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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Dear All:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Question 1):</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>For an optimization task, I need to loop Petsc (I’m
using Petsc-2.3.0). But I had problems to reinitialize Petsc after finalize,
here is a simple FORTRAN program to explain my problem:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
program petsc_test</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'># include
"include/finclude/petsc.h"</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
call PetscInitialize(PETSC_NULL_CHARACTER, ierr)</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
call PetscFinalize(ierr)</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
print*,’ierr=’,ierr</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
call PetscInitialize(PETSC_NULL_CHARACTER, ierr)</span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>
call PetscFinalize(ierr)</span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> end</span></font></p>
<p class=MsoNormal><font size=2 face="Courier New"><span style='font-size:10.0pt;
font-family:"Courier New"'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>When the program excuted to the second PetscInitial line, it
shows error message: “Error encountered before initializing MPICH”.
Can anyone help me on this? Thanks.</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Question 2):</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Follow up my previous question, I also tried to Initiallize and
Finalize Petsc only once and perform the do-loop between Petscinitialize and PetscFinalize.
I used KSP CR solver with Prometheus PCs to solver large linear equations.
After several loops, the program was interrupted by segmentation violation
error. I suppose there was a memory leak somewhere. The error message is like
this: Any suggestion for this? Thanks</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>*********Doing job -- nosort0001</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Task No. 1 Total
CPU= 52.3 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> ---------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> *********Doing job -- nosort0002</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Task No. 2 Total
CPU= 52.1 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> ---------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> *********Doing job -- nosort0003</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>--------------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Petsc Release Version 2.3.0, Patch 44, </span></font><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>April, 26, 2005</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>See docs/changes/index.html for recent updates.</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>See docs/faq.html for hints about trouble shooting.</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>See docs/index.html for manual pages.</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-----------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>../feap on a linux-gnu named GPTnode3.cl.ghiocel-tech.com by
ltwang Mon Apr 24 </span></font><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>15:25:04</span></font><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'> 2006</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Libraries linked from
/home/ltwang/Library/petsc-2.3.0/lib/linux-gnu</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Configure run at Tue Mar 14 </span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>11:19:49</span></font><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'> 2006</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Configure options --with-mpi-dir=/usr --with-debugging=0
--download-spooles=1 --download-f-blas-lapack=1 --download-parmetis=1
--download-prometheus=1 --with-shared=0</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-----------------------------------------------------------------------</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: configure using --with-debugging=yes, recompile,
link, and run </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: to get more information on the crash.</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: User provided function() line 0 in unknown
directory unknown file</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: Signal received!</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[1]PETSC ERROR: !</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[cli_1]: aborting job:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>[cli_0]: aborting job:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Fatal error in MPI_Allgather: Other MPI error, error stack:</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPI_Allgather(949)........................: MPI_Allgather(sbuf=0xbffeea14,
scount=1, MPI_INT, rbuf=0x8bf0a0c, rcount=1, MPI_INT, comm=0x84000000) failed</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPIR_Allgather(180).......................: </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPIC_Sendrecv(161)........................: </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPIC_Wait(321)............................: </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPIDI_CH3_Progress_wait(199)..............: an error
occurred while handling an event returned by MPIDU_Sock_Wait()</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPIDI_CH3I_Progress_handle_sock_event(422): </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MPIDU_Socki_handle_read(649)..............: connection
failure (set=0,sock=2,errno=104:(strerror() not found))</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>rank 1 in job 477 GPTMaster_53830 caused
collective abort of all ranks</span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> exit status of rank 1: return code 59 </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Letian </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> </span></font></p>
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