[petsc-dev] plex error in next, new

Fri Oct 30 17:58:22 CDT 2015

> On Oct 30, 2015, at 3:55 PM, Satish Balay <balay at mcs.anl.gov> wrote:
> 
> The example runs fine - if I build & run manually. Something else must
> have caused malloc failure last night..

  Ok, thanks!

> 
> Satish
> 
> ---------
> 
> petsc at n-gage:~/petsc.test/src/dm/examples/tests$ env |grep PETSC
> PETSC_ARCH=arch-opensolaris-cmplx-pkgs-dbg
> PETSC_DIR=/export/home/petsc/petsc.test
> petsc at n-gage:~/petsc.test/src/dm/examples/tests$ make ex36
> /export/home/petsc/soft/mpich-3.1.3/bin/mpicc -o ex36.o -c -g  -I/export/home/petsc/petsc.test/include -I/export/home/petsc/petsc.test/arch-opensolaris-cmplx-pkgs-dbg/include -I/export/home/petsc/soft/mpich-3.1.3/include    `pwd`/ex36.c
> /export/home/petsc/soft/mpich-3.1.3/bin/mpicc -g  -o ex36 ex36.o  -R/export/home/petsc/petsc.test/arch-opensolaris-cmplx-pkgs-dbg/lib -L/export/home/petsc/petsc.test/arch-opensolaris-cmplx-pkgs-dbg/lib  -lpetsc -R/export/home/petsc/petsc.test/arch-opensolaris-cmplx-pkgs-dbg/lib -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lscalapack -lflapack -lfblas -lparmetis -lmetis -lssl -lcrypto -ltriangle -lX11 -lm -R/export/home/petsc/soft/mpich-3.1.3/lib -L/export/home/petsc/soft/mpich-3.1.3/lib -lmpifort -R/opt/SUNWspro/lib -L/opt/SUNWspro/lib -R/opt/SUNWspro/prod/lib -L/opt/SUNWspro/prod/lib -R/usr/ccs/lib -L/usr/ccs/lib -lfui -lfai -lfsu -lsunmath -lmtsk -lm -ldl -lmpicxx -lmpi -R/opt/SUNWspro/lib/rw7:/opt/SUNWspro/lib:/usr/ccs/lib:/lib:/usr/lib -lCstd -lCrun  -ldl  -lsocket -lnsl
> /usr/bin/rm -f -f ex36.o
> petsc at n-gage:~/petsc.test/src/dm/examples/tests$ make runex36_2dp1
> petsc at n-gage:~/petsc.test/src/dm/examples/tests$ make runex36_2dp1
> petsc at n-gage:~/petsc.test/src/dm/examples/tests$ make runex36_2dp1
> petsc at n-gage:~/petsc.test/src/dm/examples/tests$ 
> 
> 
> 
> On Fri, 30 Oct 2015, Satish Balay wrote:
> 
>> Hm - the error below is from wii (freebsd). But I don't see that in tonights
>> builds.
>> 
>> The opensolaris issues looks different [out of memory]. Thats wierd.
>> 
>> I'll check if I can reproduce..
>> 
>> Satish
>> 
>> On Fri, 30 Oct 2015, Barry Smith wrote:
>> 
>>> 
>>>  The log file is http://ftp.mcs.anl.gov/pub/petsc/nightlylogs/archive/2015/10/30/examples_next_arch-opensolaris-cmplx-pkgs-dbg_n-gage.log
>>> 
>>> hence the machine name is n-gage and the PETSC_ARCH is arch-opensolaris-cmplx-pkgs-dbg
>>> 
>>> 
>>>> On Oct 30, 2015, at 2:49 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>>> 
>>>> Cool. Which machine had the error you sent. I can't find it.
>>>> 
>>>>   Matt
>>>> 
>>>> On Oct 30, 2015 2:47 PM, "Barry Smith" <bsmith at mcs.anl.gov> wrote:
>>>> 
>>>>  Satish can provide more details on how you can easily run in the EXACT environment where something broke to debug it much faster.  The model is
>>>> 
>>>> 1)  ssh petsc at login.mcs.anl.gov
>>>> 
>>>> 2) ssh testmachine  (testmachine is always the end part of the name of the log file)
>>>> 
>>>> 3) cd to either  /sandbox/petsc/petsc.test  or /home/petsc/petsc.test depending on the machine
>>>> 
>>>> 4) git fetch
