[petsc-users] How to understand these error messages
Fande Kong
fd.kong at siat.ac.cn
Mon Jun 24 02:53:58 CDT 2013
Hi Barry,
I switched to gnu compiler. I also got the similar results:
[330]PETSC ERROR: --------------------- Error Message
------------------------------------
[330]PETSC ERROR: Petsc has generated inconsistent data!
[330]PETSC ERROR: Negative MPI source: stash->nrecvs=27 i=33
MPI_SOURCE=-32766 MPI_TAG=-32766 MPI_ERROR=5243744!
[330]PETSC ERROR:
------------------------------------------------------------------------
[330]PETSC ERROR: Petsc Release Version 3.4.1, unknown
[330]PETSC ERROR: See docs/changes/index.html for recent updates.
[330]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[330]PETSC ERROR: See docs/index.html for manual pages.
[330]PETSC ERROR:
------------------------------------------------------------------------
[330]PETSC ERROR: ./linearElasticity on a arch-linux2-cxx-opt_gnu named
ys0554 by fandek Mon Jun 24 01:42:37 2013
[330]PETSC ERROR: Libraries linked from
/glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu/lib
[330]PETSC ERROR: Configure run at Mon Jun 24 00:34:40 2013
[330]PETSC ERROR: Configure options --with-valgrind=1 --with-clanguage=cxx
--with-shared-libraries=1 --with-dynamic-loading=1
--download-f-blas-lapack=1 --with-mpi=1 --download-parmetis=1
--download-metis=1 --with-64-bit-indices=1 --download-netcdf=1
--download-exodusii=1 --download-ptscotch=1 --download-hdf5=1
--with-debugging=no
[330]PETSC ERROR:
------------------------------------------------------------------------
[330]PETSC ERROR: MatStashScatterGetMesg_Private() line 633 in
/src/mat/utilsmatstash.c
[330]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 676 in
/src/mat/impls/aij/mpimpiaij.c
[330]PETSC ERROR: MatAssemblyEnd() line 4939 in /src/mat/interfacematrix.c
[330]PETSC ERROR: SpmcsDMMeshCreatVertexMatrix() line 65 in meshreorder.cpp
[330]PETSC ERROR: SpmcsDMMeshReOrderingMeshPoints() line 125 in
meshreorder.cpp
[330]PETSC ERROR: CreateProblem() line 59 in preProcessSetUp.cpp
[330]PETSC ERROR: DMmeshInitialize() line 78 in mgInitialize.cpp
[330]PETSC ERROR: main() line 71 in linearElasticity3d.cpp
Thus, I think that it has nothing to do with the compiler.
On Sun, Jun 23, 2013 at 11:45 PM, Fande Kong <fd.kong at siat.ac.cn> wrote:
> Thanks Barry，
>
> I will try impi.
>
> I have another question. In the previous email, you said If I can change
> to use another compiler. Why I need to change the compiler？
>
>
> On Mon, Jun 24, 2013 at 12:27 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> Fande,
>>
>> We've seen trouble before with IBM on large intel systems at scale.
>>
>> From the previous configure.log you sent I see
>>
>> sh: mpicc -show
>> Executing: mpicc -show
>> sh: /ncar/opt/intel/
>> 12.1.0.233/composer_xe_2011_sp1.11.339/bin/intel64/icc
>> -I/glade/apps/el6/include -I/glade/apps/el6/usr/include
>> -I/glade/apps/opt/netcdf/4.2/intel/default/include
>> -Wl,-rpath,/ncar/opt/intel/
>> 12.1.0.233/composer_xe_2011_sp1.11.339/compiler/lib/intel64 -Wl,-rpath,/ncar/opt/intel/
>> 12.1.0.233/composer_xe_2011_sp1.11.339/compiler/lib/ia32 -L/glade/apps/el6/usr/lib -L/glade/apps/el6/usr/lib64
>> -Wl,-rpath,/glade/apps/el6/usr/lib -Wl,-rpath,/glade/apps/el6/usr/lib64
>> -L/glade/apps/opt/netcdf/4.2/intel/default/lib -lnetcdf_c++4 -lnetcdff
>> -lnetcdf -Wl,-rpath,/glade/apps/opt/netcdf/4.2/intel/default/lib -m64
>> -D__64BIT__ -Wl,--allow-shlib-undefined -Wl,--enable-new-dtags
>> -Wl,-rpath,/opt/ibmhpc/pe1209/mpich2/intel/lib64 -Wl,-rpath,/ncar/opt/intel/
>> 12.1.0.233/composer_xe_2011_sp1.11.339/compiler/lib/intel64-I/opt/ibmhpc/pe1209/mpich2/intel/include64
>> -I/opt/ibmhpc/pe1209/base/include -L/opt/ibmhpc/pe1209/mpich2/intel/lib64
>> -lmpi -ldl -L/ncar/opt/intel/
>> 12.1.0.233/composer_xe_2011_sp1.11.339/compiler/lib/intel64 -lirc
>> -lpthread -lrt
>>
>> Note the -I/opt/ibmhpc/pe1209/base/include
>> -L/opt/ibmhpc/pe1209/mpich2/intel/lib64 -lmpi which is probably some IBM
>> hack job of some ancient mpich2
>>
>> Now the page
>> http://www2.cisl.ucar.edu/resources/yellowstone/software/modules-intel-dependent has the modules
>>
>>
>> impi/4.0.3.008 This module loads the Intel MPI Library. See
>> http://software.intel.com/en-us/intel-mpi-library/ for details.
