[yt-users] problem installing yt on kraken

[gso at physics.ucsd.edu]

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.  There is a working version of YT, just have to set
these environment variables:

export PATH=.:/lustre/scratch/proj/yt_common/trunk/bin:$PATH

export PYTHONPATH=/lustre/scratch/proj/yt_common/trunk/bin/python

export
LD_LIBRARY_PATH=/lustre/scratch/proj/yt_common/trunk/lib:$LD_LIBRARY_PATH

export MPLCONFIGDIR=/lustre/scratch/<user name>

If you need the latest version from the install script, probably best to
ask Stephen.  The old documentation shows some brief install steps for the
different machines (a section devoted to Kraken), but I'm not sure if
Kraken is taken into account in the new script with its strange
requirements.

From
G.S.


> Greetings,
>
> I'm trying to install yt on kraken using the install_script.  I have done
> a
> 'module swap PrgEnv-pgi PrgEnv-gnu' to switch to gnu compilers.  I have
> also
> done 'module unload mercurial' and 'module unload python' to remove the
> system mercurial and python2.6 installs.  Finally, I have added
> --enable-shared to the Python configure line in the install script, since
> I
> will try to build enzo with inline yt enabled.
>
> The build is failing on numpy with the following error:
> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3
> -Wall
> -Wstrict-prototypes -fPIC
>
> compile options: '-Inumpy/core/include
> -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy
> -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
> -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
> -Inumpy/core/src/umath
> -Inumpy/core/include
> -I/lustre/scratch/britton/yt-embedded/include/python2.6
> -Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray
> -Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c'
> gcc -pthread -shared
> build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/numpy/core/src/_sortmodule.o
> -L. -Lbuild/temp.linux-x86_64-2.6 -lm -lpython2.6 -o
> build/lib.linux-x86_64-2.6/numpy/core/_sort.so
> /usr/bin/ld: cannot find -lpython2.6
> collect2: ld returned 1 exit status
> /usr/bin/ld: cannot find -lpython2.6
> collect2: ld returned 1 exit status
>
> Because I can see the error is that it can't find the python library, I
> tried adding
> /lustre/scratch/britton/yt-embedded/lib/python2.6/config/:/lustre/scratch/britton/yt-embedded/lib
> to my $LD_LIBRARY_PATH, and restarting the install, but I get the same
> error.  I have also added the appropriate paths to PATH and PYTHONPATH and
> that has not helped either.
>
> Does anyone have any ideas?
>
> Britton
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