[Llvm-bgq-discuss] Linker error: undefined reference to `vtable for std::nested_exception'

Mon Jul 28 17:16:58 CDT 2014

Everyone... one more thing...

If you extract the 4.7.2 toolchain files from V1R2M1_base_4.7.2-files.tar.gz linked to on the wiki page, you'll likely find that dynamic linking does not work correctly. I've updated the wiki page with instructions on how to fix this.

  http://trac.alcf.anl.gov/projects/llvm-bgq/wiki/WikiStart#RPMsetc.

 -Hal

----- Original Message -----
> From: "Michael Schlottke" <m.schlottke at aia.rwth-aachen.de>
> To: "Hal Finkel" <hfinkel at anl.gov>
> Cc: llvm-bgq-discuss at lists.alcf.anl.gov, "Sandipan Mohanty" <s.mohanty at fz-juelich.de>
> Sent: Saturday, July 19, 2014 12:06:23 PM
> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined reference to `vtable for std::nested_exception'
> 
> Dear Hal,
> 
> Indeed, this seems to have been the culprit. Thank you very much for
> support. It seems like I can compile & link programs now with
> bgclang++11, and the executable also runs (at least on the frontend).
> Right now the 4.7.2 files are in a temporary location but I will
> relocate them on JUQUEEN to a more fitting place next week.
> 
> Y'all have a nice weekend
> 
> Michael
> 
> On Sa 19 Jul 2014 16:58:34 CEST, Hal Finkel wrote:
> > Sandipan, et al.,
> >
> > There is a link to V1R2M1_base_4.7.2-files.tar.gz (with some
> > explanatory text) on the wiki:
> >
> >    http://trac.alcf.anl.gov/projects/llvm-bgq/
> >
> >   -Hal
> >
> > ----- Original Message -----
> >> From: "Hal Finkel" <hfinkel at anl.gov>
> >> To: "Sandipan Mohanty" <s.mohanty at fz-juelich.de>
> >> Cc: llvm-bgq-discuss at lists.alcf.anl.gov
> >> Sent: Friday, July 18, 2014 5:57:03 PM
> >> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined reference
> >> to `vtable	for std::nested_exception'
> >>
> >> Sandipan,
> >>
> >> To solve the actual std::exception error you still need to pick up
> >> the libstdc++ libs from the 4.7.2 toolchain. If you look in the
> >> wrapper script, it looks for them in some particular places; make
> >> sure that matches you system.
> >>
> >>   -Hal
> >>
> >> ----- Original Message -----
> >>> From: "Sandipan Mohanty" <s.mohanty at fz-juelich.de>
> >>> To: llvm-bgq-discuss at lists.alcf.anl.gov
> >>> Sent: Friday, July 18, 2014 5:29:40 PM
> >>> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined reference
> >>> to `vtable	for std::nested_exception'
> >>>
> >>> Hi Hal, Michael and Roy,
> >>>      I changed the variable VLIBSTDCXX from 4.4.6 to 4.4.7 in the
> >>>      bgclang
> >>> wrapper in Jülich. Unfortunately, the error persists.
> >>>
> >>> /Sandipan
> >>>
> >>>
> >>> On Friday 18 Jul 2014 17:06:28 Hal Finkel wrote:
> >>>> Roy,
> >>>>
> >>>> Ah, that certainly explains things.
> >>>>
> >>>> Michael, if you edit the variables at the top of the bgclang
> >>>> wrapper script,
> >>>> you'll make things work again.
> >>>>
> >>>> I need to put together a new release soon anyway (upstream 3.5
> >>>> is
> >>>> almost
> >>>> out...)
> >>>>
> >>>>   -Hal
> >>>>
> >>>> ----- Original Message -----
> >>>>
> >>>>> From: "Roy Musselman" <roymuss at us.ibm.com>
> >>>>> To: "Hal Finkel" <hfinkel at anl.gov>
> >>>>> Cc: llvm-bgq-discuss at lists.alcf.anl.gov,
> >>>>> llvm-bgq-discuss-bounces at lists.alcf.anl.gov, "Michael
> >>>>> Schlottke"
> >>>>> <m.schlottke at fz-juelich.de>
> >>>>> Sent: Friday, July 18, 2014 5:02:57 PM
> >>>>> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined
> >>>>> reference
> >>>>> to
> >>>>> `vtable for std::nested_exception'
> >>>>>
> >>>>>
> >>>>>
> >>>>> Hi Hal & Michael,
> >>>>>
> >>>>> We installed V1R2M2 here at LLNL. Note that the subdirectory is
> >>>>> 4.4.7
> >>>>> for V1R2M2, not 4.4.6 as it was for V1R2M1.
> >>>>>
> >>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >>>>> Roy Musselman
