[petsc-dev] Error running on Titan with GPUs & GNU
Karl Rupp
rupp at iue.tuwien.ac.at
Wed Oct 31 05:59:38 CDT 2018
Hi Mark,
ah, I was confused by the Python information at the beginning of
configure.log. So it is picking up the correct compiler.
Have you tried uncommenting the check for GNU?
Best regards,
Karli
On 10/31/18 11:40 AM, Mark Adams wrote:
> It looks like configure is not finding the correct cc. It does not seem
> hard to find.
>
> 06:37 master= /lustre/atlas/proj-shared/geo127/petsc$ cc --version
> gcc (GCC) 6.3.0 20161221 (Cray Inc.)
> Copyright (C) 2016 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> 06:37 master= /lustre/atlas/proj-shared/geo127/petsc$ which cc
> /opt/cray/craype/2.5.13/bin/cc
> 06:38 master= /lustre/atlas/proj-shared/geo127/petsc$ which gcc
> /opt/gcc/6.3.0/bin/gcc
>
>
> On Wed, Oct 31, 2018 at 6:34 AM Mark Adams <mfadams at lbl.gov
> <mailto:mfadams at lbl.gov>> wrote:
>
>
>
> On Wed, Oct 31, 2018 at 5:05 AM Karl Rupp <rupp at iue.tuwien.ac.at
> <mailto:rupp at iue.tuwien.ac.at>> wrote:
>
> Hi Mark,
>
> please comment or remove lines 83 and 84 in
> config/BuildSystem/config/packages/cuda.py
>
> Is there a compiler newer than GCC 4.3 available?
>
>
> You mean 6.3?
>
> 06:33 ~$ module avail gcc
>
> -----------------------------------------------------
> /opt/modulefiles -----------------------------------------------------
> gcc/4.8.1 gcc/4.9.3 gcc/6.1.0
> gcc/6.3.0(default) gcc/7.2.0
> gcc/4.8.2 gcc/5.3.0 gcc/6.2.0 gcc/7.1.0
> gcc/7.3.0
>
>
> Best regards,
> Karli
>
>
>
> On 10/31/18 8:15 AM, Mark Adams via petsc-dev wrote:
> > After loading a cuda module ...
> >
> > On Wed, Oct 31, 2018 at 2:58 AM Mark Adams <mfadams at lbl.gov
> <mailto:mfadams at lbl.gov>
> > <mailto:mfadams at lbl.gov <mailto:mfadams at lbl.gov>>> wrote:
> >
> > I get an error with --with-cuda=1
> >
> > On Tue, Oct 30, 2018 at 4:44 PM Smith, Barry F.
> <bsmith at mcs.anl.gov <mailto:bsmith at mcs.anl.gov>
> > <mailto:bsmith at mcs.anl.gov <mailto:bsmith at mcs.anl.gov>>>
> wrote:
> >
> > --with-cudac=1 should be --with-cuda=1
> >
> >
> >
> > > On Oct 30, 2018, at 12:35 PM, Smith, Barry F. via
> petsc-dev
> > <petsc-dev at mcs.anl.gov <mailto:petsc-dev at mcs.anl.gov>
> <mailto:petsc-dev at mcs.anl.gov <mailto:petsc-dev at mcs.anl.gov>>>
> wrote:
> > >
> > >
> > >
> > >> On Oct 29, 2018, at 8:09 PM, Mark Adams
> <mfadams at lbl.gov <mailto:mfadams at lbl.gov>
> > <mailto:mfadams at lbl.gov <mailto:mfadams at lbl.gov>>> wrote:
> > >>
> > >> And a debug build seems to work:
> > >
> > > Well ok.
> > >
> > > Are there newer versions of the Gnu compiler
> for this
> > system? Are there any other compilers on the system
> that would
> > likely be less buggy? IBM compilers? If this simple code
> > generates a gross error with optimization who's to
> say how many
> > more subtle bugs may be induced in the library by the
> buggy
> > optimizer (there may be none but IMHO probability
> says there
> > will be others).
