[Dune] error running code with MPI

Vogelbacher Florian Florian.Vogelbacher at psi.ch
Fri Sep 3 15:02:04 CEST 2010


Hello Christian,

no, I did not use this kind of flag :-)

I'm using an opts file to compile dune. Do I have to include it into the 
CXXFLAGS or somewhere else as well?

dune.opts.file:

CONFIGURE_FLAGS="CXX='mpicxx' CC='mpicc' LD='mpicxx' 
                     CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2' 
                            CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2'
LDFLAGS=' '
           --disable-documentation
           --enable-parallel
           --enable-debug-output
           --with-boost='$HOME/extlib-scratch3-felsim/boost-trunk'
           --with-metis='$HOME/extlib-scratch3-felsim/metis-4.0'
           --with-rlog='$HOME/extlib-scratch3-felsim/rlog-1.4'
           --with-alugrid='$HOME/extlib-scratch3-felsim/ALUGrid-1.22'"

Christian Engwer wrote:
> Hi  Florian,
> 
>> 1.) the system:
>> gcc (GCC) 4.3.1
>>
>> Linux felsim01 2.6.18-194.8.1.el5 #1 SMP Thu Jul 1 16:05:53 EDT 2010
>> x86_64 x86_64 x86_64 GNU/Linux
> 
> did you compile your code with -fno-strict-aliasing?
> 
> Christian
> 
>> mpirun (Open MPI) 1.3.3
>>
>>
>> 2.) the error:
>>
>> [...]
>> Created parallel ALUSimplexGrid<3,3> from macro grid file
>> '../../../grids/spherical-capacitor.dgf'.
>>
>> process[1] : #[total leaf element]=0
>> 2010-Sep-03 10:11:07.563938 ::: hades3delectrostatic.cc:   320 :::
>> PRODUCTION  #[total leaf element]=7863
>> 2010-Sep-03 10:11:07.564055 ::: hades3delectrostatic.cc:   323 :::
>> PRODUCTION  #[process in this run]=2
>> process[0] : #[total leaf element]=7863
>> 2010-Sep-03 10:11:07.564110 :::
>> ../globaldatainterface/globaldatainterface.hh:    75 ::: PRODUCTION
>> [ Get element tags from macro grid ...
>> 2010-Sep-03 10:11:07.567824 :::
>> ../globaldatainterface/globaldatainterface.hh:   134 ::: PRODUCTION
>> all element tags from macro grid are now available on cpu 0. ]
>> 2010-Sep-03 10:11:07.567973 ::: hades3delectrostatic.cc:   353 :::
>> PRODUCTION  [parallel - #[global refinement]=0
>> 2010-Sep-03 10:11:07.568019 ::: hades3delectrostatic.cc:   374 :::
>> PRODUCTION  [parallel - initiate load balance
>> 2010-Sep-03 10:11:07.568065 ::: hades3delectrostatic:
>> parallel/gitter_pll_sti.h:732: void ALUGridSpace::LinkedObject::Identifier::read(__gnu_cxx::__normal_iterator<const
>> int*, std::vector<int, std::allocator<int> > >&, const
>> __gnu_cxx::__normal_iterator<const int*, std::vector<int,
>> std::allocator<int> > >&): Assertion `pos != end' failed.
>> [felsim01:02544] *** Process received signal ***
>> hades3delectrostatic: parallel/gitter_pll_sti.h:732: void ALUGridSpace::LinkedObject::Identifier::read(__gnu_cxx::__normal_iterator<const
>> int*, std::vector<int, std::allocator<int> > >&, const
>> __gnu_cxx::__normal_iterator<const int*, std::vector<int,
>> std::allocator<int> > >&): Assertion `pos != end' failed.
>> [felsim01:02544] Signal: Aborted (6)
>> [felsim01:02544] Signal code:  (-6)
>> [felsim01:02543] *** Process received signal ***
>> [felsim01:02543] Signal: Aborted (6)
>> [felsim01:02543] Signal code:  (-6)
>> [felsim01:02543] [ 0] /lib64/libpthread.so.0 [0x35f8a0de60]
>> [felsim01:02543] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x35f7e30045]
