[aspect-devel] Aspect hangs after several time steps
Lev Karatun
lev.karatun at gmail.com
Mon Feb 22 14:59:39 PST 2016
Hi again,
so I simplified the setup (prm file attached) to the point when I have a
box with a single compositional field, tangential velocity b.c. for all 6
faces, constant temperature throughout the entire box - so I'm literally
modelling a constant state of material with nothing happening. And the
simulation fails with the error " The residual in the last step was nan".
However, if I delete the compositional fields from the input file, the
simulation runs fine.
What can be causing this?..
Best regards,
Lev Karatun.
2016-02-22 0:07 GMT-05:00 Lev Karatun <lev.karatun at gmail.com>:
> Hi Timo,
>
> I've simplified the model to the extreme, and still the solver doesn't
> converge (The residual in the last step was nan). It's not even using any
> of the plugins that I used, so I'm really confused. The cookbooks, however,
> run without problems. (and my model in release mode runs successfully too)
>
> I'm trying to run the models on a lab computer, single core. I attached
> the prm file that I'm using, could you have a look please?
> Thanks in advance!
>
> Best regards,
> Lev Karatun.
>
> 2016-02-12 9:10 GMT-05:00 Timo Heister <heister at clemson.edu>:
>
>> Lev,
>>
>> your system setup (compiler, operating system, standard libraries)
>> doesn't allow for the debugging trick to detect floating point
>> exceptions. You could try a recent version of clang (or gcc if you
>> were using clang) and see. Sorry, I don't know a sure way to get this
>> enabled (I have no problems with it on ubuntu 14.04 using gcc or
>> clang).
>>
>> That said, convergence failures can have other reasons not detectable
>> using this technique. It is hard to tell, but you should probably
>> simplify your test problem and if it works, increase the complexity
>> one by one. Do the included files like convection-box or shell 2d/3d
>> work correctly on your machine (is it a cluster?)?
>>
>> Best,
>> Timo
>>
>> On Fri, Feb 12, 2016 at 5:21 AM, Lev Karatun <lev.karatun at gmail.com>
>> wrote:
>> > Hi Wolfgang,
>> >
>> > I fixed the issues that Timo pointed out, but I'm still getting the
>> "did not
>> > converge" error. Is there a way for me to debug it the same way Timo
>> did?
>> > What am I missing? A compiler with C++11 support? Something else?
>> >
>> > Best regards,
>> > Lev Karatun.
>> >
>> > 2016-02-03 9:20 GMT-05:00 Wolfgang Bangerth <bangerth at tamu.edu>:
>> >>
>> >>
>> >> Lev,
>> >> this is complicated.
>> >>
>> >> You switched on floating point signals by hand, but your compiler
>> support
>> >> library has functions that trip this, so your program gets stopped in a
>> >> place that is outside anyone's control (and where it doesn't actually
>> matter
>> >> much). This is why floating point exceptions were disabled
>> automatically
>> >> when you ran the ASPECT cmake script. In other words, to make
>> progress, you
>> >> need to disable floating point exceptions again.
>> >>
>> >> Of course, without being able to run FPE on your system, you won't be
>> able
>> >> to reproduce the issues Timo found on his system. But you don't have
>> to find
>> >> these issues -- he already did that for you. Just fix these places and
>> you
>> >> should be able to make progress.
>> >>
>> >> Best
>> >> W.
>> >>
>> >>
>> >> On 02/01/2016 11:00 PM, Lev Karatun wrote:
>> >>>
>> >>> Hi Wolfgang,
>> >>>
>> >>> I've tried this, the last stack frame is:
>> >>>
>> >>> #13 0x00000000012e50d5 in main (argc=2, argv=0x7fffffffe128) at
>> >>> /home/lev/aspect/aspect_debug_new/source/main.cc:513
>> >>>
>> >>>
>> >>> The 513 line in main.cc is:
>> >>>
>> >>> aspect::Simulator<3>::declare_parameters(prm);
>> >>>
>> >>>
>> >>> Looks like it stops at the attempt of reading the Start time line:
>> >>>
>> >>> #10 0x00007ffff537a569 in dealii::ParameterHandler::declare_entry
>> >>> (this=0x7fffffffdc90, entry="Start time", default_value="0",
>> >>> pattern=...,
>> >>> documentation=
>> >>> "The start time of the simulation. Units: Years if the 'Use
>> >>> years in
>> >>> output instead of seconds' parameter is set; seconds otherwise.")
