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Tim,
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<div class="">I’ve tried to set the PYTHONHOME variable a few times to see if I can force the right python version to be found but I have yet to be successful.</div>
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<div class="">Jonathan</div>
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<div class="">On Apr 21, 2015, at 9:54 AM, Tim Armstrong <<a href="mailto:tim.g.armstrong@gmail.com" class="">tim.g.armstrong@gmail.com</a>> wrote:</div>
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<div class="">It looks like the environment variable PYTHONHOME=/path/to/anaconda needs to be set for it to look in the right places for the packages. I'm looking to see if we can automatically set this up so that it does the right thing in future.<br class="">
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<div class="">- Tim<br class="">
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<div class="gmail_quote">On 20 April 2015 at 18:24, Ozik, Jonathan <span dir="ltr" class="">
<<a href="mailto:jozik@anl.gov" target="_blank" class="">jozik@anl.gov</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Tim,
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<div class="">Just for kicks I tried to create a standalone conda environment for Python 2.7 and used that as my PYTHON_INSTALL location but I still am seeing incorrect sys.version, platform.python_version(), etc. Not sure what’s going on, but like I said earlier,
it doesn’t seem to affect the running of the code.</div>
<span class="HOEnZb"><font color="#888888" class="">
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<div class="">Jonathan</div>
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<div class="">On Apr 20, 2015, at 4:56 PM, Jonathan Ozik <<a href="mailto:jozik@anl.gov" target="_blank" class="">jozik@anl.gov</a>> wrote:</div>
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<div style="word-wrap:break-word" class="">Tim,
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<div class="">I had:</div>
<div class="">PYTHON_INSTALL=/Users/jozik/anaconda</div>
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<div class="">I had to go in and undo some of the attempts I had made to fix the issue (but probably just exacerbated it), and now with everything back to its initial settings I get the intended:</div>
<div class="">Using Python lib directory: /Users/jozik/anaconda/lib<br class="">
Using Python lib name: python2.7</div>
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<div class="">If I ignore what I’m seeing returned by sys.version, it does look like the correct Python version is being picked up, at least based on the modules that are available. Maybe the sys.version issue is associated with the subtle issue you mentioned?</div>
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<div class="">In any case, thank you for the help.</div>
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<div class="">Jonathan</div>
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<blockquote type="cite" class="">
<div class="">On Apr 20, 2015, at 9:46 AM, Tim Armstrong <<a href="mailto:tim.g.armstrong@gmail.com" target="_blank" class="">tim.g.armstrong@gmail.com</a>> wrote:</div>
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<div class="">What did you have PYTHON_INSTALL set to in exm-settings? It should be printing the directory/name there.<br class="">
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I was actually able to replicate a similar problem, which may not be what you were seeing. There's a subtle issue with ordering of library dependencies where it was picking up the system Python library rather than the other one in some cases.<br class="">
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- Tim<br class="">
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<div class="gmail_quote">On 19 April 2015 at 23:28, Ozik, Jonathan <span dir="ltr" class="">
<<a href="mailto:jozik@anl.gov" target="_blank" class="">jozik@anl.gov</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">I’m not an Autoconf expert, so take this with a grain of salt, but the two lines in the turbine configure script:
<div class=""> echo "Using Python lib directory: ${USE_PYTHON_LIBDIR}"<br class="">
echo "Using Python lib name: ${USE_PYTHON_NAME}”</div>
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<div class="">were showing:</div>
<div class="">Using Python lib directory: .</div>
<div class="">Using Python lib name: 1</div>
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<div class="">so I looked at how those variables were being derived, and it looks like there might be some issues there.</div>
<div class="">Also, exm-settings.sh doesn’t mention the --with-python-lib option either.</div>
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<div class="">As for the sys.version issue that I’m seeing, it’s really strange, because it is possible that sys.version is not correct, as odd as that may sound. I know that sys.executable is not always correct, but I thought I could trust sys.version. The
python that is being used definitely has modules installed that are not in the version of python that’s being reported. Odd. But the good news is that I’m now able to move on with what we’re actually trying to do.</div>
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<div class="">Thanks again for helping me think through this,</div>
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<div class="">Jonathan</div>
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<div class="">On Apr 19, 2015, at 9:21 PM, Tim Armstrong <<a href="mailto:tim.g.armstrong@gmail.com" target="_blank" class="">tim.g.armstrong@gmail.com</a>> wrote:</div>
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<div class="">Hmm, so it's probably picking up the system Python by default. This may be an oversight on our part - I'm creating a bug to look into it. Our build should be linking it to your other python library but isn't.<br class="">
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<div class="">As a workaround, you can override this with the DYLD_LIBRARY_PATH environment variable on Mac OS X.