> >>>>> HPC Application Analyst at LLNL
> >>>>> email: roymuss at us.ibm.com
> >>>>> Cell: 507-358-8895, Home: 507-281-9565
> >>>>>
> >>>>> Inactive hide details for Hal Finkel ---07/18/2014 12:20:12
> >>>>> PM---Michael, The relevant parts of the log are:Hal Finkel
> >>>>> ---07/18/2014 12:20:12 PM---Michael, The relevant parts of the
> >>>>> log
> >>>>> are:
> >>>>>
> >>>>> From: Hal Finkel <hfinkel at anl.gov>
> >>>>> To: Michael Schlottke <m.schlottke at fz-juelich.de>
> >>>>> Cc: llvm-bgq-discuss at lists.alcf.anl.gov
> >>>>> Date: 07/18/2014 12:20 PM
> >>>>> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined
> >>>>> reference
> >>>>> to
> >>>>> `vtable for std::nested_exception'
> >>>>> Sent by: llvm-bgq-discuss-bounces at lists.alcf.anl.gov
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Michael,
> >>>>>
> >>>>> The relevant parts of the log are:
> >>>>>
> >>>>> ignoring nonexistent directory
> >>>>> "/bgsys/drivers/V1R2M2/ppc64/gnu-linux/powerpc64-bgq-linux/include/c++/4.4
> >>>>> .6"
> >>>>>
> >>>>> ignoring nonexistent directory
> >>>>> "/bgsys/drivers/V1R2M2/ppc64/gnu-linux/powerpc64-bgq-linux/include/c++/4.4
> >>>>> .6/powerpc64-bgq-linux"
> >>>>>
> >>>>> Where did these files go on your system?
> >>>>>
> >>>>> -Hal
> >>>>>
> >>>>> ----- Original Message -----
> >>>>>
> >>>>>> From: "Michael Schlottke" <m.schlottke at fz-juelich.de>
> >>>>>> To: llvm-bgq-discuss at lists.alcf.anl.gov, hfinkel at anl.gov
> >>>>>> Sent: Friday, July 18, 2014 3:23:59 AM
> >>>>>> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined
> >>>>>> reference
> >>>>>> to `vtable for std::nested_exception'
> >>>>>>
> >>>>>> Hi Hal,
> >>>>>>
> >>>>>> Thanks for checking this out. I installed the last RPMs that
> >>>>>> we
> >>>>>> knew
> >>>>>> worked before the toolchain upgrade (r201012-20140207), but
> >>>>>> to
> >>>>>> no
> >>>>>> avail.
> >>>>>> When trying to compile the same MWE program, we get a
> >>>>>> compiler
> >>>>>> (preprocessor?) error instead, but again it seems to be
> >>>>>> centered
> >>>>>> around
> >>>>>> exceptions (I've attached the log). Maybe this sheds some
> >>>>>> more
> >>>>>> light
> >>>>>> on
> >>>>>> the issues we're having.
> >>>>>>
> >>>>>> Regards,
> >>>>>>
> >>>>>> Michael
> >>>>>>
> >>>>>> P.S.: As before, the error occurs only when using bgclang++11
> >>>>>> or
> >>>>>> when
> >>>>>> manually adding -stdlib=libc++ to bgclang++. Otherwise it
> >>>>>> compiles
> >>>>>> &
> >>>>>> runs just fine.
> >>>>>>
> >>>>>> On 17.07.2014 19:21, Hal Finkel wrote:
> >>>>>>> Hi,
> >>>>>>>
> >>>>>>> This error almost always occurs when you pick up the old
> >>>>>>> libstdc++
> >>>>>>> library instead of the one from the 4.7.2 toolchain. I'll
> >>>>>>> look at
> >>>>>>> your verbose logs later.
> >>>>>>>
> >>>>>>> -Hal
> >>>>>>>
> >>>>>>> ----- Original Message -----
> >>>>>>>
> >>>>>>>> From: "Sandipan Mohanty" <s.mohanty at fz-juelich.de>
> >>>>>>>> To: llvm-bgq-discuss at lists.alcf.anl.gov
> >>>>>>>> Sent: Thursday, July 17, 2014 11:53:07 AM
> >>>>>>>> Subject: Re: [Llvm-bgq-discuss] Linker error: undefined
> >>>>>>>> reference
> >>>>>>>> to `vtable for std::nested_exception'
> >>>>>>>>
> >>>>>>>> Hi!
> >>>>>>>>
> >>>>>>>> The linker error Michael mentioned also appears for a
> >>>>>>>> simple
> >>>>>>>> hello world
> >>>>>>>> program:
> >>>>>>>>
> >>>>>>>> #include <iostream>
> >>>>>>>>
> >>>>>>>> int main()
> >>>>>>>> {
> >>>>>>>> std::cout << "Hello, World!\n";
> >>>>>>>> }
> >>>>>>>>
> >>>>>>>> Compiling it with bgclang++ is fine. Compiling with
> >>>>>>>> bgclang++11,
> >>>>>>>> which also
> >>>>>>>> links with libc++, produces the linker error he mentioned
> >>>>>>>> about
> >>>>>>>> nested_exception. The nested_exception class members are
> >>>>>>>> defined
> >>>>>>>> inside the
> >>>>>>>> exception.cpp file in the libc++ source. But there are
> >>>>>>>> lots
> >>>>>>>> of
