Is it possible atlas is linked wrongly by new binutils?

[Richard W.M. Jones]

ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
fails to link to atlas:

+ /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I examples
lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
/usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
/usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
/usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
/usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_'
collect2: error: ld returned 1 exit status

However this only happens with the very latest atlas that was built by
binutils 2.29 (atlas-3.10.2-18.fc27.x86_64).  It doesn't occur with
the previous version of atlas (atlas-3.10.2-16.fc26) even though there
seems to have been no change in atlas.

$ nm -D /usr/lib64/atlas/libtatlas.so | grep larfy
                 U clarfy_
                 U dlarfy_
                 U slarfy_
                 U zlarfy_

I looked in /usr/lib64 on my development machine which has atlas
installed but there is no .so* file that I can find which defines
these symbols.  I also couldn't work out where in the atlas code
(which is a bit strange) these references are used.

Hence the question: Is this breakage in atlas?  binutils?

Rich.

-- 
Richard Jones, Virtualization Group, Red Hat http://people.redhat.com/~rjones
Read my programming and virtualization blog: http://rwmj.wordpress.com
libguestfs lets you edit virtual machines.  Supports shell scripting,
bindings from many languages.  http://libguestfs.org

[Antonio Trande]

On 08/09/2017 11:37 AM, Richard W.M. Jones wrote:
>  
>  ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
>  fails to link to atlas:
>  
>  + /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I examples
> lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_'
>  collect2: error: ld returned 1 exit status
>  
>  However this only happens with the very latest atlas that was built by
>  binutils 2.29 (atlas-3.10.2-18.fc27.x86_64).  It doesn't occur with
>  the previous version of atlas (atlas-3.10.2-16.fc26) even though there
>  seems to have been no change in atlas.
>  
>  $ nm -D /usr/lib64/atlas/libtatlas.so | grep larfy
>                   U clarfy_
>                   U dlarfy_
>                   U slarfy_
>                   U zlarfy_
>  
>  I looked in /usr/lib64 on my development machine which has atlas
>  installed but there is no .so* file that I can find which defines
>  these symbols.  I also couldn't work out where in the atlas code
>  (which is a bit strange) these references are used.
>  
>  Hence the question: Is this breakage in atlas?  binutils?
>  
>  Rich.
>   
lapack-3.7.1 on rawhide looks affected too:
https://bugzilla.redhat.com/show_bug.cgi?id=1479567

-- 
--
Antonio Trande
sagitter AT fedoraproject dot org
See my vCard.

[Richard W.M. Jones]

On Wed, Aug 09, 2017 at 02:10:02PM +0200, Antonio Trande wrote:
>  On 08/09/2017 11:37 AM, Richard W.M. Jones wrote:
>  > 
>  > ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
>  > fails to link to atlas:
>  > 
>  > + /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I
> examples lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
>  > /usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
>  > /usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
>  > /usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
>  > /usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_'
>  > collect2: error: ld returned 1 exit status
>  > 
>  > However this only happens with the very latest atlas that was built by
>  > binutils 2.29 (atlas-3.10.2-18.fc27.x86_64).  It doesn't occur with
>  > the previous version of atlas (atlas-3.10.2-16.fc26) even though there
>  > seems to have been no change in atlas.
>  > 
>  > $ nm -D /usr/lib64/atlas/libtatlas.so | grep larfy
>  >                  U clarfy_
>  >                  U dlarfy_
>  >                  U slarfy_
>  >                  U zlarfy_
>  > 
>  > I looked in /usr/lib64 on my development machine which has atlas
>  > installed but there is no .so* file that I can find which defines
>  > these symbols.  I also couldn't work out where in the atlas code
>  > (which is a bit strange) these references are used.
>  > 
>  > Hence the question: Is this breakage in atlas?  binutils?
>  > 
>  > Rich.
>  > 
>  
>  lapack-3.7.1 on rawhide looks affected too:
>  https://bugzilla.redhat.com/show_bug.cgi?id=1479567 
As is ocaml-lacaml (OCaml bindings for lapack) ...

Rich.

