[R-sig-Debian] GotoBLAS2 breaks lapack

[Dirk Eddelbuettel]

On 26 February 2011 at 14:16, Dirk Eddelbuettel wrote:
| 
| On 26 February 2011 at 13:07, dks wrote:
| | Thanks a lot for this, which led me to my solution.  (I'm including all this
| | in case others run into this problem.)
| | 
| | It turns out that, by default GotoBLAS2 builds a single shared library that
| | includes both BLAS and Lapack, rather than producing two separate libraries,
| | which is what Debian/Ubuntu wants.  One of the things that gotoblas2-helper
| | does is to separate the single shared library into separate BLAS and Lapack
| | libraries, which is why the deb you showed looks as it does.
| | 
| | I had looked at gotoblas2-helper before, but I saw that it was built before
| | GotoBLAS adopted the BSD license (when it still required login/password to
| | download source), and so I didn't think it would still work or get the new
| | version, but I was wrong on both counts.  It worked great and installed
| | GotoBLAS2 system-wide.  For others looking at this, full instructions are on
| | the poster linked from the gbcd paper:
| | http://prs.ism.ac.jp/~nakama/debian/SC09-poster.pdf
| | 
| | You still have to get a login/password from TACC (
| | http://www.tacc.utexas.edu/?id=402) and set that and the architecture target
| | (e.g., "NEHALEM") in the site.conf file, and gotoblas2-helper does the
| | rest.  I wasn't able to get the public key to download for the ISM
| | repository, but as long as you're willing to install it unverified, it
| | should work fine.
| 
| Excellent!  I remember I had to make one or two trivial changes in the
| debian/* files but maybe that has been fixed or no longer matters on newer
| Ubuntu releases.
| 
| Glad to hear you have it working.
|  
| | (Finally, a bad hack around this is to symbolically link both libblas and
| | liblapack to point to the single GotoBLAS2 library; it works for R, but I
| | have no idea what bad consequences might ultimately result.  There are a lot
| | of web guides out there for installing GotoBLAS2 in Ubuntu, and they all
| | suggest this strategy of forcing symbolic links, so I'm including this here
| | in case people google around, so they find the better approach above.)
| 
| Yup. We always hope that good information eventually drowns out bad
| information. 

One last follow-up.  Debian's Atlas maintainer has started to work in the
OpenGoto packaging.  There will be proper Goto packages now that the license
is better, but it may take a while. It took years to get Atlas packaged
'right' so don;t expect anything too soon.  The gotoblas2-helper package is
still useful for the 'here and now'.

Dirk
 
| Dirk
|  
| | 
| | 
| | 
| | | I successfully built GotoBLAS2 from source, copied the library to /usr/lib
| | > | and created s symbolic link from libblas.so.3gf to point to the new
| | > | GotoBLAS2 library.
| | >
| | > You did that wrong.  This isn't easy stuff (as understanding how the plug &
| | > play of all the BLAS / LAPACK alternatives is implemented is non-trivial),
| | > but forcing it isn't the right approach.  Below you mention my gcbd
| | > paper/package. In it, I use a rather awesome 'gotoblas2-helper' package
| | > which
| | > _automates_ creating a deb from the gotoblas2 sources.
| | >
| | > I suspect your problem comes from the fact that you only took half of what
| | > GotoBlas can give.  If I look at the deb created from the helper:
| | >
| | > edd at max:~/atlas$ dpkg -c
| | > /var/spool/gotoblas2-helper/archive/gotoblas2_1.13-1_amd64.deb |grep lib
| | > drwxr-xr-x root/root         0 2010-07-05 18:57 ./usr/lib/
| | > drwxr-xr-x root/root         0 2010-07-05 19:00 ./usr/lib/gotoblas2/
| | > -rw-r--r-- root/root  10445138 2010-07-05 19:00
| | > ./usr/lib/gotoblas2/libblas.a
| | > -rw-r--r-- root/root   8672978 2010-07-05 19:00
| | > ./usr/lib/gotoblas2/liblapack.a
| | > -rw-r--r-- root/root   5491025 2010-07-05 19:00
| | > ./usr/lib/gotoblas2/libblas.so.3gf.0
| | > -rw-r--r-- root/root   7427273 2010-07-05 19:00
| | > ./usr/lib/gotoblas2/liblapack.so.3gf.0
| | > edd at max:~/atlas$
| | >
| | > you see that I got libblas.so and liblapack.so.
| | >
| | > So your crashes / lack of lapack success may well be due to Goto assuming
| | > its
| | > own lapack, but not getting it.
| | >
| | > Dirk
| | >
| | 
| | 	[[alternative HTML version deleted]]
| | 
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| -- 
| Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
| 
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com