> >>>>>>>> macros
> >>>>>>>> influencing what sections get compiled. Is the libc++ in
> >>>>>>>> the
> >>>>>>>> RPM
> >>>>>>>> compiled with
> >>>>>>>> libsupc++, libcxxrt or libcxxabi as the LIBCXX_CXX_ABI ?
> >>>>>>>>
> >>>>>>>> /Sandipan
> >>>>>>>>
> >>>>>>>> On Thursday 17 Jul 2014 11:30:35 Rob Latham wrote:
> >>>>>>>>> See
> >>>>>>>>> http://www.alcf.anl.gov/user-guides/bgclang-compiler#faq
> >>>>>>>>> ,
> >>>>>>>>> which
> >>>>>>>>> I
> >>>>>>>>> myself was just staring at last night:
> >>>>>>>>>
> >>>>>>>>> Linking code compiled with bgclang++ together with code
> >>>>>>>>> compiled
> >>>>>>>>> with
> >>>>>>>>> bgclang++11 does not work, why?
> >>>>>>>>>
> >>>>>>>>> Code compiled using bgclang++ uses the same libstdc++
> >>>>>>>>> standard
> >>>>>>>>> template
> >>>>>>>>> library (STL) implementation as the system-default GNU
> >>>>>>>>> powerpc64-bgq-linux-g++ compiler. This provides
> >>>>>>>>> compatibility
> >>>>>>>>> with
> >>>>>>>>> C++
> >>>>>>>>> libraries, including some system libraries, compiled with
> >>>>>>>>> the
> >>>>>>>>> GNU
> >>>>>>>>> toolchain. This STL implementation, however, cannot
> >>>>>>>>> provide
> >>>>>>>>> a
> >>>>>>>>> conforming
> >>>>>>>>> C++11 programming environment, and so bgclang++11 uses an
> >>>>>>>>> up-to-date STL
> >>>>>>>>> implementation derived from LLVM's libc++. Unfortunately,
> >>>>>>>>> this
> >>>>>>>>> STL
> >>>>>>>>> implementation is incompatible with libstdc++, and so
> >>>>>>>>> linking
> >>>>>>>>> errors
> >>>>>>>>> will result for functions that use STL objects as part of
> >>>>>>>>> their
> >>>>>>>>> signatures (i.e. parameter or return types).
> >>>>>>>>>
> >>>>>>>>> ==rob
> >>>>>>>>>
> >>>>>>>>> On 07/17/2014 08:48 AM, Michael Schlottke wrote:
> >>>>>>>>>> Hi Hal,
> >>>>>>>>>>
> >>>>>>>>>> We tried to install the new version of clang on the BG/Q
> >>>>>>>>>> @
> >>>>>>>>>> FZ
> >>>>>>>>>> Juelich
> >>>>>>>>>> from your rpms, which worked like a breeze (thanks again
> >>>>>>>>>> for
> >>>>>>>>>> your
> >>>>>>>>>> effors!). However, with the new installation we are not
> >>>>>>>>>> able
> >>>>>>>>>> to
> >>>>>>>>>> link
> >>>>>>>>>> even simple problems against libcxx, as all attempts end
> >>>>>>>>>> with
> >>>>>>>>>> the
> >>>>>>>>>> following error:
> >>>>>>>>>>
> >>>>>>>>>> /bgsys/local/clang/r209570-20140527/libc++/lib/libc++.a(exception.c
> >>>>>>>>>> pp.o):(
> >>>>>>>>>> .toc+0x0): undefined reference to `vtable for
> >>>>>>>>>> std::nested_exception'
> >>>>>>>>>> clang: error: linker command failed with exit code 1
> >>>>>>>>>> (use
> >>>>>>>>>> -v
> >>>>>>>>>> to
> >>>>>>>>>> see
> >>>>>>>>>> invocation)
> >>>>>>>>>>
> >>>>>>>>>> It happens as soon as we try to compile & link a dummy
> >>>>>>>>>> program
> >>>>>>>>>> that has
> >>>>>>>>>> at least one std library include file. If we use
> >>>>>>>>>> bgclang++,
> >>>>>>>>>> the
> >>>>>>>>>> error
> >>>>>>>>>> does not occur, but it does when using either
> >>>>>>>>>> -stdlib=libc++
> >>>>>>>>>> or
> >>>>>>>>>> bgclang++11.
> >>>>>>>>>>
> >>>>>>>>>> Do you have any idea what the source of the problem
> >>>>>>>>>> could
> >>>>>>>>>> be?
> >>>>>>>>>> I
> >>>>>>>>>> attached
> >>>>>>>>>> a MWE and the output of running bgclang++11 with -v.
> >>>>>>>>>>
> >>>>>>>>>> Regards,
> >>>>>>>>>>
> >>>>>>>>>> Michael
> >>>>>>>>>>
> >>>>>>>>>> P.S.: We had a driver/toolchain upgrade on JUQUEEN and
> >>>>>>>>>> thus
> >>>>>>>>>> our
> >>>>>>>>>> old
> >>>>>>>>>> clang installations are not working anymore. Maybe this
> >>>>>>>>>> could
> >>>>>>>>>> be
> >>>>>>>>>> related
> >>>>>>>>>> to the problem?
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> -------------------------------------------------------------------
> >>>>>>>>>> -------
> >>>>>>>>>> ----------------------
> >>>>>>>>>> -------------------------------------------------------------------
> >>>>>>>>>> ------
