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@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@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]] | | | | _______________________________________________ | | R-SIG-Debian mailing list | | R-SIG-Debian@r-project.org | | https://stat.ethz.ch/mailman/listinfo/r-sig-debian | | -- | Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com | | _______________________________________________ | R-SIG-Debian mailing list | R-SIG-Debian@r-project.org | https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