>> impi/4.1.0.030 This module loads the Intel MPI Library. See
>> http://software.intel.com/en-us/intel-mpi-library/ for details.
>>
>> Perhaps you could load those modules with the Intel compilers and avoid
>> the IBM MPI? If that solves the problem then we know the IBM MPI is too
>> blame. We are interested in working with you to determine the problem.
>>
>> Barry
>>
>>
>>
>>
>> On Jun 23, 2013, at 9:14 PM, Fande Kong <fd.kong at siat.ac.cn> wrote:
>>
>> > Thanks Barry,
>> > Thanks Jed,
>> >
>> > The computer I am using is Yellowstone
>> http://en.wikipedia.org/wiki/Yellowstone_(supercomputer), or
>> http://www2.cisl.ucar.edu/resources/yellowstone. The compiler is
>> intel compiler. The mpi is IBM mpi which is a part of IBM PE.
>> >
>> > With less unknowns (about 5 \times 10^7), the code can correctly run.
>> With unknowns (4 \times 10^8), the code produced the error messages. But
>> with so large unknowns (4 \times 10^8), the code can also run with less
>> cores. This is very strange.
>> >
>> > When I switch to gnu compiler, I can not install petsc, I got the
>> following errors:
>> >
>> >
>> *******************************************************************************
>> > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log
>> for details):
>> >
>> -------------------------------------------------------------------------------
>> > Downloaded exodusii could not be used. Please check install in
>> /glade/p/work/fandek/petsc/arch-linux2-cxx-opt_gnu
>> >
>> *******************************************************************************
>> > File "./config/configure.py", line 293, in petsc_configure
>> > framework.configure(out = sys.stdout)
>> > File
>> "/glade/p/work/fandek/petsc/config/BuildSystem/config/framework.py", line
>> 933, in configure
>> > child.configure()
>> > File
>> "/glade/p/work/fandek/petsc/config/BuildSystem/config/package.py", line
>> 556, in configure
>> > self.executeTest(self.configureLibrary)
>> > File "/glade/p/work/fandek/petsc/config/BuildSystem/config/base.py",
>> line 115, in executeTest
>> > ret = apply(test, args,kargs)
>> > File
>> "/glade/p/work/fandek/petsc/config/BuildSystem/config/packages/exodusii.py",
>> line 36, in configureLibrary
>> > config.package.Package.configureLibrary(self)
>> > File
>> "/glade/p/work/fandek/petsc/config/BuildSystem/config/package.py", line
>> 484, in configureLibrary
>> > for location, directory, lib, incl in self.generateGuesses():
>> > File
>> "/glade/p/work/fandek/petsc/config/BuildSystem/config/package.py", line
>> 238, in generateGuesses
>> > raise RuntimeError('Downloaded '+self.package+' could not be used.
>> Please check install in '+d+'\n')
>> >
>> >
>> > The configure.log is attached.
>> >
>> > Regards,
>> > On Mon, Jun 24, 2013 at 1:03 AM, Jed Brown <jedbrown at mcs.anl.gov>
>> wrote:
>> > Barry Smith <bsmith at mcs.anl.gov> writes:
>> >
>> > > What kind of computer system are you running? What MPI does it
>> use? These values are nonsense MPI_SOURCE=-32766 MPI_TAG=-32766
>> >
>> > From configure.log, this is Intel MPI. Can you ask their support what
>> > this error condition is supposed to mean? It's not clear to me that
>> > MPI_SOURCE or MPI_TAG contain any meaningful information (though it
>> > could be indicative of an internal overflow), but this value of
>> > MPI_ERROR should mean something.
