[yt-users] HaloProfiler Troubles

[Nathan Goldbaum]

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.

The logic that handles forthon/gfortran detection is in the setup.py file
in the top level of the yt source distribution:
https://bitbucket.org/yt_analysis/yt/src/be524f912750b192aab75b9e5aacdab3421b2e6c/setup.py?at=yt#cl-28

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".

If gfortran is available, you'll see something like this (near the top of
about a hundred lines of other output):

$ python setup.py develop

*snip*
running build_forthon
Building package fKD
  Forthon fKD.v
  F90Free fKD_p.F90
  F90Free fKD_source.f90
  F90Free fKD.F90
  Preprocess Forthon.h
  Preprocess Forthon.c
  Setup fKD
*snip*

If forthon/gfortran are not available, you'll see something like this in
the same place:

$ python setup.py develop

*snip*
running build_forthon
fKDpy.so won't be built due to missing Forthon/gfortran
*snip*

"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".

Hope that helps.  Let us know if you continue to have trouble.

-Nathan




On Thu, Dec 5, 2013 at 11:37 PM, Britton Smith <brittonsmith at gmail.com>wrote:

> Hi Claire,
>
> It's tough to tell for certain, but if you are working with an Enzo
> dataset, the HaloProfiler usually looks for the halo 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
> HaloProfiler 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.
>
> 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.
>
> Britton
>
>
>
> On Fri, Dec 6, 2013 at 2:53 AM, Claire Kopenhafer <clairekope at gmail.com>wrote:
>
>> Hello, my name is Claire. Recently, I've been having some very odd
>> trouble with HaloProfiler.
>>
>> 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!
>>
>> HaloProfiler then goes on to run HaloFinder, which would be totally cool
>> except that that fails, too. Parallel_hop_interface.py cannot open fKD.
>>
>> Any ideas? Thanks!!
>> -Claire
>>
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>>
>
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