[petsc-users] Re-initializing petsc again
Suraj Prabhakaran
suraj.prabhakaran at gmail.com
Wed Sep 4 11:22:36 CDT 2013
Dear Barry and Satish,
Thank you for your responses and help. I got it all cleared now.
If it will be interesting for you, what I am trying to do is spawn (using MPI_COMM_SPAWN) new processes and re-initialize petsc along with the parents and children in one communicator. At the moment, after a couple of tests, it seems to work fine with Petsc 3.4.0.
Best,
Suraj
On Sep 4, 2013, at 6:18 PM, Satish Balay wrote:
> On Wed, 4 Sep 2013, Barry Smith wrote:
>
>>
>>>> In file included from /opt/petsc-3.4.2/include/petsc.h:8,
>>>> from Main/time_integration_dir/compute_tau_w_mean.c:91:
>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
>>>> /opt/petsc-3.4.2/include/petscbt.h:33: error: invalid storage class for function ‘PetscBTLength’
>>>> /opt/petsc-3.4.2/include/petscbt.h:38: error: invalid storage class for function ‘PetscBTMemzero’
>>>> /opt/petsc-3.4.2/include/petscbt.h:43: error: invalid storage class for function ‘PetscBTDestroy’
>>
>>
>> Ok, nothing wrong with the static inline or build; There must be something wonky in compute_tau_w_mean.c or a file it includes that is causing the error.
>>
>> I would start debugging by removing stuff from compute_tau_w_mean.c before the #include "petsc.h" until the error goes away and that will show the culprit.
>
> Also you have a huge list of -I dirs. Make sure a wrong petscconf.h isn't getting
> included from one of these locations.
>
> I would do a 'make CFLAGS=-E' compute_tau_w_mean.o
>
> and look at the preprocessed 'PetscBTLength' reference in there.
>
> Also 'grep petscconf.h compute_tau_w_mean.o'
>
> Satish
>
>
>>
>> Barry
>>
>>
>>
>> On Sep 3, 2013, at 10:21 PM, Suraj Prabhakaran <suraj.prabhakaran at gmail.com> wrote:
>>
>>> Hi Barry,
>>>
>>> Thanks a lot! Here are the files attached.
>>>
>>> Suraj
>>>
>>> <configure.log><make.log>
>>>
>>> On Sep 4, 2013, at 5:13 AM, Barry Smith wrote:
>>>
>>>>
>>>> Something is going wrong with the PETSC_STATIC_INLINE definition. Please send configure.log and make.log
>>>>
>>>> Barry
>>>>
>>>> On Sep 3, 2013, at 10:01 PM, Suraj Prabhakaran <suraj.prabhakaran at gmail.com> wrote:
>>>>
>>>>> Thanks a lot for the confirmation!!
>>>>> I am now compiling it with 3.4.2, but I get a strange error and could be great if someone can just point out whats wrong. (Might be something stupid, but just in case...)
>>>>>
>>>>> Thanks in advance!
>>>>>
>>>>> Suraj
>>>>>
>>>>> -------------------------------ERROR-----------------------------
>>>>>
>>>>> In file included from /opt/petsc-3.4.2/include/petsc.h:8,
>>>>> from Main/time_integration_dir/compute_tau_w_mean.c:91:
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:33: error: invalid storage class for function ‘PetscBTLength’
>>>>> /opt/petsc-3.4.2/include/petscbt.h:38: error: invalid storage class for function ‘PetscBTMemzero’
>>>>> /opt/petsc-3.4.2/include/petscbt.h:43: error: invalid storage class for function ‘PetscBTDestroy’
>>>>> /opt/petsc-3.4.2/include/petscbt.h:48: error: invalid storage class for function ‘PetscBTLookup’
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTLookup’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:47: warning: declaration of ‘index’ shadows a global declaration
>>>>> /usr/include/string.h:489: warning: shadowed declaration is here
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:59: error: invalid storage class for function ‘PetscBTView’
>>>>> /opt/petsc-3.4.2/include/petscbt.h:74: error: invalid storage class for function ‘PetscBTCreate’
>>>>> /opt/petsc-3.4.2/include/petscbt.h:79: error: invalid storage class for function ‘PetscBTLookupSet’
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTLookupSet’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:78: warning: declaration of ‘index’ shadows a global declaration
>>>>> /usr/include/string.h:489: warning: shadowed declaration is here
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:91: error: invalid storage class for function ‘PetscBTSet’
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTSet’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:90: warning: declaration of ‘index’ shadows a global declaration
>>>>> /usr/include/string.h:489: warning: shadowed declaration is here
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:103: error: invalid storage class for function ‘PetscBTLookupClear’
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTLookupClear’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:102: warning: declaration of ‘index’ shadows a global declaration
>>>>> /usr/include/string.h:489: warning: shadowed declaration is here
