[yt-users] problem installing yt on kraken

[Britton Smith]

Hi Matt,

Just for the record, I tried this and it does work.  Thanks!

Britton

On Thu, Jan 27, 2011 at 11:20 AM, Matthew Turk <matthewturk at gmail.com>wrote:

> Hi Britton,
>
> I'm not sure.  It should be the same outcome. ... except that I think
> I meant to write in my email that you should put:
>
> export LDFLAGS="-L${DEST_DIR}/lib"
>
> instead of just setting the variable.  I think that may have been the
> problem.  I'm glad that it works now, however -- and I'm sorry for my
> typo.
>
> -Matt
>
> On Thu, Jan 27, 2011 at 11:14 AM, Britton Smith <brittonsmith at gmail.com>
> wrote:
> > Hi Matt and all,
> >
> > Thanks for the advice.  I tried setting the LDFLAGS variable, but got the
> > same outcome.  I tried again after adding the appropriate stuff to PATH,
> > PYTHONPATH, and LD_LIBRARY_PATH, with no luck.  Then, I simple went into
> the
> > numpy source dir that was created by the install script and did "python
> > setup.py install" and everything went fine.  Matt, what is different
> about
> > the install script than just doing what I did?
> >
> > Britton
> >
> > On Thu, Jan 27, 2011 at 8:29 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> Hi all,
> >>
> >> Geoffrey -- Stephen's right Britton's experimenting with using shared
> >> libraries as linked from Enzo, which isn't quite as applicable.  The
> >> idea being that a static compilation is a great deal of work; most
> >> (but not all) of the time spent in symbol loading is frontloaded to
> >> the calculation, so a shared library loading can be efficient at
> >> medium scales.  (Certainly more efficient that building statically, if
> >> you look at wall clock time from the beginning of your time investment
> >> to the end results.)
> >>
> >> Additionally, I believe that the static compile option is now somewhat
> >> easier than we previously thought, because in recent memory Python has
> >> added the option to explicitly request the CXX compiler be used for
> >> linking rather than LD or CC.  I tested this myself last month and I
> >> was able to get a static build without too much trouble; I was not,
> >> however, able to get "Freeze" to work on it, which would have frozen
> >> the .py files into .c files, built a single executable containing all
> >> the symbols, and all around been pretty rad.
> >>
> >> Britton -- I've run a set of tests on triton and I was not able to
> >> replicate the problem you see.  BUT, in doing so, I think I remember
> >> seeing this with a hand-built installation a while back.  I believe
> >> the solution is to set the environment variable LDFLAGS in the
> >> install_script.sh.  There may be a more permanent way of doing this,
> >> but I don't know what it is.  I set mine (back then) in my environment
> >> variables, but you should be able to add this line:
> >>
> >> LDFLAGS="-L${DEST_DIR}/lib"
> >>
> >> just below the line YT_DIR="" in the installation script.  If you can
> >> give that a shot, I think it might clear things up.  As a quick note,
> >> you should avoid linking against the whatever/config/ directory,
> >> because it contains the .a file, whereas you want the .so file which
> >> is just under lib.
> >>
> >> Good luck,
> >>
> >> Matt
> >>
> >> On Wed, Jan 26, 2011 at 6:49 PM, Stephen Skory <stephenskory at yahoo.com>
> >> wrote:
> >> > Geoffrey,
> >> >
> >> >> Stephen is the expert for YT on Kraken, something about the scratch
> >> >> disk
> >> >> cannot see the home directories when running jobs and requires static
> >> >> linked libraries.
> >> >
> >> > That is not entirely correct anymore, and I don't think that is what
> >> > Britton's problem is. Yes, the compute nodes cannot see the home disk,
> but I
> >> > think Britton is building things using a login node. So disk
> visibility
> >> > should not be his problem. Also, Kraken now supports shared object
> loading,
> >> > so the static build option that I am renowned for (?!) isn't necessary
> >> > unless you want to run python/yt inline, which is what Britton is
> trying to
> >> > do. As to Britton's problem, I don't know what is going on, sorry!
> >> >
> >> >
> >> >  Stephen Skory
> >> > stephenskory at yahoo.com
> >> > http://stephenskory.com/
> >> > 510.621.3687 <tel:+15106213687> (google voice)
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