[yt-users] Building yt on Hopper

[Andrew Myers]

Hi Nathan,

Done.

On Michael's point about having a yt module at NERSC, I personally think
that would be a great thing to have. I can ask the NERSC people about doing
this - I can always go bother them in person, after all.

-Andrew


On Sun, Feb 2, 2014 at 11:19 AM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> 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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