Seems that deleting python is not an option in Ubuntu, and I can't really replace it by default with 3.XX anyway.<br><br><br>So as you suggested, I went inside build/pylith/pythia-0.8.1.14/ , and executed the command,<br>
so that in the folder<br>$HOME/build/pylith/pythia-0.8.1.14/mpi/<br>I have all the files you mentioned, although the install.log [file attached] contains errors at the beginning<br><br>Should I move them manually into $PREFIX/lib/python2.7/site-packages/mpi/ ?<br>
<br>Regards<br>Niz<br><br>PS: Should I always answer to cig-short@geodynamics?<br><div class="gmail_quote">2012/8/21 Brad Aagaard <span dir="ltr"><<a href="mailto:baagaard@usgs.gov" target="_blank">baagaard@usgs.gov</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">We have not tested PyLith with Python 3.x yet, so I don't advise doing using Python 3.x. You are using Python 2.7.3, so distutils is coming from there, which should be fine.<br>
<br>
I suggest that you try installing pythia again by running<br>
<br>
python setup.py install --prefix=$PREFIX >& install.log<br>
<br>
in the pythia source directory. If you see errors in the install.log or all of the files in the mpi directory are not there, send us the install.log file.<br>
<br>
Regards,<br>
Brad<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
On 08/21/2012 01:59 PM, Niz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
in $PREFIX/lib/python2.7/site-<u></u>packages/mpi/ I do not have:<br>
cmpi.pxd<br>
the folder launchers is not here too:<br>
launchers/<br>
nor are these files<br>
_mpi.c<br>
_mpi.pxd<br>
mpi.pxd<br>
_mpi.pyx<br>
pympi.h<br>
<br>
and the folder scripts contains<br>
-rw-rw-r-- 1 tora tora 340 May 25 2011 __init__.py<br>
-rw-rw-r-- 1 tora tora 156 Aug 21 15:07 __init__.pyc<br>
-rw-rw-r-- 1 tora tora 377 May 25 2011 mpistart.py<br>
-rw-rw-r-- 1 tora tora 217 Aug 21 15:07 mpistart.pyc<br>
and not this:<br>
scripts/<br>
__vault__.odb<br>
<br>
------------------------------<u></u>--<br>
As for the python version, I get this:<br>
python<br>
Python 2.7.3 (default, Aug 1 2012, 05:14:39)<br>
[GCC 4.6.3] on linux2<br>
Type "help", "copyright", "credits" or "license" for more information.<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
import distutils<br>
distutils.__version__<br>
</blockquote></blockquote></blockquote>
'2.7.3'<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
</blockquote></blockquote></blockquote>
<br>
I doubt I could revert to 2.7.2. So I shall test with the python 3.X.X<br>
instead, or delete python and add it in the configure. maybe the later<br>
would be more successful.<br>
<br>
<br>
2012/8/21 Brad Aagaard <<a href="mailto:baagaard@usgs.gov" target="_blank">baagaard@usgs.gov</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The config.log files for the other packages are probably not relevant,<br>
assuming the packages installed without errors.<br>
<br>
The config.log from nemesis shows the following error message:<br>
<br>
merlin.UnknownExtra: pythia 0.8.1.14 has no such extra feature 'mpi'<br>
<br>
This suggests that the pythia install did not proceed correctly. There<br>
is no config.log for that install because it is a pure python package.<br>
This may indicate a distutils problem.<br>
<br>
Look in $PREFIX/lib/python2.7/site-<u></u>packages/pythia-0.8.1.14-py2.<u></u>7.egg.<br>
You should see an "mpi" directory and it should contain:<br>
<br>
Application.py*<br>
<br>
<br>
CartesianCommunicator.py*<br>
<br>
<br>
cmpi.pxd<br>
<br>
<br>
CommunicatorGroup.py*<br>
<br>
<br>
Communicator.py*<br>
<br>
<br>
__init__.py*<br>
<br>
<br>
LauncherMPICH.py*<br>
<br>
<br>
Launcher.py*<br>
<br>
<br>
launchers/<br>
<br>
<br>
_mpi.c<br>
<br>
<br>
_mpi.pxd<br>
<br>
<br>
mpi.pxd<br>
<br>
<br>
_mpi.pyx<br>
<br>
<br>
Port.py*<br>
<br>
<br>
pympi.h<br>
scripts/<br>
__vault__.odb<br>
<br>
Do you have all of these files and directories? If you run<br>
<br>
python<br>
import distutils<br>
distutils.__version__<br>
<br>
what do you see?<br>
<br>
On my ubuntu 11.11 machine I get<br>
<br>
python<br>
Python 2.7.2+ (default, Oct 4 2011, 20:06:09)<br>
[GCC 4.6.1] on linux2<br>
Type "help", "copyright", "credits" or "license" for more information.<br>
>>> import distutils<br>
>>> distutils.__version__<br>
'2.7.2'<br>
<br>
<br>
</blockquote>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regards,<br>
Brad<br>
<br>
On 08/21/2012 09:59 AM, Niz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
here is both config.log, from the nemeis and the global one. are there<br>
other config files relevant?<br>
<br>
Regards<br>
<br>
2012/8/21 Brad Aagaard <<a href="mailto:baagaard@usgs.gov" target="_blank">baagaard@usgs.gov</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
As Matt noted, we need the config.log from the configure of nemesis to<br>
know for sure what is going wrong.<br>
<br>
I can say that there is a build issue with merlin (one of the Python<br>
packages that we use) and Python version 2.7 and later. Merlin is<br>
