[yt-users] activating yt

[Desika Narayanan]

Hi Nathan and Matt,

Thanks for your help (both via email and IRC chat) yesterday.   I suspect
(as I think you do) that it was an issue with my environment.

I ended up resetting my environment to bash, and simplifying my bashrc
(again, this is a test computer, so it's no big deal to experiment)  to the
point where I only have the following (yt is the only thing I'm trying to
install):

export CC=cc
export CXX=g++

and of course

longtrail:~ desika$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

when installing the red (bleeding edge; but I get the same problem trying
the yellow development version), I get the following errors at the time of
HDF5 installation.  Have these been seen before?  I post the entire output
file at:

http://ajax.as.arizona.edu/~desika/yt_install.log


thanks,
Desika



Installing HDF5
********************************************
        FAILURE REPORT:
********************************************

sed -e 's/-L/:/g' -e 's/ //g'`"                               \
 ./H5make_libsettings > H5lib_settings.c  ||                               \
    (test $HDF5_Make_Ignore && echo "*** Error ignored") ||          \
    (rm -f H5lib_settings.c ; exit 1)
dyld: Library not loaded: libz.so.1.2.8
  Referenced from:
/Users/desika/yt-x86_64/src/hdf5-1.8.11/src/./H5make_libsettings
  Reason: image not found
/bin/sh: line 1: 61656 Trace/BPT trap: 5
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/Users/desika/yt-x86_64/lib/
-L/Users/desika/yt-x86_64/lib64/ -L/Users/desika/yt-x86_64/lib/
-L/Users/desika/yt-x86_64/lib64/ -L/Users/desika/yt-x86_64/lib/
-L/Users/desika/yt-x86_64/lib64/ -L/Users/desika/yt-x86_64/lib/
-L/Users/desika/yt-x86_64/lib64/ |                   sed -e 's/-L/:/g' -e
's/ //g'`" ./H5make_libsettings > H5lib_settings.c
make[1]: *** [H5lib_settings.c] Error 1
make: *** [install-recursive] Error 1

********************************************
********************************************
Failure.  Check /Users/desika/yt-x86_64/yt_install.log.  The last 10 lines
are above.





On Wed, Nov 20, 2013 at 12:56 PM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> Hi Desika,
>
> Is the yt bin directory in your $PATH after running the activate script?
>
> I know not many of us are csh/tcsh users - it’s possible there’s a bug in
> activate.csh.
>
> -Nathan
>
> On November 20, 2013 at 11:41:11 AM, Desika Narayanan (
> dnarayan at haverford.edu <//dnarayan at haverford.edu>) wrote:
>
> Hey Team,
>
> I'm trying a fresh install of yt on mac os x (mountain lion).  I've done
> this before successfully a few times, so am surprised at my problems.  I'm
> downloading the bleeding edge version.
>
> The install script ran fine, but then nothing in the bin directory
> actually runs.  For example:
>
>  longtrail:~] desika% which pip
> /Users/desika/yt-3.0/yt-x86_64/bin/pip
> [longtrail:~] desika% which python
> /Users/desika/yt-3.0/yt-x86_64/bin/python
> [longtrail:~] desika% pip install scipy
> pip: Command not found.
>
> So - maybe I should run 'activate', right?  So, then I do (I'm in csh):
>
>  longtrail:~] desika% echo $YT_DST
> YT_DST: Undefined variable.
> [longtrail:~] desika% echo $SHELL
> /bin/csh
> [longtrail:~] desika% echo $YT_DEST
> /Users/desika/yt-3.0/yt-x86_64/
> [longtrail:~] desika% source $YT_DEST/bin/activate.csh
> [yt-x86_64] [longtrail:~] desika%
> [yt-x86_64] [longtrail:~] desika% which pip
> /Users/desika/yt-3.0/yt-x86_64/bin/pip
> [yt-x86_64] [longtrail:~] desika% pip install scipy
> pip: Command not found.
> [yt-x86_64] [longtrail:~] desika% ipython
> ipython: Command not found.
>
>
> So then I try doing things manually....
>
>  yt-x86_64] [longtrail:~] desika% echo $LD_LIBRARY_PATH
> /Users/desika/yt-3.0/yt-x86_64/lib:
> [yt-x86_64] [longtrail:~] desika% echo $PYTHONPATH
> /Users/desika/python_packages/dn_python_packages:/Users/desika/hyperion-dust-0.1.0/dust_files:/Users/desika/powderday/:/Users/desika/toolbox/python_tools:/Users/desika/yt-3.0/yt-x86_64/bin/:/Users/desika/yt-3.0/yt-x86_64/lib/python2.7/site-packages/
> [yt-x86_64] [longtrail:~] desika%
> [yt-x86_64] [longtrail:~] desika% pip install sicpy
> pip: Command not found.
>
>
> So now I'm super confused....am I missing something obvious?
>
> thanks,
> desika
>
>
>
>
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