[gentoo-science] failure to merge sage due to unavailability of cblas
Hello, I'm trying to emerge sage from the sage-on-gentoo overlay. Unfortunately this always fails with errors like the following: === x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -ggdb -fno-strict-aliasing /var/tmp/portage/sci-mathematics/sage-5.6/work/sage-5.6-python2_7/temp.linux-x86_64-2.7/sage/gsl/callback.o -L/usr//lib -L/usr/lib64 -lcsage -lgsl -lgslcblas -lstdc++ -lntl -lpython2.7 -o /var/tmp/portage/sci-mathematics/sage-5.6/work/sage-5.6-python2_7/lib/sage/gsl/callback.so /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/../../../../x86_64-pc-linux-gnu/bin/ld: cannot find -lgslcblas collect2: error: ld returned 1 exit status === I have the science overlay installed. I understand that there are quite some changes in the overlay on how the scientific libraries are handled -- so I come here for help. ;) I've installed both gsl and atlas and invoked eselect several times to make sure, that everything is set up properly, but to no avail. I have a file /usr/lib64/libgslcblas.so on my system, so I don't see what's wrong here. Any clues appreciated. :) Markus -- Aoccdrnig to a threoy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer are in the rghit pclae. The rset can be a taotl mses and you can sitll raed it in msot csaes. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. And I awlyas thought slpeling was ipmorantt.
Re: [gentoo-science] failure to merge sage due to unavailability of cblas
At Tue, 05 Mar 2013 11:51:58 +1300, Francois Bissey wrote: pkg-config 0.28 is what is wrong. I thought we had fixed 5.6 for it but obviously not. Try 5.7 or downgrade pkgconfig to 0.27 5.7 works fine. :) Thanks Markus -- Aoccdrnig to a threoy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer are in the rghit pclae. The rset can be a taotl mses and you can sitll raed it in msot csaes. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. And I awlyas thought slpeling was ipmorantt.
Re: [gentoo-science] BLAS and LAPACK dependecy resolution
Hi, I did the following, which seems to have done the trick: 1. add the package.mask entries 2. merge eselect::science 3. remerge all libraries that come from the science overlay (everything from 'eix -I --in-overlay science') 4. remove /usr/lib/libblas.so (which was kept by preserve-libs) that is actually do 'rm /usr/lib/libblas.so' 5. remerge lapack-reference (which provided /usr/lib/libblas.so) 6. remerge umfpack (which depended on /usr/lib/libblas.so) In between 3. and 4. I tried 'emerge @preserved-rebuild' which did not improve the situation (i.e. the preserved /usr/lib/libblas.so was still used by the newly built packages). Step 6 is probably collateral damage which is hard to formalize. [2 blas.mask text/plain (base64)] The entry =app-shells/bash-completion-2.1 should probably be added, since the newer versions require =eselect-1.3.8 which is only available in the main tree. Once the mask file is available via overlay it would probably be nice to have the above steps documented. I would volunteer to write a short piece for the wiki (but afaik I'm not allowed to edit https://wiki.gentoo.org/wiki/Project:Science/Overlay so somebody else would have to add it). Markus -- Aoccdrnig to a threoy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer are in the rghit pclae. The rset can be a taotl mses and you can sitll raed it in msot csaes. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. And I awlyas thought slpeling was ipmorantt.
Re: [gentoo-science] BLAS and LAPACK dependecy resolution
Hi, I tried my hand at a wiki blurb which can be found at [1]. I changed the procedure to disable preserved-libs which will probably give the most reproducible results. Comments welcome. Markus [1] https://wiki.gentoo.org/wiki/User_talk:Houseofsuns -- Aoccdrnig to a threoy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer are in the rghit pclae. The rset can be a taotl mses and you can sitll raed it in msot csaes. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. And I awlyas thought slpeling was ipmorantt.
Re: [gentoo-science] BLAS and LAPACK dependecy resolution
Hi, At Thu, 12 Sep 2013 11:19:11 +0200, Markus wrote: 4. remove /usr/lib/libblas.so (which was kept by preserve-libs) that is actually do 'rm /usr/lib/libblas.so' I see something really strange: repeatedly merging lapack-reference causes it to bounce between two states. Where in one state there are three additional files installed by the package: /usr/lib/debug/usr/lib64/libblas.so.debug /usr/lib64/libblas.so /usr/lib64/pkgconfig/blas.pc I tried it a larger number of times and the package alternates predictably between the two states. Any hints on how this can happen? Also it seems that in the state where the files are not there other packages have difficulties finding BLAS -- so the woes do not seem to be over yet. *sigh* Markus -- Aoccdrnig to a threoy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer are in the rghit pclae. The rset can be a taotl mses and you can sitll raed it in msot csaes. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. And I awlyas thought slpeling was ipmorantt.
Re: [gentoo-science] BLAS and LAPACK dependecy resolution
Hi, At Sat, 14 Sep 2013 21:33:35 +1200, Francois Bissey wrote: So the solution is: properly eselect a blas and make sure it is a valid and sane configuration. thanks, that worked. I modified the wiki piece to prevent this accident. Markus -- Aoccdrnig to a threoy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer are in the rghit pclae. The rset can be a taotl mses and you can sitll raed it in msot csaes. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. And I awlyas thought slpeling was ipmorantt.