>> >
>> > > Is it possible to run the code with valgrind?
>> > >
>> > > Any chance of running the code with a different compiler?
>> > >
>> > > Barry
>> > >
>> > >
>> > >
>> > > On Jun 23, 2013, at 4:12 AM, Fande Kong <fd.kong at siat.ac.cn> wrote:
>> > >
>> > >> Thanks Jed,
>> > >>
>> > >> I added your code into the petsc. I run my code with 10240 cores. I
>> got the following error messages:
>> > >>
>> > >> [6724]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > >> [6724]PETSC ERROR: Petsc has generated inconsistent data!
>> > >> [6724]PETSC ERROR: Negative MPI source: stash->nrecvs=8 i=11
>> MPI_SOURCE=-32766 MPI_TAG=-32766 MPI_ERROR=20613892!
>> > >> [6724]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > >> [6724]PETSC ERROR: Petsc Release Version 3.4.1, unknown
>> > >> [6724]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > >> [6724]PETSC ERROR: See docs/faq.html for hints about trouble
>> shooting.
>> > >> [6724]PETSC ERROR: See docs/index.html for manual pages.
>> > >> [6724]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > >> [6724]PETSC ERROR: ./linearElasticity on a arch-linux2-cxx-debug
>> named ys4350 by fandek Sun Jun 23 02:58:23 2013
>> > >> [6724]PETSC ERROR: Libraries linked from
>> /glade/p/work/fandek/petsc/arch-linux2-cxx-debug/lib
>> > >> [6724]PETSC ERROR: Configure run at Sun Jun 23 00:46:05 2013
>> > >> [6724]PETSC ERROR: Configure options --with-valgrind=1
>> --with-clanguage=cxx --with-shared-libraries=1 --with-dynamic-loading=1
>> --download-f-blas-lapack=1 --with-mpi=1 --d
>> > >> ownload-parmetis=1 --download-metis=1 --with-64-bit-indices=1
>> --download-netcdf=1 --download-exodusii=1 --download-ptscotch=1
>> --download-hdf5=1 --with-debugging=yes
>> > >> [6724]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > >> [6724]PETSC ERROR: MatStashScatterGetMesg_Private() line 633 in
>> /src/mat/utilsmatstash.c
>> > >> [6724]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 676 in
>> /src/mat/impls/aij/mpimpiaij.c
>> > >> [6724]PETSC ERROR: MatAssemblyEnd() line 4939 in
>> /src/mat/interfacematrix.c
>> > >> [6724]PETSC ERROR: SpmcsDMMeshCreatVertexMatrix() line 65 in
>> meshreorder.cpp
>> > >> [6724]PETSC ERROR: SpmcsDMMeshReOrderingMeshPoints() line 125 in
>> meshreorder.cpp
>> > >> [6724]PETSC ERROR: CreateProblem() line 59 in preProcessSetUp.cpp
>> > >> [6724]PETSC ERROR: DMmeshInitialize() line 78 in mgInitialize.cpp
>> > >> [6724]PETSC ERROR: main() line 71 in linearElasticity3d.cpp
>> > >> Abort(77) on node 6724 (rank 6724 in comm 1140850688): application
>> called MPI_Abort(MPI_COMM_WORLD, 77) - process 6724
>> > >> [2921]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > >> [2921]PETSC ERROR: Petsc has generated inconsistent data!
>> > >> [2921]PETSC ERROR: Negative MPI source: stash->nrecvs=15 i=3
>> MPI_SOURCE=-32766 MPI_TAG=-32766 MPI_ERROR=3825270!
>> > >> [2921]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > >> [2921]PETSC ERROR: Petsc Release Version 3.4.1, unknown
>> > >> [2921]PETSC ERROR: See docs/changes/index.html for recent updates.
>> > >> [2921]PETSC ERROR: See docs/faq.html for hints about trouble
>> shooting.
>> > >> [2921]PETSC ERROR: See docs/index.html for manual pages.
