[R-sig-Debian] GotoBLAS2 breaks lapack

[Dirk Eddelbuettel]

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. 

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