>> >>> at
>> >>>
>> >>>
>> /home/lev/distrib/dealii_debug_new/source/base/parameter_handler.cc:1628
>> >>>
>> >>>
>> >>> but it's just "set Start time = 0", I never changed it.
>> >>>
>> >>> Full backtrace:
>> >>>
>> >>> Program received signal SIGFPE, Arithmetic exception.
>> >>> __mpn_lshift () at ../sysdeps/x86_64/lshift.S:26
>> >>> 26 movq -8(%rsi,%rdx,8), %mm7
>> >>> (gdb) bt
>> >>> #0 __mpn_lshift () at ../sysdeps/x86_64/lshift.S:26
>> >>> #1 0x0000003db304a53e in ___printf_fp (fp=0x7fffffff71b0,
>> >>> info=0x7fffffff70b0, args=<value optimized out>) at
>> printf_fp.c:483
>> >>> #2 0x0000003db30458a0 in _IO_vfprintf_internal (s=<value
>> optimized
>> >>> out>,
>> >>> format=<value optimized out>, ap=<value optimized out>) at
>> >>> vfprintf.c:1640
>> >>> #3 0x0000003db306f752 in _IO_vsnprintf (string=0x7fffffff7420 "",
>> >>> maxlen=<value optimized out>, format=0x7fffffff74f0 "%.*g",
>> >>> args=0x7fffffff7310)
>> >>> at vsnprintf.c:120
>> >>> #4 0x0000003dbd87eb4f in std::__convert_from_v (__cloc=<value
>> >>> optimized
>> >>> out>, __out=0x7fffffff7420 "", __size=45, __fmt=0x7fffffff74f0
>> >>> "%.*g")
>> >>> at
>> >>>
>> >>>
>> /usr/src/debug/gcc-4.4.7-20120601/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/x86_64-redhat-linux/bits/c++locale.h:89
>> >>> #5 0x0000003dbd880f23 in std::num_put<char,
>> >>> std::ostreambuf_iterator<char, std::char_traits<char> >
>> >>> >::_M_insert_float<double> (this=0x3dbdaf22e0, __s=..., __io=
>> >>> ..., __fill=32 ' ', __mod=<value optimized out>,
>> >>> __v=-1.7976931348623157e+308)
>> >>> at
>> >>>
>> >>>
>> /usr/src/debug/gcc-4.4.7-20120601/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/locale_facets.tcc:980
>> >>> #6 0x0000003dbd881249 in std::num_put<char,
>> >>> std::ostreambuf_iterator<char, std::char_traits<char> > >::do_put
>> >>> (this=<value optimized out>, __s=...,
>> >>> __io=<value optimized out>, __fill=<value optimized out>,
>> >>> __v=<value
>> >>> optimized out>)
>> >>> at
>> >>>
>> >>>
>> /usr/src/debug/gcc-4.4.7-20120601/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/locale_facets.tcc:1127
>> >>> #7 0x0000003dbd89487f in put (this=0x7fffffff7630,
>> >>> __v=-1.7976931348623157e+308)
>> >>> at
>> >>>
>> >>>
>> /usr/src/debug/gcc-4.4.7-20120601/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/locale_facets.h:2390
>> >>> #8 std::basic_ostream<char, std::char_traits<char>
>> >>> >::_M_insert<double>
>> >>> (this=0x7fffffff7630, __v=-1.7976931348623157e+308)
>> >>> at
>> >>>
>> >>>
>> /usr/src/debug/gcc-4.4.7-20120601/obj-x86_64-redhat-linux/x86_64-redhat-linux/libstdc++-v3/include/bits/ostream.tcc:73
>> >>> #9 0x00007ffff5373468 in dealii::Patterns::Double::description
>> >>> (this=0x1f92620) at
>> >>>
>> >>>
>> /home/lev/distrib/dealii_debug_new/source/base/parameter_handler.cc:290
>> >>> #10 0x00007ffff537a569 in dealii::ParameterHandler::declare_entry
>> >>> (this=0x7fffffffdc90, entry="Start time", default_value="0",
>> >>> pattern=...,
>> >>> documentation=
>> >>> "The start time of the simulation. Units: Years if the 'Use
>> >>> years in
>> >>> output instead of seconds' parameter is set; seconds otherwise.")
