[petsc-users] How to understand these error messages
Fande Kong
fd.kong at siat.ac.cn
Mon Jun 24 00:45:02 CDT 2013
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
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