[CIG-SHORT] problem with installation of pylith 64bit from source code
Makoto Hoshino
m-hoshino at aist.go.jp
Tue Oct 7 20:16:54 PDT 2008
Brad,
As you said, I deleted the directory pylith-1.3.0-linux-i686 and tried
again "tar xvf pylith-1.3.0-linux-i686.tgz".
Next I changed the current directory to the new umcompressed
src/pylith/exmpale/3d/hex8,
and ran Pylith that I have installed from the source code.
However, I found that the same error messages appeared.
In this procedure, I used the clean version of the Cubit file (I didn't
generate the Cubit file by myself).
Two points I want to emphasize are
1)The file "the box_hex8_1000m.exo" that we used here is not corrupt.
I made sure that another run of Pylith, the binary executable version,
finished successfully for the same Cubit datafile.
2)It seems that I was able to have installed Pylith from the source
code except a module used to read Cubit files because test runs finished
successfully as long as I used Lagrit or ascii formats (e.g.,
src/pylith/examples/3d/tet4 or src/pylith/examples/twocells).
I haven’t solved this problem of importing Cubit files yet. I'm happy
if the above facts are useful to provide another comment.
Makoto
Brad Aagaard wrote:
> Makoto-
>
> The assertion that was triggered is a consistency check to make sure that the
> size of the coordinates array is the number of vertices times the spatial
> dimension. This error seems to indicate that the box_hex8_1000m.exo file is
> corrupt. Did you run CUBIT and generate the file or are you using the file
> from the source code? I would extract a clean version of this file from the
> source tarball (or repository if you used the SVN repository) and then try
> again.
>
> Brad
>
>
> On Monday 06 October 2008 5:28:19 pm Leif Strand wrote:
>
>> Sorry, I just noticed that your last e-mail didn't go to Matt or the
>> cig-short list.
>>
>> I don't know what that assertion means... I've CC'd Brad, who should be
>> able to help.
>>
>> --Leif
>>
>> Makoto Hoshino wrote:
>>
>>> Matt and Leif,
>>>
>>> Thanks for your prompt reply.
>>>
>>> As you pointed out, I actually built Nemesis by running 'setup.py'. So
>>> I deleted the directory
>>> /usr/local2/lib/python2.5/site-packages/nemesis-1.0-py2.5.egg
>>> and installed Nemesis and Pylith again. After all, Pylith started to run
>>> correctly, but only when a meshfile made by Lagrit was used. For example,
>>> a test run
>>> cd src/pylith/examples/3d/tet4; pylith dislocation.cfg
>>> seemed to go well, but another run “cd src/pylith/examples/3d/hex8;
>>> pylith dislocation.cfg”
>>> ended with error messages:
>>>
>>> [dry at n102 hex8]$ pylith dislocation.cfg
>>>
>>> /usr/local2/lib/python2.5/site-packages/pylith/utils/PetscManager.py:47:i
>>> nitialize
>>>
>>> -- petsc(info)
>>> -- Initializing PETSc.
>>>
>>> >> /usr/local2/lib/python2.5/site-packages/pylith/meshio/MeshIO.py:45:re
>>> >>ad
>>>
>>> -- meshiocubit(info)
>>> -- Reading finite-element mesh
>>>
>>> >> meshio/MeshIOCubit.cc:138:<unknown>
>>>
>>> -- meshiocubit(info)
>>> -- Reading 245 vertices.
>>> mpinemesis: meshio/MeshIOCubit.cc:154: void
>>> pylith::meshio::MeshIOCubit::_readVertices(NcFile&,
>>> pylith::double_array*, int*, int*) const: Assertion
>>> `(*numVertices)*(*numDims) == size' failed.
>>> rank 0 in job 5 n102_53796 caused collective abort of all ranks
>>> exit status of rank 0: killed by signal 6
>>> --pyre-start: mpirun: exit 6
>>> /usr/local2/bin/pylith: /usr/local2/bin/nemesis: exit 1
>>>
>>> Should I install any library related to Cubit?
>>>
>>>
>>> On Thu, 02 Oct 2008 11:57:11 -0700
>>> Leif Strand <leif at geodynamics.org> wrote:
>>>
>>> As Matt said, something probably went wrong when you installed
>>>
>>> 'nemesis'. I notice that in your 'sys.path', you have:
>>>
>>>> /usr/local2/lib/python2.5/site-packages/nemesis-1.0-py2.5.egg
>>>>
>>>> This directory should not exist. If it does exist, it suggests you ran
>>>> the Nemesis 'setup.py' script. But the nemesis 'setup.py' script
>>>> should not be run directly. Instead, install 'nemesis' as follows:
>>>>
>>>> ./configure --prefix=/usr/local2
>>>> make
>>>> make install
>>>>
>>>> Make sure the correct MPI tools are on your path when you do this.
>>>> Also make sure the correct 'python' is on your path.
>>>>
>>>> Afterwards, you should have a 'nemesis' executable
>>>> (/usr/local2/bin/nemesis) which behaves just like Python, except that
>>>> it knows about '_mpi':
>>>>
>>>> [dry at n100 ~]$ nemesis
>>>> Python 2.5.2 (r252:60911, Sep 25 2008, 15:56:45)
>>>> [GCC 3.4.6 20060404 (Red Hat 3.4.6-3)] on linux2
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>
>>>>
>>>>>>> import _mpi
>>>>>>>
>>>> I must confess that I'm baffled by the error message you sent:
>>>>
>>>> ImportError: No module named _mpi
>>>>
>>>> If you installed 'nemesis' incorrectly, then you wouldn't have a
>>>> 'nemesis' program, and you wouldn't be able to run 'pylith' at all.