> >>>>>>>>>> ----------------------- Forschungszentrum Juelich GmbH
> >>>>>>>>>> 52425 Juelich
> >>>>>>>>>> Sitz der Gesellschaft: Juelich
> >>>>>>>>>> Eingetragen im Handelsregister des Amtsgerichts Dueren
> >>>>>>>>>> Nr.
> >>>>>>>>>> HR
> >>>>>>>>>> B
> >>>>>>>>>> 3498
> >>>>>>>>>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen
> >>>>>>>>>> Huthmacher
> >>>>>>>>>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt
> >>>>>>>>>> (Vorsitzender),
> >>>>>>>>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing.
> >>>>>>>>>> Harald
> >>>>>>>>>> Bolt,
> >>>>>>>>>> Prof. Dr. Sebastian M. Schmidt
> >>>>>>>>>> -------------------------------------------------------------------
> >>>>>>>>>> -------
> >>>>>>>>>> ----------------------
> >>>>>>>>>> -------------------------------------------------------------------
> >>>>>>>>>> ------
> >>>>>>>>>> -----------------------
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> llvm-bgq-discuss mailing list
> >>>>>>>>>> llvm-bgq-discuss at lists.alcf.anl.gov
> >>>>>>>>>> https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> llvm-bgq-discuss mailing list
> >>>>>>>> llvm-bgq-discuss at lists.alcf.anl.gov
> >>>>>>>> https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> >>>>>>
> >>>>>> ------------------------------------------------------------------------
> >>>>>> ------------------------
> >>>>>> -----------------------------------------------------------------------
> >>>>>> ------------------------- Forschungszentrum Juelich GmbH
> >>>>>> 52425 Juelich
> >>>>>> Sitz der Gesellschaft: Juelich
> >>>>>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR
> >>>>>> B
> >>>>>> 3498
> >>>>>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen
> >>>>>> Huthmacher
> >>>>>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt
> >>>>>> (Vorsitzender),
> >>>>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald
> >>>>>> Bolt,
> >>>>>> Prof. Dr. Sebastian M. Schmidt
> >>>>>> ------------------------------------------------------------------------
> >>>>>> ------------------------
> >>>>>> -----------------------------------------------------------------------
> >>>>>> ------------------------->
> >>>>> --
> >>>>> Hal Finkel
> >>>>> Assistant Computational Scientist
> >>>>> Leadership Computing Facility
> >>>>> Argonne National Laboratory
> >>>>> _______________________________________________
> >>>>> llvm-bgq-discuss mailing list
> >>>>> llvm-bgq-discuss at lists.alcf.anl.gov
> >>>>> https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> >>>
> >>>
> >>> ------------------------------------------------------------------------------------------------
> >>> ------------------------------------------------------------------------------------------------
> >>> Forschungszentrum Juelich GmbH
> >>> 52425 Juelich
> >>> Sitz der Gesellschaft: Juelich
> >>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B
> >>> 3498
> >>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> >>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt
> >>> (Vorsitzender),
> >>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald
> >>> Bolt,
> >>> Prof. Dr. Sebastian M. Schmidt
> >>> ------------------------------------------------------------------------------------------------
> >>> ------------------------------------------------------------------------------------------------
> >>>
> >>>
> >>> _______________________________________________
> >>> llvm-bgq-discuss mailing list
> >>> llvm-bgq-discuss at lists.alcf.anl.gov
> >>> https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> >>>
> >>
> >> --
> >> Hal Finkel
> >> Assistant Computational Scientist
> >> Leadership Computing Facility
> >> Argonne National Laboratory
> >>
> >
> 

-- 
Hal Finkel
Assistant Computational Scientist
Leadership Computing Facility
Argonne National Laboratory