[petsc-users] Petsc/3.5.0 make test failed

Fri Jul 25 15:55:08 CDT 2014

Wonderful! Thanks so much for all of your help!

Kai

On Fri, Jul 25, 2014 at 3:50 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   Well it is running. It is just producing annoying warning messages. You
> need to talk to your local MPI expert on that system for how to get rid of
> the problem.
>
>    Barry
>
> On Jul 25, 2014, at 3:23 PM, Kai Song <ksong at lbl.gov> wrote:
>
> > Hi Barry,
> >
> > I indeed deleted some of the OpenMPI related warning messages, it should
> be irrelevant. Here is the full output:
> > ======================
> > [kaisong at n0009 petsc-3.5.0]$ sh petsc-3.5.0-gcc.sh
> > Running test examples to verify correct installation
> > Using PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0
> and PETSC_ARCH=arch-linux2-c-debug
> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
> process
> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >
> --------------------------------------------------------------------------
> > WARNING: There is at least non-excluded one OpenFabrics device found,
> > but there are no active ports detected (or Open MPI was unable to use
> > them).  This is most certainly not what you wanted.  Check your
> > cables, subnet manager configuration, etc.  The openib BTL will be
> > ignored for this job.
> >
> >   Local host: n0009.scs00
> >
> --------------------------------------------------------------------------
> > lid velocity = 0.0016, prandtl # = 1, grashof # = 1
> > Number of SNES iterations = 2
> > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI
> processes
> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >
> --------------------------------------------------------------------------
> > WARNING: There is at least non-excluded one OpenFabrics device found,
> > but there are no active ports detected (or Open MPI was unable to use
> > them).  This is most certainly not what you wanted.  Check your
> > cables, subnet manager configuration, etc.  The openib BTL will be
> > ignored for this job.
> >
> >   Local host: n0009.scs00
> >
> --------------------------------------------------------------------------
> > lid velocity = 0.0016, prandtl # = 1, grashof # = 1
> > Number of SNES iterations = 2
> > [n0009.scs00:07638] 1 more process has sent help message
> help-mpi-btl-openib.txt / no active ports found
> > [n0009.scs00:07638] Set MCA parameter "orte_base_help_aggregate" to 0 to
> see all help / error messages
> > Possible error running Fortran example src/snes/examples/tutorials/ex5f
> with 1 MPI process
> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >
> --------------------------------------------------------------------------
> > WARNING: There is at least non-excluded one OpenFabrics device found,
> > but there are no active ports detected (or Open MPI was unable to use
> > them).  This is most certainly not what you wanted.  Check your
> > cables, subnet manager configuration, etc.  The openib BTL will be
> > ignored for this job.
> >
> >   Local host: n0009.scs00
> >
> --------------------------------------------------------------------------
> > Number of SNES iterations =     4
> > Completed test examples
> > =========================================
> > Now to evaluate the computer systems you plan use - do:
> > make PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0
> PETSC_ARCH=arch-linux2-c-debug streams NPMAX=<number of MPI processes you
> intend to use>
> > ======================
> >
> > I also followed your suggestion and built ex19 separately, and made sure
> using the same compiler that built petsc. Here is the complete output:
> > ======================
> > [kaisong at n0009 tutorials]$ mpiexec -n 2 ./ex19
> >
> --------------------------------------------------------------------------
> > WARNING: There is at least non-excluded one OpenFabrics device found,
> > but there are no active ports detected (or Open MPI was unable to use
> > them).  This is most certainly not what you wanted.  Check your
> > cables, subnet manager configuration, etc.  The openib BTL will be
