[petsc-users] Petsc/3.5.0 make test failed

Fri Jul 25 15:23:14 CDT 2014

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
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