>>>> Note that the very first line of the 'pylith' script is:
>>>>
>>>> #!/usr/bin/env nemesis
>>>>
>>>> On the other hand, if 'nemesis' does exist, then it must have been
>>>> successfully installed... and it should be able to "import _mpi".
>>>>
>>>> --Leif
>>>>
>>>> Matthew Knepley wrote:
>>>>
>>>>> This is a problem with the nemesis installation, since this is what
>>>>> loads the
>>>>> _mpi module for Python. It is common (if you have multiple MPI
>>>>> installations)
>>>>> to select the wrong one at nemesis installation time. You muse have the
>>>>> correct 'mpirun' or 'mpiexec' in your path when installing nemesis.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>> 2008/10/2 Makoto Hoshino <m-hoshino at aist.go.jp>:
>>>>>
>>>>>> Dear pylith developers,
>>>>>>
>>>>>> As written in the previous email from Ikuo, I have installed Pylith
>>>>>> from
>>>>>> the source code into a 64bit computer machine with specification:
>>>>>>
>>>>>> OS: CentOS release 4.4 (Final)
>>>>>> linux: 2.6.9-42.0.10.ELsmp x86_64
>>>>>> CPU(64bit): Intel(R) Xeon(R) X5355 @ 2.66GHz
>>>>>>
>>>>>> As a note, I installed Python2.5 to /usr/local2/ and export
>>>>>> PYTHONPATH=/usr/local2/lib/python2.5/site-packages,
>>>>>> and installed pylith so that it does NOT depend on MPICH but MPICH2.
>>>>>>
>>>>>> No noticeable warning was found in the installation process of Pylith,
>>>>>> but I was not able to run it correctly. To be specific, I tried to run
>>>>>> Pylith in the directory src/pylith/examples/3d/hex8 by typing " pylith
>>>>>> dislocation.cfg". However, I only obtained the following messages.
>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>> File "/usr/local2/bin/pylith", line 31, in <module>
>>>>>> from pylith.PyLithApp import PyLithApp
>>>>>> File "/usr/local2/lib/python2.5/site-packages/pylith/PyLithApp.py",
>>>>>> line
>>>>>> 17, in <module>
>>>>>> from mpi import Application
>>>>>> File
>>>>>> "/usr/local2/lib/python2.5/site-packages/pythia-0.8.1.7-py2.5.egg/mpi/
>>>>>> __init__.py",
>>>>>>
>>>>>> line 14, in <module>
>>>>>> from _mpi import *
>>>>>> ImportError: No module named _mpi
>>>>>>
>>>>>> Could you tell me what happened? I think the following information
>>>>>> obtained from the python shell is useful to make a diagnosis.
>>>>>>
>>>>>> [dry at n100 ~]$ python
>>>>>> Python 2.5.2 (r252:60911, Sep 25 2008, 15:56:45)
>>>>>> [GCC 3.4.6 20060404 (Red Hat 3.4.6-3)] on linux2
>>>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>>
>>>>>>
>>>>>>>>>>>> import sys
>>>>>>>>>>>> sys.path
>>>>>>>>>>>>
>>>>>> ['', '/usr/local2/lib/python2.5/site-packages/merlin-1.4.egg',
>>>>>> '/usr/local2/lib/python2.5/site-packages/Cheetah-2.0.1-py2.5-linux-x86
>>>>>> _64.egg',
>>>>>>
>>>>>> '/usr/local2/lib/python2.5/site-packages/pythia-0.8.1.7-py2.5.egg',
>>>>>> '/usr/local2/lib/python2.5/site-packages/nemesis-1.0-py2.5.egg',
>>>>>> '/usr/local2/lib/python2.5/site-packages',
>>>>>> '/usr/local2/lib/python25.zip', '/usr/local2/lib/python2.5',
>>>>>> '/usr/local2/lib/python2.5/plat-linux2',
>>>>>> '/usr/local2/lib/python2.5/lib-tk',
>>>>>> '/usr/local2/lib/python2.5/lib-dynload']
>>>>>>
>>>>>>
>>>>>>>>>>>> import mpi
>>>>>>>>>>>>
>>>>>> Traceback (most recent call last):
>>>>>> File "<stdin>", line 1, in <module>
>>>>>> File
>>>>>> "/usr/local2/lib/python2.5/site-packages/pythia-0.8.1.7-py2.5.egg/mpi/
>>>>>> __init__.py",
>>>>>>
>>>>>> line 14, in <module>
>>>>>> from _mpi import *
>>>>>> ImportError: No module named _mpi
>>>>>>
>>>>>> ------------------------------------------------------
>>>>>> Makoto HOSHINO
>>>>>> Seismogenic Process Research Group
>>>>>> Institute of Geology and Geoinformation
>>>>>> National Institute of Advanced Industrial Science and Technology
>>>>>> tel; 029-861-2460, fax; 029-861-3682
>>>>>> email; m-hoshino at aist.go.jp
>>>>>> -------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> CIG-SHORT mailing list
>>>>>> CIG-SHORT at geodynamics.org
>>>>>> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>>>>
>
>
>
>
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