installed during "downloading missing Python dependencies". If merlin is<br>
already installed, then an infinite loop can be encountered when merlin<br>
tries to get installed again. The remedy is to remove all merlin related<br>
files (*merlin*) from the installation directory ($PREFIX) and then<br>
continue the installation from where things go wrong.<br>
<br>
</blockquote>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Regards,<br>
Brad<br>
<br>
<br>
On 08/21/2012 06:15 AM, Niz wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2012/8/21 Niz <<a href="mailto:niz.moussatat@gmail.com" target="_blank">niz.moussatat@gmail.com</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This is the<br>
/home/tora/build/pylith/<u></u>nemesis-build/config.log<br>
PS: It happens when I run make command, that the compilation stopps<br>
earlier on a loop command [it is not systematic]. If I reran it again,<br>
</blockquote></blockquote>
and<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
again i reach also this point.<br>
<br>
<br>
2012/8/21 Matthew Knepley <<a href="mailto:knepley@mcs.anl.gov" target="_blank">knepley@mcs.anl.gov</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Tue, Aug 21, 2012 at 2:59 AM, Niz <<a href="mailto:niz.moussatat@gmail.com" target="_blank">niz.moussatat@gmail.com</a>><br>
</blockquote></blockquote></blockquote></blockquote></blockquote>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello Pylith People<br>
<br>
I never seem to get this instalation process right.<br>
I did the following:<br>
mkdir -p $HOME/src/pylith<br>
cd $HOME/src/pylith<br>
mv $HOME/Downloads/pylith-<u></u>installer-1.7.1-0.tgz .<br>
tar -zxf pylith-installer-1.7.1-0.tgz<br>
<br>
mkdir -p $HOME/build/pylith<br>
cd $HOME/build/pylith<br>
$HOME/src/pylith/pylith-<u></u>installer-1.7.1-0/configure \<br>
--with-make-threads=2 \<br>
--prefix=$HOME/pylith<br>
source setup.sh<br>
make LDFLAGS+=-ldl<br>
<br>
%% I added the LDFLAGS because of a previous error<br>
%% and cleaned the build folder<br>
<br>
</blockquote>
<br>
Yes, this is the correct fix. The cppunit configure must be<br>
</blockquote></blockquote></blockquote></blockquote></blockquote>
imperfect.<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The install process advances further till it hits:<br>
checking whether -lpython2.7 is a shared library... yes<br>
configure: downloading missing Python dependencies<br>
configure: error: in `/home/tora/build/pylith/<u></u>nemesis-build':<br>
configure: error: cannot download missing Python dependencies<br>
See `config.log' for more details<br>
<br>
</blockquote>
<br>
This could be a connectivity issue with this machine. Can you send<br>
/home/tora/build/pylith/<u></u>nemesis-build/config.log?<br>
<br>
Thanks,<br>
<br>
Matt<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
make[3]: Entering directory<br>
</blockquote></blockquote></blockquote></blockquote></blockquote></blockquote>
`/home/tora/build/pylith/<u></u>nemesis-build'<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
make[3]: *** No targets specified and no makefile found. Stop.<br>
make[3]: Leaving directory `/home/tora/build/pylith/<u></u>nemesis-build'<br>
make[2]: *** [nemesis] Error 2<br>
make[2]: Leaving directory `/home/tora/build/pylith'<br>
make[1]: *** [installed_nemesis] Error 2<br>
make[1]: Leaving directory `/home/tora/build/pylith'<br>
make: *** [installed_pylith] Error 2<br>
<br>
As said in the Config.log, I run a Ubuntu 12.04 64bit, its a clean<br>
slate, meaning I am trying to make pylith work with 2 thread before<br>
installing anything else.<br>
<br>
<br>
Regards<br>
<br>
<br>
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<br>
</blockquote>
<br>
<br>
--<br>
What most experimenters take for granted before they begin their<br>
experiments is infinitely more interesting than any results to which<br>
</blockquote></blockquote></blockquote>
their<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
experiments lead.<br>
-- Norbert Wiener<br>
<br>
</blockquote>
<br>
<br>
<br>
--<br>
******************************<u></u>*************************<br>
MOUSSATAT Nizar - PhD Student<br>
ISTerre - Maison des Geosiences - Equipe risques<br>
Bureau 1121 (1er étage)<br>
Université de Grenoble, 38041 Grenoble Cedex 9, France<br>
E-mail: <a href="mailto:nizar.moussatat@obs.ujf-grenoble.fr" target="_blank">nizar.moussatat@obs.ujf-<u></u>grenoble.fr</a><br>
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<br>
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<br>
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<br>
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<br>
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<br>
</blockquote>
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<br>MOUSSATAT Nizar - PhD Student
<br>ISTerre - Maison des Geosiences - Equipe risques
<br>Bureau 1121 (1er étage)
<br>Université de Grenoble, 38041 Grenoble Cedex 9, France
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