>> [felsim01:02543] [ 2] /lib64/libc.so.6(abort+0x110) [0x35f7e31ae0]
>> [felsim01:02543] [ 3] /lib64/libc.so.6(__assert_fail+0xf6) [0x35f7e29756]
>> [felsim01:02543] [ 4] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace8identifyINS_6Gitter5hedgeEEEvNS_14AccessIteratorIT_E6HandleERSt6vectorISt4pairISt4listIS6_SaIS6_EESB_ESaISC_EERKNS_13MpAccessLocalE+0x1645)
>> [0x898de5]
>> [felsim01:02543] [ 5] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace9GitterPll14MacroGitterPll14identificationERNS_13MpAccessLocalE+0x386)
>> [0x82bd16]
>> [felsim01:02543] [ 6] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace9GitterPll22notifyMacroGridChangesEv+0x75)
>> [0x80eba5]
>> [felsim01:02543] [ 7] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace9GitterPll29loadBalancerGridChangesNotifyEv+0x448)
>> [0x8129a8]
>> [felsim01:02543] [ 8] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace13GitterDunePll15duneLoadBalanceEv+0xd)
>> [0x80c25d]
>> [felsim01:02543] [ 9]
>> ../../../hades3delectrostatic/hades3delectrostatic(main+0x199e)
>> [0x6369ae]
>> [felsim01:02543] [10] /lib64/libc.so.6(__libc_start_main+0xf4)
>> [0x35f7e1d8a4]
>> [felsim01:02543] [11] ../../../hades3delectrostatic/hades3delectrostatic(_ZNSt8ios_base4InitD1Ev+0x51)
>> [0x632b39]
>> [felsim01:02543] *** End of error message ***
>> [felsim01:02544] [ 0] /lib64/libpthread.so.0 [0x35f8a0de60]
>> [felsim01:02544] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x35f7e30045]
>> [felsim01:02544] [ 2] /lib64/libc.so.6(abort+0x110) [0x35f7e31ae0]
>> [felsim01:02544] [ 3] /lib64/libc.so.6(__assert_fail+0xf6) [0x35f7e29756]
>> [felsim01:02544] [ 4] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace8identifyINS_6Gitter5hedgeEEEvNS_14AccessIteratorIT_E6HandleERSt6vectorISt4pairISt4listIS6_SaIS6_EESB_ESaISC_EERKNS_13MpAccessLocalE+0x1645)
>> [0x898de5]
>> [felsim01:02544] [ 5] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace9GitterPll14MacroGitterPll14identificationERNS_13MpAccessLocalE+0x386)
>> [0x82bd16]
>> [felsim01:02544] [ 6] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace9GitterPll22notifyMacroGridChangesEv+0x75)
>> [0x80eba5]
>> [felsim01:02544] [ 7] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace9GitterPll29loadBalancerGridChangesNotifyEv+0x448)
>> [0x8129a8]
>> [felsim01:02544] [ 8] ../../../hades3delectrostatic/hades3delectrostatic(_ZN12ALUGridSpace13GitterDunePll15duneLoadBalanceEv+0xd)
>> [0x80c25d]
>> [felsim01:02544] [ 9]
>> ../../../hades3delectrostatic/hades3delectrostatic(main+0x199e)
>> [0x6369ae]
>> [felsim01:02544] [10] /lib64/libc.so.6(__libc_start_main+0xf4)
>> [0x35f7e1d8a4]
>> [felsim01:02544] [11] ../../../hades3delectrostatic/hades3delectrostatic(_ZNSt8ios_base4InitD1Ev+0x51)
>> [0x632b39]
>> [felsim01:02544] *** End of error message ***
>> --------------------------------------------------------------------------
>> mpirun noticed that process rank 1 with PID 2544 on node felsim01
>> exited on signal 6 (Aborted).
>> --------------------------------------------------------------------------
>>
>>

-- 
---------------------------
Paul Scherrer Institut
Florian Vogelbacher
WBCA/004
5232 Villigen PSI
Switzerland

Mail: 	Florian.Vogelbacher at psi.ch
Phone:	+41 (0) 563105019
Web:	www.psi.ch
---------------------------



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