[Debian-med-packaging] Bug#936609: Advent calendar bug squashing issue (Was: Bug#936609: cblas / gsl hint needed (Was: Bug#936609: Ported ghmm to Python3 but issues with clapack))
Dirk Eddelbuettel
edd at debian.org
Sat Dec 5 14:32:33 GMT 2020
On 5 December 2020 at 12:09, Andreas Tille wrote:
| this issue is something for our advent calendar. Anybody with cblas
| knowledge?
I am the GNU GSL maintainer, and I at one point also worked a lot with the
Atlas and other LAPACK/BLAS packages. I think Mo may be wrong here: I did the
same approach of "oh we can just skip GSL's cblas". I think that is
wrong. The way the C interface of the GNU GSL works appears to be require GSL
+ GSL CBLAS. That is what every package I know using GSL does -- even though
that "looks weird and redundant".
>From a quick look at http://ghmm.org it also looks like GLS is purely
optional and for RNGs only -- just like my RcppZiggurat (upstream) package
does which just relies on my RcppGSL (upstream) package which just export
`gsl-config --libs`, and has for years.
So I'd give the GSL defaults here a try.
(That said Mo knows a lot more than I do about BLAS, but I've watched a lot
of GSL build too over the decades I looked after that package.)
Dirk
| Kind regards
|
| Andreas.
|
| On Mon, Jan 27, 2020 at 10:55:25AM +0100, Andreas Tille wrote:
| > Hi again,
| >
| > with my last mail I wanted to express: Hmmmm, to stupid to turn
| > this hint into real code. Any more detailed hint / patch would be
| > really welcome.
| >
| > Kind regards
| >
| > Andreas.
| >
| > On Mon, Jan 06, 2020 at 12:56:17PM +0100, Andreas Tille wrote:
| > > Hi Mo,
| > >
| > > On Sun, Jan 05, 2020 at 08:19:07AM +0000, Mo Zhou wrote:
| > > > GSL provides a set of CBLAS API/ABI, delivered with shared object
| > > > "libgslcblas.so" and header "gsl_cblas.h". That subset becomes
| > > > redundant once you include the headers of any standard/compatible
| > > > (C)BLAS library. That's what the compilation error means.
| > >
| > > Seems you want to tell me to not include gsl_cblas.h header. However,
| > > the code has no hit for
| > >
| > > grep -R gsl_cblas
| > >
| > > so the header is not included explicitly. So while your hint explains
| > > the error I need to admit I have no idea yet, how to fix it.
| > >
| > > > Make sure that the code only use one CBLAS implementation. In the
| > > > context of debian, I'd recommend you use the CBLAS ABI from libblas-dev,
| > > > and avoid linking against -lcblas. Link against -lblas instead.
| > >
| > > OK, once I'm at the linking step I might come back to this hint.
| > >
| > > Kind regards
| > >
| > > Andreas.
| > >
| > > > On Sun, Jan 05, 2020 at 07:55:05AM +0100, Andreas Tille wrote:
| > > > > Control: tags -1 help
| > > > >
| > > > > Hi,
| > > > >
| > > > > I was asking upstream about this issue[1] and an issue about gsl usage
| > > > > is suspected. Any hint how this can be fixed?
| > > > >
| > > > > > Finally I have a question about building with lapack. I get:
| > > > > >
| > > > > > ...
| > > > > > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -DDTD_LOC=\"/usr/share/ghmm/ghmm.dtd.1.0\" -g -O2 "-fdebug-prefix-map=/build/ghmm-0.9~rc3=." -fstack-protector-strong - Wformat -Werror=format-security -I/usr/include -I/usr/include/x86_64-linux-gnu -I/usr/include/libxml2 -c rng.c -fPIC -DPIC -o .libs/rng.o
| > > > > > In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,
| > > > > > from matrixop.c:48:
| > > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:9: error: nested redefinition of 'enum CBLAS_ORDER'
| > > > > > 5 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };
| > > > > > | ^~~~~~~~~~~
| > > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:9: error: redeclaration of 'enum CBLAS_ORDER'
| > > > > > In file included from /usr/include/gsl/gsl_blas_types.h:28,
| > > > > > from /usr/include/gsl/gsl_blas.h:29,
| > > > > > from /usr/include/gsl/gsl_linalg.h:30,
| > > > > > from matrixop.c:44:
| > > > > > /usr/include/gsl/gsl_cblas.h:46:6: note: originally defined here
| > > > > > 46 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
| > > > > > | ^~~~~~~~~~~
| > > > > > In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,
| > > > > > from matrixop.c:48:
| > > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:22: error: redeclaration of enumerator 'CblasRowMajor'
| > > > > > 5 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };
| > > > > > | ^~~~~~~~~~~~~
| > > > > > In file included from /usr/include/gsl/gsl_blas_types.h:28,
| > > > > > from /usr/include/gsl/gsl_blas.h:29,
| > > > > > from /usr/include/gsl/gsl_linalg.h:30,
| > > > > > from matrixop.c:44:
| > > > > > /usr/include/gsl/gsl_cblas.h:46:19: note: previous definition of 'CblasRowMajor' was here
| > > > > > 46 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
| > > > > > | ^~~~~~~~~~~~~
| > > > > > In file included from /usr/include/x86_64-linux-gnu/clapack.h:4,
| > > > > > from matrixop.c:48:
| > > > > > /usr/include/x86_64-linux-gnu/cblas.h:5:41: error: redeclaration of enumerator 'CblasColMajor'
| > > > > > 5 | enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102 };
| > > > > > | ^~~~~~~~~~~~~
| > > > > >
| > > > > >
| > > > >
| > > > > Kind regards
| > > > >
| > > > > Andreas.
| > > > >
| > > > >
| > > > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=936609#19
| > > > >
| > > > > --
| > > > > http://fam-tille.de
| > > > >
| > > >
| > >
| > > --
| > > http://fam-tille.de
| > >
| > >
| >
| > --
| > http://fam-tille.de
| >
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https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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