-- 
Richard Jones, Virtualization Group, Red Hat http://people.redhat.com/~rjones
Read my programming and virtualization blog: http://rwmj.wordpress.com
libguestfs lets you edit virtual machines.  Supports shell scripting,
bindings from many languages.  http://libguestfs.org

[Jerry James]

On Wed, Aug 9, 2017 at 3:37 AM, Richard W.M. Jones <rjones(a)redhat.com&gt; wrote:
>  ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
>  fails to link to atlas:
>
>  + /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I examples
> lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_'
>  collect2: error: ld returned 1 exit status 
Something is definitely afoot.  The latest opengrm-ngram build just
failed with the same list of undefined symbols.
-- 
Jerry James
http://www.jamezone.org/

[Tom Callaway]

On 08/09/2017 05:37 AM, Richard W.M. Jones wrote:
>  
>  ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
>  fails to link to atlas:
>  
>  + /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I examples
> lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
>  /usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_' 
This is because I bumped lapack in rawhide. Atlas uses liblapack.a, and
the first lapack 3.7.1 builds were missing some symbols. Everything is
fixed now in lapack in rawhide, but I forgot atlas was doing this. I
have an atlas rebuild going now that should resolve the error.

~tom

[Tom Callaway]

On 08/16/2017 04:34 PM, Tom Callaway wrote:
>  
>  
>  On 08/09/2017 05:37 AM, Richard W.M. Jones wrote:
> >
> > ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
> > fails to link to atlas:
> >
> > + /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I examples
> lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
> > /usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
> > /usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
> > /usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
> > /usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_'
>  
>  This is because I bumped lapack in rawhide. Atlas uses liblapack.a, and
>  the first lapack 3.7.1 builds were missing some symbols. Everything is
>  fixed now in lapack in rawhide, but I forgot atlas was doing this. I
>  have an atlas rebuild going now that should resolve the error. 
Or, it would, if it wasn't failing on s390x. I miss secondary architectures.

https://koji.fedoraproject.org/koji/taskinfo?taskID=21267770

~tom

[Jakub Martisko]

It should work now [1].

Jakub

[1]:
https://koji.fedoraproject.org/koji/taskinfo?taskID=21296324

On 9.8.2017 11:37, Richard W.M. Jones wrote:
> 
> ocaml-gsl (OCaml bindings for GNU Scientific Library) currently
> fails to link to atlas:
> 
> + /usr/bin/ocamlfind ocamlopt -g -I lib -linkpkg -package bigarray -I lib -I examples
lib/gsl.cmxa examples/blas_ex.cmx -o examples/blas_ex.native
> /usr/lib64/atlas/libsatlas.so: undefined reference to `dlarfy_'
> /usr/lib64/atlas/libsatlas.so: undefined reference to `slarfy_'
> /usr/lib64/atlas/libsatlas.so: undefined reference to `clarfy_'
> /usr/lib64/atlas/libsatlas.so: undefined reference to `zlarfy_'
> collect2: error: ld returned 1 exit status
> 
> However this only happens with the very latest atlas that was built by
> binutils 2.29 (atlas-3.10.2-18.fc27.x86_64).  It doesn't occur with
> the previous version of atlas (atlas-3.10.2-16.fc26) even though there
> seems to have been no change in atlas.
> 
> $ nm -D /usr/lib64/atlas/libtatlas.so | grep larfy
>                  U clarfy_
>                  U dlarfy_
>                  U slarfy_
>                  U zlarfy_
> 
> I looked in /usr/lib64 on my development machine which has atlas
> installed but there is no .so* file that I can find which defines
> these symbols.  I also couldn't work out where in the atlas code
> (which is a bit strange) these references are used.
> 
> Hence the question: Is this breakage in atlas?  binutils?
> 
> Rich.
>

[Richard W.M. Jones]

On Fri, Aug 18, 2017 at 08:04:52AM +0200, Jakub Martisko wrote:
>  It should work now [1].
>  
>  Jakub
>  
>  [1]:
>  https://koji.fedoraproject.org/koji/taskinfo?taskID=21296324 
Thanks, I'll try to rebuild ocaml-gsl & ocaml-lacaml shortly.

Rich.

-- 
Richard Jones, Virtualization Group, Red Hat http://people.redhat.com/~rjones
Read my programming and virtualization blog: http://rwmj.wordpress.com
libguestfs lets you edit virtual machines.  Supports shell scripting,
bindings from many languages.  http://libguestfs.org