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If you add the directory with your preferred python .dylib file to that environment variable, it should link against that version of python instead of the system one.<br class="">
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<div class="">E.g. <br class="">
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export DYLD_LIBRARY_PATH=/path/to/anaconda/lib<br class="">
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<div class="">I *think* this should give you a way to work around it in the meantime.<br class="">
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<div class="">- Tim<br class="">
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<div class="gmail_quote">On 19 April 2015 at 20:19, Ozik, Jonathan <span dir="ltr" class="">
<<a href="mailto:jozik@anl.gov" target="_blank" class="">jozik@anl.gov</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Thanks Tim. Here’s what I get on OS X:
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<div class="">XioMBP:swift_simphony_example_DEAP jozik$ otool -L /Users/jozik/work/swift_t/install/turbine/lib/libtclturbine.dylib <br class="">
/Users/jozik/work/swift_t/install/turbine/lib/libtclturbine.dylib:<br class="">
<span style="white-space:pre-wrap" class=""></span>/Users/jozik/work/swift_t/install/turbine/lib/libtclturbine.dylib (compatibility version 0.0.0, current version 0.0.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/Users/jozik/work/swift_t/install/lb/lib/libadlb.dylib (compatibility version 0.0.0, current version 0.0.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/Users/jozik/work/swift_t/install/c-utils/lib/libexmcutils.dylib (compatibility version 0.0.0, current version 0.0.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/opt/tcl-tk/lib/libtcl8.6.dylib (compatibility version 8.6.0, current version 8.6.3)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/lib/libmpi.12.dylib (compatibility version 13.0.0, current version 13.4.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/lib/libsz.2.dylib (compatibility version 3.0.0, current version 3.0.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/lib/libhdf5.8.dylib (compatibility version 9.0.0, current version 9.2.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/lib/libhdf5_hl.8.dylib (compatibility version 9.0.0, current version 9.2.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/lib/libpmpi.12.dylib (compatibility version 13.0.0, current version 13.4.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)<br class="">
<span style="white-space:pre-wrap" class=""></span>/usr/local/Cellar/gcc/4.9.2/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)</div>
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<div class="">Which doesn’t answer our question of which libpython2.7.dylib is being linked to… If there’s a build log file that you want to point me to, I can do some more digging.</div>
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<div class="">Jonathan</div>
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<blockquote type="cite" class="">
<div class="">On Apr 19, 2015, at 7:36 PM, Tim Armstrong <<a href="mailto:tim.g.armstrong@gmail.com" target="_blank" class="">tim.g.armstrong@gmail.com</a>> wrote:</div>
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<div class="">It might be helpful to get some linker information from your installation to see which Python version it's linking against.<br class="">
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In linux:<br class="">
ldd /path/to/turbine/lib/libtclturbine.so <br class="">
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In OS X I think it's something like:<br class="">
otool -L /path/to/turbine/lib/libtclturbine.dylib
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<div class="">- Tim<br class="">
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<div class="gmail_quote">On 19 April 2015 at 15:55, Ozik, Jonathan <span dir="ltr" class="">
<<a href="mailto:jozik@anl.gov" target="_blank" class="">jozik@anl.gov</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
An update. I looked to see whether this was a PATH issue, and saw that there was a difference between how my bash and zsh shells populate the PATH variable. I have made them compatible now, but am still seeing the same issue with the wrong python being picked
up.<br class="">
<span class=""><font color="#888888" class=""><br class="">
Jonathan<br class="">
</font></span>
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<div class=""><br class="">
> On Apr 18, 2015, at 11:21 PM, Ozik, Jonathan <<a href="mailto:jozik@anl.gov" target="_blank" class="">jozik@anl.gov</a>> wrote:<br class="">
><br class="">
> Hi all,<br class="">
><br class="">
> I’ve run up against an issue where Swift/T’s python and python_persist are using the wrong Python version. I’ve checked and rebuilt and it looks like the Python install location specified in exm-settings.sh is being used in the build log but when I run a
simple test:<br class="">
> string ss = python_persist("import sys\nsys.version”);<br class="">
> I’m getting the Python installation at /usr/bin/python rather than the Python version installed as part of the Anaconda distribution (which is what the exm-settings.sh is configured to use).<br class="">
> Any advice on how I might better diagnose this would be appreciated. I’m on Mac OS X (10.10.3).<br class="">
><br class="">
> Jonathan<br class="">
><br class="">
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