#15045: ATLAS: multiple definition of `ATL_SetAtomicCount'
-------------------------------------------------+-------------------------
Reporter: jdemeyer | Owner:
Type: defect | Status:
Priority: blocker | needs_review
Component: packages: standard | Milestone: sage-5.12
Keywords: | Resolution:
Authors: Volker Braun | Merged in:
Report Upstream: Reported upstream. No | Reviewers:
feedback yet. | Work issues:
Branch: | Commit:
Dependencies: | Stopgaps:
-------------------------------------------------+-------------------------
Changes (by vbraun):
* status: needs_work => needs_review
Old description:
> This non-reproducible problem which can occur during the ATLAS build
> (with atlas-3.10.1.p3.spkg from #14754) was supposed to be fixed but it
> actually is not fixed:
> {{{
> make[5]: Entering directory
> `/home/buildbot/build/sage/lena-1/lena_full/build/sage-5.12.beta1/spkg/build/atlas-3.10.1.p3
> /ATLAS-build/lib'
> gcc -fPIC -m64 -shared -o libsatlas.so \
> -Wl,"rpath-link
> /home/buildbot/build/sage/lena-1/lena_full/build/sage-5.12.beta1/local/lib"
> \
> -Wl,--whole-archive liblapack.a libf77blas.a libcblas.a
> libatlas.a -Wl,--no-whole-archive
> -L/usr/local/gcc-4.7.0/x86_64-Linux-k10-fc/lib/gcc/x86_64-unknown-linux-
> gnu/4.7.0/../../../../lib64 -lgfortran -lc -lpthread -lm -lgcc
> /usr/local/binutils-2.22/x86_64-Linux-k10-fc-gcc-4.6.2-rh/bin/ld: cannot
> find rpath-link
> /home/buildbot/build/sage/lena-1/lena_full/build/sage-5.12.beta1/local/lib:
> No such file or directory
> libatlas.a(ATL_SetAtomicCount_mut.o): In function `ATL_SetAtomicCount':
> ATL_SetAtomicCount_mut.c:(.text+0x0): multiple definition of
> `ATL_SetAtomicCount'
> libatlas.a(ATL_SetAtomicCount_arch.o):ATL_SetAtomicCount_arch.c:(.text+0x0):
> first defined here
> libatlas.a(ATL_ResetAtomicCount_mut.o): In function
> `ATL_ResetAtomicCount':
> ATL_ResetAtomicCount_mut.c:(.text+0x0): multiple definition of
> `ATL_ResetAtomicCount'
> libatlas.a(ATL_ResetAtomicCount_amd64.o):(.text+0x0): first defined here
> libatlas.a(ATL_DecAtomicCount_mut.o): In function `ATL_DecAtomicCount':
> ATL_DecAtomicCount_mut.c:(.text+0x0): multiple definition of
> `ATL_DecAtomicCount'
> libatlas.a(ATL_DecAtomicCount_amd64.o):(.text+0x0): first defined here
> libatlas.a(ATL_FreeAtomicCount_mut.o): In function `ATL_FreeAtomicCount':
> ATL_FreeAtomicCount_mut.c:(.text+0x0): multiple definition of
> `ATL_FreeAtomicCount'
> libatlas.a(ATL_FreeAtomicCount_arch.o):ATL_FreeAtomicCount_arch.c:(.text+0x0):
> first defined here
> collect2: error: ld returned 1 exit status
> make[5]: *** [GCCTRY] Error 1
> }}}
>
> [http://build.sagemath.org/sage/builders/Skynet%20lena%20%28Fedora%2016%20x86_64%29/builds/174/steps/shell_5/logs/atlas
> full ATLAS build log]
>
> Upstream: [http://sourceforge.net/p/math-atlas/support-requests/907/]
>
> New spkg:
> http://boxen.math.washington.edu/home/vbraun/spkg/atlas-3.10.1.p4.spkg
New description:
This non-reproducible problem which can occur during the ATLAS build (with
atlas-3.10.1.p3.spkg from #14754) was supposed to be fixed but it actually
is not fixed:
{{{
make[5]: Entering directory
`/home/buildbot/build/sage/lena-1/lena_full/build/sage-5.12.beta1/spkg/build/atlas-3.10.1.p3
/ATLAS-build/lib'
gcc -fPIC -m64 -shared -o libsatlas.so \
-Wl,"rpath-link
/home/buildbot/build/sage/lena-1/lena_full/build/sage-5.12.beta1/local/lib"
\
-Wl,--whole-archive liblapack.a libf77blas.a libcblas.a
libatlas.a -Wl,--no-whole-archive
-L/usr/local/gcc-4.7.0/x86_64-Linux-k10-fc/lib/gcc/x86_64-unknown-linux-
gnu/4.7.0/../../../../lib64 -lgfortran -lc -lpthread -lm -lgcc
/usr/local/binutils-2.22/x86_64-Linux-k10-fc-gcc-4.6.2-rh/bin/ld: cannot
find rpath-link
/home/buildbot/build/sage/lena-1/lena_full/build/sage-5.12.beta1/local/lib:
No such file or directory
libatlas.a(ATL_SetAtomicCount_mut.o): In function `ATL_SetAtomicCount':
ATL_SetAtomicCount_mut.c:(.text+0x0): multiple definition of
`ATL_SetAtomicCount'
libatlas.a(ATL_SetAtomicCount_arch.o):ATL_SetAtomicCount_arch.c:(.text+0x0):
first defined here
libatlas.a(ATL_ResetAtomicCount_mut.o): In function
`ATL_ResetAtomicCount':
ATL_ResetAtomicCount_mut.c:(.text+0x0): multiple definition of
`ATL_ResetAtomicCount'
libatlas.a(ATL_ResetAtomicCount_amd64.o):(.text+0x0): first defined here
libatlas.a(ATL_DecAtomicCount_mut.o): In function `ATL_DecAtomicCount':
ATL_DecAtomicCount_mut.c:(.text+0x0): multiple definition of
`ATL_DecAtomicCount'
libatlas.a(ATL_DecAtomicCount_amd64.o):(.text+0x0): first defined here
libatlas.a(ATL_FreeAtomicCount_mut.o): In function `ATL_FreeAtomicCount':
ATL_FreeAtomicCount_mut.c:(.text+0x0): multiple definition of
`ATL_FreeAtomicCount'
libatlas.a(ATL_FreeAtomicCount_arch.o):ATL_FreeAtomicCount_arch.c:(.text+0x0):
first defined here
collect2: error: ld returned 1 exit status
make[5]: *** [GCCTRY] Error 1
}}}
[http://build.sagemath.org/sage/builders/Skynet%20lena%20%28Fedora%2016%20x86_64%29/builds/174/steps/shell_5/logs/atlas
full ATLAS build log]
Upstream: [http://sourceforge.net/p/math-atlas/support-requests/907/]
New spkg:
http://boxen.math.washington.edu/home/vbraun/spkg/atlas-3.10.1.p5.spkg
--
Comment:
I've made the change to force `iForceUseMutex` and that indeed reproduces
the bug reliably. I made the change that Nils suggested and always use the
assembly version, this fixes it for me.
--
Ticket URL: <http://trac.sagemath.org/ticket/15045#comment:28>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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