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘compute_tau_w_mean’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:115: error: invalid storage class for function ‘PetscBTClear’
>>>>> /opt/petsc-3.4.2/include/petscbt.h: In function ‘PetscBTClear’:
>>>>> /opt/petsc-3.4.2/include/petscbt.h:114: warning: declaration of ‘index’ shadows a global declaration
>>>>> /usr/include/string.h:489: warning: shadowed declaration is here
>>>>> In file included from /opt/petsc-3.4.2/include/petsc.h:9,
>>>>> from Main/time_integration_dir/compute_tau_w_mean.c:91:
>>>>> /opt/petsc-3.4.2/include/petscctable.h: In function ‘compute_tau_w_mean’:
>>>>> /opt/petsc-3.4.2/include/petscctable.h:20: error: invalid storage class for function ‘PetscHash’
>>>>> /opt/petsc-3.4.2/include/petscctable.h:40: error: invalid storage class for function ‘PetscTableAdd’
>>>>> In file included from /opt/petsc-3.4.2/include/petsc.h:9,
>>>>> from Main/time_integration_dir/compute_tau_w_mean.c:91:
>>>>> /opt/petsc-3.4.2/include/petscctable.h:83: error: invalid storage class for function ‘PetscTableAddCount’
>>>>> /opt/petsc-3.4.2/include/petscctable.h:120: error: invalid storage class for function ‘PetscTableFind’
>>>>> In file included from /opt/petsc-3.4.2/include/petscsnesfas.h:3,
>>>>> from /opt/petsc-3.4.2/include/petsc.h:27,
>>>>> from Main/time_integration_dir/compute_tau_w_mean.c:91:
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:585: error: invalid storage class for function ‘SNESGetSNESLineSearch’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:586: error: invalid storage class for function ‘SNESSetSNESLineSearch’
>>>>> Main/time_integration_dir/compute_tau_w_mean.c:223: warning: implicit declaration of function ‘wall_thermoquants’
>>>>> Main/time_integration_dir/compute_tau_w_mean.c:155: warning: unused variable ‘iface_plus_one’
>>>>> Main/time_integration_dir/compute_tau_w_mean.c:330: warning: value computed is not used
>>>>> Main/time_integration_dir/compute_tau_w_mean.c:116: warning: unused variable ‘ierr’
>>>>> Main/time_integration_dir/compute_tau_w_mean.c:111: warning: unused variable ‘icell’
>>>>> Main/time_integration_dir/compute_tau_w_mean.c:105: warning: unused variable ‘mach’
>>>>> /opt/petsc-3.4.2/include/petscts.h:328: warning: unused variable ‘TSRegisterAllCalled’
>>>>> /opt/petsc-3.4.2/include/petscts.h:327: warning: unused variable ‘TSList’
>>>>> /opt/petsc-3.4.2/include/petscts.h:168: warning: unused variable ‘DMTS_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscts.h:167: warning: unused variable ‘TS_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscts.h:163: warning: unused variable ‘TSExactFinalTimeOptions’
>>>>> /opt/petsc-3.4.2/include/petscts.h:101: warning: unused variable ‘TSConvergedReasons’
>>>>> /opt/petsc-3.4.2/include/petscts.h:80: warning: unused variable ‘TSEquationTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnesfas.h:19: warning: unused variable ‘SNESFASTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:679: warning: unused variable ‘SNESQNRestartTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:675: warning: unused variable ‘SNESQNScaleTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:667: warning: unused variable ‘SNESNCGTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:654: warning: unused variable ‘SNESNGMRESSelectTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:648: warning: unused variable ‘SNESNGMRESRestartTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:474: warning: unused variable ‘SNESLineSearch_Apply’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:473: warning: unused variable ‘SNESLineSearchList’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:472: warning: unused variable ‘SNESLineSearchRegisterAllCalled’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:471: warning: unused variable ‘SNESLINESEARCH_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:470: warning: unused variable ‘SNESList’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:469: warning: unused variable ‘SNESRegisterAllCalled’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:356: warning: unused variable ‘SNESNormTypes’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:217: warning: unused variable ‘SNESConvergedReasons’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:50: warning: unused variable ‘DMSNES_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscsnes.h:49: warning: unused variable ‘SNES_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petsccharacteristic.h:44: warning: unused variable ‘CharacteristicList’