> > >
> > > Is there any chance that valgrind runs on this
> machine;
> > you could run the optimized version through it and
> see what it says.
> > >
> > > Barry
> > >
> > >>
> > >> 21:04 1 master=
> /lustre/atlas/proj-shared/geo127/petsc$ make
> >
> PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
> > PETSC_ARCH="" test
> > >> Running test examples to verify correct installation
> > >> Using
> >
> PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
> > and PETSC_ARCH=
> > >> *******************Error detected during compile or
> > link!*******************
> > >> See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
> > ex19
> > >>
> >
> *********************************************************************************
> > >> cc -o ex19.o -c -g
> >
> -I/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/include `pwd`/ex19.c
> > >> cc -g -o ex19 ex19.o
> >
> -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> >
> -Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> >
> -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> > -lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
> > In function `PetscDLOpen':
> > >>
> >
> /lustre/atlas1/geo127/proj-shared/petsc/src/sys/dll/dlimpl.c:108: warning:
> > Using 'dlopen' in statically linked applications
> requires at
> > runtime the shared libraries from the glibc version
> used for linking
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(send.o):
> > In function `PetscOpenSocket':
> > >>
> >
> /lustre/atlas1/geo127/proj-shared/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
> > warning: Using 'gethostbyname' in statically linked
> applications
> > requires at runtime the shared libraries from the
> glibc version
> > used for linking
> > >> true ex19
> > >> rm ex19.o
> > >> Possible error running C/C++
> > src/snes/examples/tutorials/ex19 with 1 MPI process
> > >> See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > >> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> > >> Number of SNES iterations = 2
> > >> Application 19081049 resources: utime ~1s, stime
> ~1s, Rss
> > ~17112, inblocks ~36504, outblocks ~111043
> > >> Possible error running C/C++
> > src/snes/examples/tutorials/ex19 with 2 MPI processes
> > >> See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > >> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> > >> Number of SNES iterations = 2
> > >> Application 19081050 resources: utime ~1s, stime
> ~1s, Rss
> > ~19816, inblocks ~36527, outblocks ~111043
> > >> 5a6
> > >>> Application 19081051 resources: utime ~1s, stime
> ~0s, Rss
> > ~13864, inblocks ~36527, outblocks ~111043
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
> > >> Possible problem with ex19_hypre, diffs above
> > >> =========================================
> > >> *******************Error detected during compile or
> > link!*******************
> > >> See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
> > ex5f
> > >>
> *********************************************************
> > >> ftn -c -g
> >
> -I/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/include
> > -o ex5f.o ex5f.F90
> > >> ftn -g -o ex5f ex5f.o
> >
> -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> >
> -Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> >
> -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> > -lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
> > In function `PetscDLOpen':
> > >>
> >
> /lustre/atlas1/geo127/proj-shared/petsc/src/sys/dll/dlimpl.c:108: warning:
> > Using 'dlopen' in statically linked applications
> requires at
> > runtime the shared libraries from the glibc version
> used for linking
> > >>
> >
> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(send.o):
> > In function `PetscOpenSocket':
> > >>
> >
> /lustre/atlas1/geo127/proj-shared/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
> > warning: Using 'gethostbyname' in statically linked
> applications
> > requires at runtime the shared libraries from the
> glibc version
> > used for linking
> > >> rm ex5f.o
> > >> Possible error running Fortran example
> > src/snes/examples/tutorials/ex5f with 1 MPI process
> > >> See
> http://www.mcs.anl.gov/petsc/documentation/faq.html
> > >> Number of SNES iterations = 4
> > >> Application 19081055 resources: utime ~1s, stime
> ~0s, Rss
> > ~12760, inblocks ~36800, outblocks ~111983
> > >> Completed test examples
> > >> 21:06 master= /lustre/atlas/proj-shared/geo127/petsc$
> > >
> >
>
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