[yt-users] yt on verne

[Matthew Turk]

Hi Stephen,

In all likelihood, this is related to not having /lib64/ in the
linking directions.  You can see this in the linking line:

-L/usr/lib

is present, but not /usr/lib64 , which is where the 'compatible'
libraries will likely be found.  You might be able to get around this
by setting the variable LD_LIBRARY_PATH to include /usr/lib64 before
running the installer script.

If that doesn't work, you can try copying
$DEST_DIR/src/numpy-1.2.1/site.cfg.example to
$DEST_DIR/src/numpy-1.2.1/site.cfg .  If you edit it, you should be
able to manually specify that /usr/lib64 be included in the linking
commands.

Alternatively, I checked in a new version of the install script
yesterday that allows you to specify NumPy build arguments, but I
cannot recall how to specify manual linking directories on the command
line.  I'm sure it's in the setup.py help documentation somewhere, but
you may need to use both the "config_fc" and "config_cc" commands.  I
am sorry I don't have an answer for that off-hand.

Good luck, and let us know if this fixes it,

Matt

On Fri, May 1, 2009 at 10:55 AM, Stephen Skory <stephenskory at yahoo.com> wrote:
>
> Hi,
>
> I am trying to build yt on the new analysis machine at NICS, called Verne. I am using the PE-gnu environment, and I set export CC=cc;export CXX=CC, like on Kraken. During the numpy step, I am getting the error below. It's confusing because it doesn't like any of the libraries here, including libm, but I can see from the yt_install.log that it's linked to -lm before without complaining. Thoughts?
>
> Thanks!
>
> building 'numpy.linalg.lapack_lite' extension
> compiling C sources
> C compiler: cc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
>
> creating build/temp.linux-x86_64-2.6/numpy/linalg
> compile options: '-DNO_ATLAS_INFO=1 -Inumpy/core/include -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/nics/c/home/sskory/yt-verne/include/python2.6 -c'
> cc: numpy/linalg/python_xerbla.c
> cc: numpy/linalg/lapack_litemodule.c
> /usr/bin/gfortran -Wall -L/nics/c/home/sskory/yt-verne/lib/ -L/nics/c/home/sskory/yt-verne/lib64/ build/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.6/numpy/linalg/python_xerbla.o -L/usr/lib -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.6/numpy/linalg/lapack_lite.so
> /usr/bin/ld: skipping incompatible /usr/lib/liblapack.so when searching for -llapack
> /usr/bin/ld: skipping incompatible /usr/lib/liblapack.a when searching for -llapack
> /usr/bin/ld: skipping incompatible /usr/lib/libblas.so when searching for -lblas
> /usr/bin/ld: skipping incompatible /usr/lib/libblas.a when searching for -lblas
> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc
>
>
>  _______________________________________________________
> sskory at physics.ucsd.edu           o__  Stephen Skory
> http://physics.ucsd.edu/~sskory/ _.>/ _Graduate Student
> ________________________________(_)_\(_)_______________
>
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