>> >>> at
>> >>>
>> >>>
>> /home/lev/distrib/dealii_debug_new/source/base/parameter_handler.cc:1628
>> >>> #11 0x000000000103fef2 in
>> aspect::Parameters<3>::declare_parameters
>> >>> (prm=...) at
>> >>>
>> /home/lev/aspect/aspect_debug_new/source/simulator/parameters.cc:88
>> >>> #12 0x000000000104e2e8 in aspect::Simulator<3>::declare_parameters
>> >>> (prm=...) at
>> >>>
>> /home/lev/aspect/aspect_debug_new/source/simulator/parameters.cc:1283
>> >>> #13 0x00000000012e50d5 in main (argc=2, argv=0x7fffffffe128) at
>> >>> /home/lev/aspect/aspect_debug_new/source/main.cc:513
>> >>>
>> >>>
>> >>>
>> >>> Best regards,
>> >>> Lev Karatun.
>> >>>
>> >>> 2016-02-01 21:34 GMT-05:00 Wolfgang Bangerth <bangerth at tamu.edu
>> >>> <mailto:bangerth at tamu.edu>>:
>> >>>
>> >>> On 02/01/2016 06:42 PM, Lev Karatun wrote:
>> >>>
>> >>>
>> >>> Could you please tell me what I'm doing wrong?..
>> >>> Thanks in advance.
>> >>>
>> >>>
>> >>> I don't think you *need* any of these packages. You may not get to
>> >>> see the
>> >>> exact location where the error happened in BLAS or some other
>> >>> low-level
>> >>> library, but ultimately you only want to know the place where you
>> >>> were in
>> >>> your own code. In other words, if the debugger stops at the
>> location
>> >>> where
>> >>> the error happens, get a backtrace and go to the last stack frame
>> in
>> >>> your
>> >>> code. Your task is then to find out what is wrong in that line.
>> >>>
>> >>> Best
>> >>> W.
>> >>>
>> >>> --
>> >>>
>> >>>
>> ------------------------------------------------------------------------
>> >>> Wolfgang Bangerth email: bangerth at math.tamu.edu
>> >>> <mailto:bangerth at math.tamu.edu>
>> >>> www:
>> >>> http://www.math.tamu.edu/~bangerth/
>> >>>
>> >>> _______________________________________________
>> >>> Aspect-devel mailing list
>> >>> Aspect-devel at geodynamics.org <mailto:Aspect-devel at geodynamics.org
>> >
>> >>>
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> _______________________________________________
>> >>> Aspect-devel mailing list
>> >>> Aspect-devel at geodynamics.org
>> >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>> >>>
>> >>
>> >>
>> >> --
>> >>
>> ------------------------------------------------------------------------
>> >> Wolfgang Bangerth email:
>> bangerth at math.tamu.edu
>> >> www:
>> http://www.math.tamu.edu/~bangerth/
>> >>
>> >> _______________________________________________
>> >> Aspect-devel mailing list
>> >> Aspect-devel at geodynamics.org
>> >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>> >
>> >
>> >
>> > _______________________________________________
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>>
>>
>>
>> --
>> Timo Heister
>> http://www.math.clemson.edu/~heister/
>> _______________________________________________
>> Aspect-devel mailing list
>> Aspect-devel at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>
>
>
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