[yt-users] Building yt on Hopper

[Nathan Goldbaum]

Wow, good catch Andrew!

Can you open a pull request for this?  I think we were planning on doing a
2.6.2 release due to an issue with our source distribution that was
recently fixed - it would be good if this fix was part of that.

On Sunday, February 2, 2014, Andrew Myers <atmyers2 at gmail.com> wrote:

> I think I found the problem. The install script first builds the ZeroMQ
> library, and then tries to build PyZMQ bindings for it. The problem was
> that the script was not passing in the location of the newly-built ZeroMQ
> when it ran setup.py for PyZMQ. Instead, PyZMQ tries to use a bundled zmq,
> which doesn't work correctly. The fix was to manually re-build PyZMQ,
> passing in the location of the new libraries. The install script picked up
> from there normally.
>
> Why didn't the script work? Looking at the function that calls setup for
> each package:
>
> function do_setup_py{    [ -e $1/done ] && return    LIB=$1    shift    if [ -z "$@" ]    then        echo "Installing $LIB"    else        echo "Installing $LIB (arguments: '$@')"    fi    [ ! -e $LIB/extracted ] && tar xfz $LIB.tar.gz    touch $LIB/extracted    cd $LIB    if [ ! -z `echo $LIB | grep h5py` ]    then        shift	( ${DEST_DIR}/bin/python2.7 setup.py build --hdf5=${HDF5_DIR} $* 2>&1 ) 1>> ${LOG_FILE} || do_exit    else        shift        ( ${DEST_DIR}/bin/python2.7 setup.py build   $* 2>&1 ) 1>> ${LOG_FILE} || do_exit    fi    ( ${DEST_DIR}/bin/python2.7 setup.py install    2>&1 ) 1>> ${LOG_FILE} || do_exit    touch done    cd ..}
>
> When this function is called, the name of the script is at $0, the library
> name is at $1, and the rest of the variables hold arguments that should be
> passed to setup.py. After the first call to shift, the additional args
> start at $1. The script then calls shift once more, whichever way it
> branches, so that the first additional argument is no longer contained in
> $*. So, this function loses the first arg. For PyZMQ, the first arg is the
> location of the zmq library. If I remove the second and third shifts and
> re-run the install script from the beginning, everything works for me.
>
> -Andrew
>
>
>
>
> On Sat, Feb 1, 2014 at 3:16 PM, Andrew Myers <atmyers2 at gmail.com> wrote:
>
> Hi Hilary,
>
> Thanks for the suggestion. Unfortunately, it didn't work for me - if I
> install ipython manually, it still fails with the same error message.
>
> I think I'll try to ask this at StackOverflow as well, as per Nathan's
> suggestion.
>
> Thanks,
> Andrew
>
>
> On Sat, Feb 1, 2014 at 10:09 AM, Hilary Egan <hilaryye at gmail.com> wrote:
>
> I saw the same problem when I was installing on CU's janus machine. I'm
> pretty sure that I got around it by building just ipython by hand and
> making sure I was on the compile node when I tried it- no idea if there is
> an equivalent for Hopper.
>
> -download and untar ipython.tar.gz (http://archive.ipython.org/release/)
>  -cd ipython
> -python setup.py install
> -touch done
>
> Caveat: I have no idea why this worked when the install script didn't, and
> I'm just basing my answer on the note I jotted down a few months ago.
> There's definitely some sort of discussion out there already about this
> being a problem in some versions in pyzmq (
> https://github.com/zeromq/pyzmq/pull/218).  Hope that helps!
>
> -Hilary
>
>
> On Sat, Feb 1, 2014 at 10:49 AM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:
>
> Hi Andrew,
>
> Unfortunately I'm not sure what the issue is.
>
> You might try asking this question on StackOverflow (tagging it with
> IPython and ZMQ) or the IPython-dev mailing list, some of the ZMQ/IPy
> devs will be more likely to see it.
>
> Nathan
>
>
> On Saturday, February 1, 2014, Andrew Myers <atmyers2 at gmail.com> wrote:
>
> Hi Folks,
>
> I'm trying to install the development version of yt-2.7 on NERSC's Hopper
> machine using the install script. I get to the part where it tries to build
> IPython, and then the script fails with the following error message:
>
>
> ============================================================================
> BUILDING IPYTHON
>                 python: 2.7.6 (default, Jan 31 2014, 21:52:04)  [GCC 4.8.1
>                         20130531 (Cray Inc.)]
>               platform: linux2
>
> OPTIONAL DEPENDENCIES
>                 sphinx: Not found (required for docs and nbconvert)
>               pygments: Not found (required for docs and nbconvert)
>                   nose: 1.3.0
>                pexpect: no (required for running standalone doctests)
> Traceback (most recent call last):
>   File "setup.py", line 342, in <module>
>
>
>
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