>> > >> [2921]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > >> [2921]PETSC ERROR: ./linearElasticity on a arch-linux2-cxx-debug
>> named ys0270 by fandek Sun Jun 23 02:58:23 2013
>> > >> [2921]PETSC ERROR: Libraries linked from
>> /glade/p/work/fandek/petsc/arch-linux2-cxx-debug/lib
>> > >> [2921]PETSC ERROR: Configure run at Sun Jun 23 00:46:05 2013
>> > >> [2921]PETSC ERROR: Configure options --with-valgrind=1
>> --with-clanguage=cxx --with-shared-libraries=1 --with-dynamic-loading=1
>> --download-f-blas-lapack=1 --with-mpi=1 --download-parmetis=1
>> --download-metis=1 --with-64-bit-indices=1 --download-netcdf=1
>> --download-exodusii=1 --download-ptscotch=1 --download-hdf5=1
>> --with-debugging=yes
>> > >> [2921]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > >> [2921]PETSC ERROR: MatStashScatterGetMesg_Private() line 633 in
>> /src/mat/utilsmatstash.c
>> > >> [2921]PETSC ERROR: MatAssemblyEnd_MPIAIJ() line 676 in
>> /src/mat/impls/aij/mpimpiaij.c
>> > >> [2921]PETSC ERROR: MatAssemblyEnd() line 4939 in
>> /src/mat/interfacematrix.c
>> > >> [2921]PETSC ERROR: SpmcsDMMeshCreatVertexMatrix() line 65 in
>> meshreorder.cpp
>> > >> [2921]PETSC ERROR: SpmcsDMMeshReOrderingMeshPoints() line 125 in
>> meshreorder.cpp
>> > >> [2921]PETSC ERROR: CreateProblem() line 59 in preProcessSetUp.cpp
>> > >> [2921]PETSC ERROR: DMmeshInitialize() line 78 in mgInitialize.cpp
>> > >> [2921]PETSC ERROR: main() line 71 in linearElasticity3d.cpp
>> > >> :
>> > >>
>> > >> On Fri, Jun 21, 2013 at 4:33 AM, Jed Brown <jedbrown at mcs.anl.gov>
>> wrote:
>> > >> Fande Kong <fd.kong at siat.ac.cn> writes:
>> > >>
>> > >> > The code works well with less cores. And It also works well with
>> > >> > petsc-3.3-p7. But it does not work with petsc-3.4.1. Thus, If you
>> can check
>> > >> > the differences between petsc-3.3-p7 and petsc-3.4.1, you can
>> figure out
>> > >> > the reason.
>> > >>
>> > >> That is one way to start debugging, but there are no changes to the
>> core
>> > >> MatStash code, and many, many changes to PETSc in total. The
>> relevant
>> > >> snippet of code is here:
>> > >>
>> > >> if (stash->reproduce) {
>> > >> i = stash->reproduce_count++;
>> > >> ierr =
>> MPI_Wait(stash->recv_waits+i,&recv_status);CHKERRQ(ierr);
>> > >> } else {
>> > >> ierr =
>> MPI_Waitany(2*stash->nrecvs,stash->recv_waits,&i,&recv_status);CHKERRQ(ierr);
>> > >> }
>> > >> if (recv_status.MPI_SOURCE < 0)
>> SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Negative MPI source!");
>> > >>
>> > >> So MPI returns correctly (stash->reproduce will be FALSE unless you
>> > >> changed it). You could change the line above to the following:
>> > >>
>> > >> if (recv_status.MPI_SOURCE < 0)
>> SETERRQ5(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Negative MPI source:
>> stash->nrecvs=%D i=%d MPI_SOURCE=%d MPI_TAG=%d MPI_ERROR=%d",
>> > >>
>> stash->nrecvs,i,recv_status.MPI_SOURCE,recv_status.MPI_TAG,recv_status.MPI_ERROR);
>> > >>
>> > >>
>> > >> It would help to debug --with-debugging=1, so that more checks for
>> > >> corrupt data are performed. You can still make the compiler
>> optimize if
>> > >> it takes a long time to reach the error condition.
>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> Fande Kong
>> > >> ShenZhen Institutes of Advanced Technology
>> > >> Chinese Academy of Sciences
>> >
>> >
>> >
>> > --
>> > Fande Kong
>> > ShenZhen Institutes of Advanced Technology
>> > Chinese Academy of Sciences
>> > <configure.zip>
>>
>>
>>
>
>
> --
> Fande Kong
> ShenZhen Institutes of Advanced Technology
> Chinese Academy of Sciences
>
--
Fande Kong
ShenZhen Institutes of Advanced Technology
Chinese Academy of Sciences
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