>>>>> /opt/petsc-3.4.2/include/petsccharacteristic.h:43: warning: unused variable ‘CharacteristicRegisterAllCalled’
>>>>> /opt/petsc-3.4.2/include/petscdmda.h:27: warning: unused variable ‘DMDABoundaryTypes’
>>>>> /opt/petsc-3.4.2/include/petscpf.h:50: warning: unused variable ‘PFRegisterAllCalled’
>>>>> /opt/petsc-3.4.2/include/petscpf.h:40: warning: unused variable ‘PF_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscpf.h:12: warning: unused variable ‘PFList’
>>>>> /opt/petsc-3.4.2/include/petscdm.h:34: warning: unused variable ‘DMRegisterAllCalled’
>>>>> /opt/petsc-3.4.2/include/petscdm.h:33: warning: unused variable ‘DMList’
>>>>> /opt/petsc-3.4.2/include/petscdm.h:11: warning: unused variable ‘DM_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscdraw.h:239: warning: unused variable ‘PETSC_DRAWHG_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscdraw.h:225: warning: unused variable ‘PETSC_DRAWSP_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscdraw.h:206: warning: unused variable ‘PETSC_DRAWLG_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscdraw.h:195: warning: unused variable ‘PETSC_DRAWAXIS_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscdraw.h:26: warning: unused variable ‘PetscDrawList’
>>>>> /opt/petsc-3.4.2/include/petscdraw.h:9: warning: unused variable ‘PETSC_DRAW_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscmatlab.h:8: warning: unused variable ‘MATLABENGINE_CLASSID’
>>>>> /opt/petsc-3.4.2/include/petscthreadcomm.h:35: warning: unused variable ‘PetscThreadCommReductionOps’
>>>>> /opt/petsc-3.4.2/include/petscthreadcomm.h:32: warning: unused variable ‘PetscThreadCommList’
>>>>>
>>>>>
>>>>>
>>>>> On Sep 3, 2013, at 9:03 PM, Satish Balay wrote:
>>>>>
>>>>>> Also you would have to call MPI_Init() before the first PetscInitialize() [and
>>>>>> similarly MPI_Finalize() after the last call to PetscFinalize()]
>>>>>>
>>>>>> Satish
>>>>>>
>>>>>> On Tue, 3 Sep 2013, Barry Smith wrote:
>>>>>>
>>>>>>>
>>>>>>> There is a problem with the 3.3 series when reinitializing PETSc. Can you switch to PETSc 3.4 which properly supports calling PetscInitialize() several times.
>>>>>>>
>>>>>>> Barry
>>>>>>>
>>>>>>> On Sep 3, 2013, at 1:58 PM, Suraj Prabhakaran <suraj.prabhakaran at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hello,
>>>>>>>>
>>>>>>>> Again, this relates to finalizing and initializing petsc in my application. I basically want to finalize petsc and initialize it again with a different MPI communicator. A rough sketch of my quite huge application is as follows.
>>>>>>>>
>>>>>>>>
>>>>>>>> main()
>>>>>>>> {
>>>>>>>> PetscInitialize()
>>>>>>>> ...
>>>>>>>> ...
>>>>>>>> AOCreate()..
>>>>>>>> AO operations..
>>>>>>>> AODestroy()..
>>>>>>>> ...
>>>>>>>> ...
>>>>>>>> PetscFinalize()
>>>>>>>> PETSC_COMM_WORLD = A new communicator (which includes more processes)
>>>>>>>> PetscInitialize()
>>>>>>>> ...
>>>>>>>> ...
>>>>>>>> AOCreate()..
>>>>>>>> AO operations..
>>>>>>>> AODestroy()
>>>>>>>> ...
>>>>>>>> ...
>>>>>>>> PetscFinalize()
>>>>>>>> }
>>>>>>>>
>>>>>>>> So after finalizing and initializing it back, I always get an error with one of the AO calls. Given below is the complete error I get when running with 8 procs. Can anyone give me a hint what the problem could be? I was told earlier, that finalizing and initializing petsc should not be a problem!
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Suraj
>>>>>>>>
>>>>>>>> -------------------------ERROR starts here-------------------------------
>>>>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>>>>>>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [0]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [0]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [0]PETSC ERROR: is given.
>>>>>>>> [0]PETSC ERROR: [0] PetscStrcmp line 414 /root/petsc/petsc-3.3-p7/src/sys/utils/str.c
>>>>>>>> [0]PETSC ERROR: [0] PetscFListAdd line 202 /root/petsc/petsc-3.3-p7/src/sys/dll/reg.c
>>>>>>>> [0]PETSC ERROR: [0] AORegister line 99 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/aoreg.c
>>>>>>>> [0]PETSC ERROR: [0] AORegisterAll line 28 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/aoregall.c
>>>>>>>> [0]PETSC ERROR: [0] AOInitializePackage line 49 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/dlregisdm.c
>>>>>>>> [0]PETSC ERROR: [0] AOCreate line 530 /root/petsc/petsc-3.3-p7/src/dm/ao/interface/ao.c
>>>>>>>> [0]PETSC ERROR: [0] AOCreateBasicIS line 381 /root/petsc/petsc-3.3-p7/src/dm/ao/impls/basic/aobasic.c
>>>>>>>> [0]PETSC ERROR: [0] AOCreateBasic line 336 /root/petsc/petsc-3.3-p7/src/dm/ao/impls/basic/aobasic.c
>>>>>>>> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [0]PETSC ERROR: Signal received!