> > ignored for this job.
> >
> >   Local host: n0009.scs00
> >
> --------------------------------------------------------------------------
> > lid velocity = 0.0625, prandtl # = 1, grashof # = 1
> > Number of SNES iterations = 2
> > [n0009.scs00:09124] 1 more process has sent help message
> help-mpi-btl-openib.txt / no active ports found
> > [n0009.scs00:09124] Set MCA parameter "orte_base_help_aggregate" to 0 to
> see all help / error messages
> > ======================
> >
> > Thanks,
> >
> > Kai
> >
> >
> >
> > On Fri, Jul 25, 2014 at 1:32 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> > On Jul 25, 2014, at 12:23 PM, Kai Song <ksong at lbl.gov> wrote:
> >
> > > Hi All,
> > >
> > > Thanks for all the suggestions! I took Satish's advice, removed the
> source, and did a fresh built.
> > >
> > > It got through the test compiling, but the tests failed as follow:
> > > ==================
> > > Running test examples to verify correct installation
> > > Using PETSC_DIR=/clusterfs/voltaire/home/software/modules/petsc/3.5.0
> and PETSC_ARCH=arch-linux2-c-debug
> > > 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
> > > Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2
> MPI processes
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > …
> >
> >    Surely it did not print … here? What was the complete message?
> >
> >    Usually this happens due to an incompatible mpiexec being used
> because it appears earlier in the path.
> >
> >    What happens if you do
> >
> > cd src/snes/examples/tutorials
> > make ex19
> > mpiexec -n 2 ./ex19
> >
> > for mpiexec use the one associated with the MPI that you built PETSc with
> >
> >   Barry
> >
> > > ==================
> > >
> > > I tried to go into src/snes/examples/tutorials/ex19, but didn't find
> any logs. Is this error for the test Okay?
> > >
> > > Thanks,
> > >
> > > Kai
> > >
> > >
> > >
> > > On Fri, Jul 25, 2014 at 11:06 AM, Satish Balay <balay at mcs.anl.gov>
> wrote:
> > > Its probably best to do a fresh build with the latest petsc-3.5.1
> tarball and see
> > > if the problem is reproduceable [with --with-shared-libraries=0]
> > >
> > > Satish
> > >
> > > On Fri, 25 Jul 2014, Jed Brown wrote:
> > >
> > > > Matthew Knepley <knepley at gmail.com> writes:
> > > >
> > > > > On Thu, Jul 24, 2014 at 5:33 PM, Kai Song <ksong at lbl.gov> wrote:
> > > > >
> > > > >> Hi Satish,
> > > > >>
> > > > >> Thanks for the quick response. I attached the make.log in this
> email, and
> > > > >> a quick glance, I didn't see any obvious errors.
> > > > >>
> > > > >
> > > > > This never built the MUMPS directory, even though you have
> PETSC_HAVE_MUMPS
> > > > > defined. I can see two
> > > > > possible reasons for this:
> > > > >
> > > > >   1) You distribution as missing files
> > > > >
> > > > >   2) You have two copies of PETSc fighting each other here (old
> PETSC_DIR?)
> > > > >
> > > > > Can you make sure you have the file mumps.c in
> > > > >
> > > > >   src/mat/impls/aij/mpi/mumps
> > > > >
> > > > > Jed, how do we check what make is doing here?
> > > >
> > > > mumps.c should be listed in $PETSC_ARCH/conf/files after the code
> > > > generator runs.  Possibly a file system problem or tinkering caused
> it
> > > > to appear up-to-date after reconfiguring?  (Just speculating because
> we
> > > > haven't seen this problem before.)
> > > >
> > >
> > >
> > >
> > >
> > > --
> > > Kai Song
> > > <ksong at lbl.gov> 1.510.495.2180
> > > 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209
> > > High Performance Computing Services (HPCS)
> > > Lawrence Berkeley National Laboratory - http://scs.lbl.gov
> >
> >
> >
> >
> > --
> > Kai Song
> > <ksong at lbl.gov> 1.510.495.2180
> > 1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209
> > High Performance Computing Services (HPCS)
> > Lawrence Berkeley National Laboratory - http://scs.lbl.gov
>
>

-- 
Kai Song
<ksong at lbl.gov> 1.510.495.2180
1 Cyclotron Rd. Berkeley, CA94720, MS-50B 3209
High Performance Computing Services (HPCS)
Lawrence Berkeley National Laboratory - http://scs.lbl.gov
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