>>>> 
>>>> 5) git checkout the broken branch
>>>> 
>>>> 6) set PETSC_ARCH=arch of broken machine, this is in the name of the log filename
>>>> 
>>>> 7) ./config/examples/${PETSC_ARCH}.py
>>>> 
>>>> 8) build PETSc and debug away.
>>>> 
>>>>  If you have any trouble with this let Satish and I know. It is the intention that debugging on the test machines should be very straightforward and not require getting help from anyone or following convoluted instructions.
>>>> 
>>>>  Barry
>>>> 
>>>>> On Oct 30, 2015, at 2:15 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>>>> 
>>>>> I ran it through valgrind on my machine with no problems. Checking logs
>>>>> 
>>>>>   Matt
>>>>> 
>>>>> On Thu, Oct 29, 2015 at 5:09 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>> 
>>>>> <   [3] Roots referenced by my leaves, by rank
>>>>> < Symmetric gradient null space: PASS
>>>>> < Function tests pass for order 0 at tolerance 1e-10
>>>>> < Function tests pass for order 0 derivatives at tolerance 1e-10
>>>>> ---
>>>>>> [2]PETSC ERROR: #1 PetscCommDuplicate() line 178 in /usr/home/balay/petsc.clone-3/src/sys/objects/tagm.c
>>>>>> [2]PETSC ERROR: #2 PetscHeaderCreate_Private() line 60 in /usr/home/balay/petsc.clone-3/src/sys/objects/inherit.c
>>>>>> [2]PETSC ERROR: #3 PetscSFCreate() line 44 in /usr/home/balay/petsc.clone-3/src/vec/is/sf/interface/sf.c
>>>>>> [2]PETSC ERROR: #4 DMPlexDistribute() line 1562 in /usr/home/balay/petsc.clone-3/src/dm/impls/plex/plexdistribute.c
>>>>>> [2]PETSC ERROR: #5 CreateMesh() line 232 in /usr/home/balay/petsc.clone-3/src/dm/impls/plex/examples/tests/ex3.c
>>>>>> [2]PETSC ERROR: #6 main() line 911 in /usr/home/balay/petsc.clone-3/src/dm/impls/plex/examples/tests/ex3.c
>>>>>> [2]PETSC ERROR: PETSc Option Table entries:
>>>>>> [2]PETSC ERROR: -dim 3
>>>>>> [2]PETSC ERROR: -dm_plex_max_projection_height 2
>>>>>> [2]PETSC ERROR: -dm_view ascii::ASCII_INFO_DETAIL
>>>>>> [2]PETSC ERROR: -malloc_dump
>>>>>> [2]PETSC ERROR: -nox
>>>>>> [2]PETSC ERROR: -nox_warning
>>>>>> [2]PETSC ERROR: -num_comp 3
>>>>>> [2]PETSC ERROR: -petscpartitioner_type simple
>>>>>> [2]PETSC ERROR: -petscspace_order 1
>>>>>> [2]PETSC ERROR: -petscspace_poly_tensor
>>>>>> [2]PETSC ERROR: -qorder 1
>>>>>> [2]PETSC ERROR: -simplex 0
>>>>>> [2]PETSC ERROR: -test_fe_jacobian
>>>>>> [2]PETSC ERROR: -tree
>>>>>> [2]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>>>>>> [cli_2]: aborting job:
>>>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>>>>>> 
>>>>>> ===================================================================================
>>>>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>>>> =   PID 15231 RUNNING AT wii
>>>>>> =   EXIT CODE: 1
>>>>>> =   CLEANING UP REMAINING PROCESSES
>>>>>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>>>> ===================================================================================
>>>>> /usr/home/balay/petsc.clone-3/src/dm/impls/plex/examples/tests
>>>>> Possible problem with with runex3_nonconforming_tensor_3, diffs above
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>>>> -- Norbert Wiener
>>>> 
>>> 
>>> 
>> 
>> 
> 