>>>>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [0]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [0]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>>>>>>> with errorcode 59.
>>>>>>>>
>>>>>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>>>>>> You may or may not see output from other processes, depending on
>>>>>>>> exactly when Open MPI kills them.
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [1]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [1]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [1]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [1]PETSC ERROR: is given.
>>>>>>>> [1]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [1]PETSC ERROR: Signal received!
>>>>>>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [1]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [1]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [1]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [1]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [1]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [2]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [2]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [2]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [2]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [2]PETSC ERROR: is given.
>>>>>>>> [2]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [2]PETSC ERROR: Signal received!
>>>>>>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [2]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [2]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [2]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [2]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [2]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [2]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [2]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [3]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [3]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [3]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [3]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [3]PETSC ERROR: is given.
>>>>>>>> [3]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [3]PETSC ERROR: Signal received!
>>>>>>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [3]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [3]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [3]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [3]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [3]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [3]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> [4]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [4]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [4]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [4]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [4]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [4]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [4]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [4]PETSC ERROR: is given.
>>>>>>>> [4]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [4]PETSC ERROR: Signal received!
>>>>>>>> [4]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [4]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [4]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [4]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [4]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [4]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [4]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [4]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [4]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [4]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [4]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [4]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> [5]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [5]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [5]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [5]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [5]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [5]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [5]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [5]PETSC ERROR: is given.
>>>>>>>> [5]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [5]PETSC ERROR: Signal received!
>>>>>>>> [5]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [5]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [5]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [5]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [5]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [5]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [5]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [5]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [5]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [5]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [5]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [5]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> [6]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [6]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [6]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[6]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [6]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [6]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [6]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [6]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [6]PETSC ERROR: is given.
>>>>>>>> [6]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [6]PETSC ERROR: Signal received!
>>>>>>>> [6]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [6]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [6]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [6]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [6]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [6]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [6]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [6]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [6]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [6]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [6]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [6]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> [7]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [7]PETSC ERROR: Caught signal number 15 Terminate: Somet process (or the batch system) has told this process to end
>>>>>>>> [7]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>>>> [7]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[7]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>>>>>>> [7]PETSC ERROR: likely location of problem given in stack below
>>>>>>>> [7]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>>>>>>> [7]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>>>>>>> [7]PETSC ERROR: INSTEAD the line number of the start of the function
>>>>>>>> [7]PETSC ERROR: is given.
>>>>>>>> [7]PETSC ERROR: --------------------- Error Message ------------------------------------
>>>>>>>> [7]PETSC ERROR: Signal received!
>>>>>>>> [7]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [7]PETSC ERROR: Petsc Release Version 3.3.0, Patch 7, Sat May 11 22:15:24 CDT 2013
>>>>>>>> [7]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>>>>> [7]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>>>>> [7]PETSC ERROR: See docs/index.html for manual pages.
>>>>>>>> [7]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [7]PETSC ERROR: ./quadflow on a arch-linu named grsacc17 by grsprabh Tue Sep 3 20:56:21 2013
>>>>>>>> [7]PETSC ERROR: Libraries linked from /opt/petsc3.3-1/lib
>>>>>>>> [7]PETSC ERROR: Configure run at Mon Aug 19 13:56:50 2013
>>>>>>>> [7]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpiCC --download-f-blas-lapack --prefix=/opt/petsc3.3-1 --with-debugging
>>>>>>>> [7]PETSC ERROR: ------------------------------------------------------------------------
>>>>>>>> [7]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> mpiexec has exited due to process rank 0 with PID 2670 on
>>>>>>>> node grsacc17 exiting improperly. There are two reasons this could occur:
>>>>>>>>
>>>>>>>> 1. this process did not call "init" before exiting, but others in
>>>>>>>> the job did. This can cause a job to hang indefinitely while it waits
>>>>>>>> for all processes to call "init". By rule, if one process calls "init",
>>>>>>>> then ALL processes must call "init" prior to termination.
>>>>>>>>
>>>>>>>> 2. this process called "init", but exited without calling "finalize".
>>>>>>>> By rule, all processes that call "init" MUST call "finalize" prior to
>>>>>>>> exiting or it will be considered an "abnormal termination"
>>>>>>>>
>>>>>>>> This may have caused other processes in the application to be
>>>>>>>> terminated by signals sent by mpiexec (as reported here).
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
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