<div dir="ltr">In particular, if you don't have both gfortran and a supplementary python package named Forthon available then the fortran kdtree will not be built. Forthon is built by the install script if it finds a fortran compiler. If you didn't install using the install script, you'll need to install it manually. "pip install forthon" should work. We don't mandate a fortran compiler to run the install script since installing one can be a pain on OS X.<div>
<br></div><div>The logic that handles forthon/gfortran detection is in the setup.py file in the top level of the yt source distribution: </div><div><a href="https://bitbucket.org/yt_analysis/yt/src/be524f912750b192aab75b9e5aacdab3421b2e6c/setup.py?at=yt#cl-28">https://bitbucket.org/yt_analysis/yt/src/be524f912750b192aab75b9e5aacdab3421b2e6c/setup.py?at=yt#cl-28</a></div>
<div><br></div><div>You'll know whether they're built or not built depending on the stdout output you see when running "python setup.py develop" in the root of the yt source distribution. If you installed using the install script, this will be in "/path/to/yt-x86_64/src/yt-hg".</div>
<div><br></div><div>If gfortran is available, you'll see something like this (near the top of about a hundred lines of other output):</div><div><br></div><div>$ python setup.py develop</div><div><br></div><div>*snip*</div>
<div><div>running build_forthon</div><div>Building package fKD</div><div> Forthon fKD.v</div><div> F90Free fKD_p.F90</div><div> F90Free fKD_source.f90</div><div> F90Free fKD.F90</div><div> Preprocess Forthon.h</div>
<div>
Preprocess Forthon.c</div><div> Setup fKD</div></div><div>*snip*</div><div><br></div><div>If forthon/gfortran are not available, you'll see something like this in the same place:</div><div><br></div><div>$ python setup.py develop</div>
<div><br></div><div>*snip*</div><div><div>running build_forthon</div><div>fKDpy.so won't be built due to missing Forthon/gfortran</div><div>*snip*</div></div><div><br></div><div>"setup.py develop" just builds the source distribution in-place. If you prefer to install yt in the same location as the rest of your python packages, you can also do "setup.py install".</div>
<div><br></div><div>Hope that helps. Let us know if you continue to have trouble.</div><div><br></div><div>-Nathan</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Dec 5, 2013 at 11:37 PM, Britton Smith <span dir="ltr"><<a href="mailto:brittonsmith@gmail.com" target="_blank">brittonsmith@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div dir="ltr" style="font-family:arial,sans-serif;font-size:13px">Hi Claire,<div><br></div><div>It's tough to tell for certain, but if you are working with an Enzo dataset, the <span>HaloProfiler</span> usually looks for the <span>halo</span> catalog file to be in the directory of the dataset itself. There might be a problem if you are using a dataset where all the data is in a single file as the <span>HaloProfiler</span> makes an assumption that each dataset is contained within its own directory. If this is the case, let me know and we should be able to fix this issue.</div>
<div><br></div><div>The second issue comes from not having the fortran kdtree installed with your yt installation. It should be install by default now, so you may have an out of date installation. In that case, you may want to run "yt update --all" to update your yt install stack. If you are running on a Mac, you will also need to make sure that you have gfortran installed.</div>
<div><br></div><div>Britton</div><div><br></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On Fri, Dec 6, 2013 at 2:53 AM, Claire Kopenhafer <span dir="ltr"><<a href="mailto:clairekope@gmail.com" target="_blank">clairekope@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><p dir="ltr" style="font-family:arial,sans-serif;font-size:12.499999046325684px">
Hello, my name is Claire. Recently, I've been having some very odd trouble with HaloProfiler.</p>
<p dir="ltr" style="font-family:arial,sans-serif;font-size:12.499999046325684px">
When I try to initiate HaloProfiler, it cannot open HopAnalysis.out, even when I feed it the full file path. This has happened on two different systems, but only with one particular data set!</p><p dir="ltr" style="font-family:arial,sans-serif;font-size:12.499999046325684px">
HaloProfiler then goes on to run HaloFinder, which would be totally cool except that that fails, too. Parallel_hop_interface.py cannot open fKD.</p><p dir="ltr" style="font-family:arial,sans-serif;font-size:12.499999046325684px">
Any ideas? Thanks!!</p><span><font color="#888888"><div><div dir="ltr">-Claire</div></div>
</font></span></div>
<br></div></div>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>
<br>_______________________________________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a><br>
<br></blockquote></div><br></div>