[SciPy-user] Installing on Ubuntu with mkl 10.0.2: libimf.so not found

[Anand Patil]

Hi all,

Sorry to post again for help installing. I recently got numpy installed with mkl 10.0.2. I pared the site.cfg file down to just

[mkl]

library_dirs = /opt/intel/mkl/10.0.2.018/lib/em64t

lapack_libs = mkl, mkl_lapack

mkl_libs = mkl, guide

and everything seems to work fine.

Now I'm trying to install scipy with the Intel compilers. The build went fine, but when I go to do python setup.py install I get:

/working_copies/scipy$ sudo python setup.py install

[sudo] password for anand: 

Traceback (most recent call last):

  File "setup.py", line 92, in <module>

    setup_package()

  File "setup.py", line 63, in setup_package

    from numpy.distutils.core import setup

  File "/usr/lib/python2.5/site-packages/numpy/__init__.py", line 130, in <module>

    import add_newdocs

  File "/usr/lib/python2.5/site-packages/numpy/add_newdocs.py", line 9, in <module>

    from lib import add_newdoc

  File "/usr/lib/python2.5/site-packages/numpy/lib/__init__.py", line 152, in <module>

    from type_check import *

  File "/usr/lib/python2.5/site-packages/numpy/lib/type_check.py", line 8, in <module>

    import numpy.core.numeric as _nx

  File "/usr/lib/python2.5/site-packages/numpy/core/__init__.py", line 5, in <module>

    import multiarray

ImportError: libimf.so: cannot open shared object file: No such file or directory

I'm having a hard time debugging this because first, I can import setup from numpy.distutils.core directly in Python:

/working_copies/scipy$ python

Python 2.5.2 (r252:60911, Jul 31 2008, 17:31:22) 

[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2

Type "help", "copyright", "credits" or "license" for more information.

>>> from numpy.distutils.core import setup

>>> 

Second, libimf.so is on my LD_LIBRARY_PATH;

/working_copies/scipy$ echo $LD_LIBRARY_PATH

:/usr/lib64:/lib64:/usr/local/lib64:/usr/lib:/usr/local/lib:/lib:/opt/intel/fce/10.1.018/lib:/opt/intel/ipp/5.3.4.080/em64t/sharedlib:/opt/intel/cce/10.1.018/lib:/opt/intel/mkl/10.0.2.018/lib/em64t

/working_copies/scipy$ ls /opt/intel/ipp/5.3.4.080/em64t/sharedlib/libimf.so

/opt/intel/ipp/5.3.4.080/em64t/sharedlib/libimf.so

Has anyone seen anything like this before?

Thanks,

ANand

[David Cournapeau]

On Tue, Nov 4, 2008 at 9:06 PM, Anand Patil
<anand.prab...@gmail.com> wrote:
> Hi all,
> Sorry to post again for help installing. I recently got numpy installed with
> mkl 10.0.2. I pared the site.cfg file down to just

I think that's a bug in the MKL. AFAIK, nobody has been able to track
it down (you're not the first one to report this problem with this
version of the MKL).

cheers,

David
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[Anand Patil]

On Tue, Nov 4, 2008 at 12:20 PM, David Cournapeau <cour...@gmail.com> wrote:

On Tue, Nov 4, 2008 at 9:06 PM, Anand Patil
<anand.prab...@gmail.com> wrote:
> Hi all,
> Sorry to post again for help installing. I recently got numpy installed with
> mkl 10.0.2. I pared the site.cfg file down to just

I think that's a bug in the MKL. AFAIK, nobody has been able to track
it down (you're not the first one to report this problem with this
version of the MKL).

Thanks David,

I couldn't find the ticket in the scipy bug tracker. Should I open a new one? Also, what's the most recent version of MKL that's known to work?

Anand

[Matthieu Brucher]

Before doing that, try without the sudo. The fact that imf is not
found is not MKL related, but system dependent IMHO.
For instance try (after checking the availability of libimf.so in the
library path):
python setup.py install --prefix=/somewhere/where/I/put/garbage

Matthieu

2008/11/4 Anand Patil <anand.prab...@gmail.com>:

> _______________________________________________
> SciPy-user mailing list
> SciPy...@scipy.org
> http://projects.scipy.org/mailman/listinfo/scipy-user
>
>

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Website: http://matthieu-brucher.developpez.com/
Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
LinkedIn: http://www.linkedin.com/in/matthieubrucher

[Anand Patil]

On Tue, Nov 4, 2008 at 2:10 PM, Matthieu Brucher <matthieu...@gmail.com> wrote:

Before doing that, try without the sudo. The fact that imf is not
found is not MKL related, but system dependent IMHO.
For instance try (after checking the availability of libimf.so in the
library path):
python setup.py install --prefix=/somewhere/where/I/put/garbage

Matthieu

That worked! So I can install scipy, but for packages that have binaries like PyTables I still need root permissions. How can I make the library available when I use sudo?

Thanks,

Anand

[Matthieu Brucher]

> That worked! So I can install scipy, but for packages that have binaries
> like PyTables I still need root permissions. How can I make the library
> available when I use sudo?
> Thanks,
> Anand

Well, it should have worked with the sudo :|
Is it an installation for all users or just for you ? If it is the
latter, I suggest you to create a local folder in your home directory
where you will put everything (every decent installation tool has the
--prefix options which will correctly populate the local folder, you
just have to set the environment variables correctly, but you already
modified LD_LIBRARY_PATH, it won't much more trouble). This way, you
don't need root permission and you won't mess up with the system
installation. This is what I did on every computer even where I had
sudo capabilities. Less trouble in the long run ;)

Matthieu

[Anand Patil]

On Tue, Nov 4, 2008 at 2:54 PM, Matthieu Brucher <matthieu...@gmail.com> wrote:

> That worked! So I can install scipy, but for packages that have binaries
> like PyTables I still need root permissions. How can I make the library
> available when I use sudo?
> Thanks,
> Anand

Well, it should have worked with the sudo :|
Is it an installation for all users or just for you ? If it is the
latter, I suggest you to create a local folder in your home directory
where you will put everything (every decent installation tool has the
--prefix options which will correctly populate the local folder, you
just have to set the environment variables correctly, but you already
modified LD_LIBRARY_PATH, it won't much more trouble). This way, you
don't need root permission and you won't mess up with the system
installation. This is what I did on every computer even where I had
sudo capabilities. Less trouble in the long run ;)

Will do... that's really weird, but I'm glad to have my Python environment up and running anyway!

Thanks,

Anand