup. First, make sure you are using the bash shell.
>>>
>>> echo $SHELL
>>>
>>> The output should be "/bin/bash". If the output is not /bin/bash, then
>>> simply startup a bash shell before running "source setup.sh" by typing
>>> "bash". If you are using the bash shell, then please try the following
>> >from the top-level pylith directory (where setup.sh) is:
>>>
>>> unset PYTHONPATH
>>> unset DYLD_LIBRARY_PATH
>>> PATH=/bin:/usr/bin
>>> source setup.sh
>>> cd src/pylith/examples/twocells/twotri3
>>> pylith axialdisp.cfg
>>>
>>> Regards,
>>> Brad
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>>
>>
>>
>>
>
>
>
>
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