On Sun, May 6, 2012 at 8:42 AM, Alexander Grayver <span dir="ltr"><<a href="mailto:agrayver@gfz-potsdam.de" target="_blank">agrayver@gfz-potsdam.de</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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On 06.05.2012 14:27, Matthew Knepley wrote:
<blockquote type="cite">On Sun, May 6, 2012 at 7:28 AM, Alexander Grayver <span dir="ltr"><<a href="mailto:agrayver@gfz-potsdam.de" target="_blank">agrayver@gfz-potsdam.de</a>></span>
wrote:<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hello,<br>
<br>
I use KSP and random rhs to compute largest singular value:<br>
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<div>1) Is this the whole program? If not, this can be caused by
memory corruption somewhere else. This is what I suspect.</div>
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<br>
Matt,<br>
<br>
I can reproduce error using attached test programm and this matrix
(7 mb):<br>
<a href="http://dl.dropbox.com/u/60982984/A.dat" target="_blank">http://dl.dropbox.com/u/60982984/A.dat</a></div></blockquote><div><br></div><div>I run it fine with the latest petsc-dev:</div><div><br></div><div> 1.405802e+00</div>
<div><br></div><div>Can you valgrind it on your machine?</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#ffffff" text="#000000">
<br>
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<br>
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<div>2) You can put in CHKMEMQ; throughout the code to find
exactly where the memory corruption happens.</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"> ! create solver and set options for
singular value estimation<br>
call KSPCreate(MPI_COMM_WORLD,ksp,ierr);CHKERRQ(ierr)<br>
call KSPSetType(ksp,KSPGMRES,ierr);CHKERRQ(ierr)<br>
call KSPSetTolerances(ksp,solvertol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,its,ierr);CHKERRQ(ierr)<br>
call KSPGMRESSetRestart(ksp, its, ierr);CHKERRQ(ierr)<br>
call KSPSetComputeSingularValues(ksp, flg,
ierr);CHKERRQ(ierr)<br>
call KSPSetFromOptions(ksp,ierr);CHKERRQ(ierr)<br>
<br>
! generate random RHS<br>
call PetscRandomCreate(PETSC_COMM_WORLD,rctx,ierr)<br>
call PetscRandomSetFromOptions(rctx,ierr)<br>
call VecSetRandom(b,rctx,ierr)<br>
<br>
!no preconditioning<br>
call KSPGetPC(ksp,pc,ierr);CHKERRQ(ierr)<br>
call PCSetType(pc,PCNONE,ierr);CHKERRQ(ierr)<br>
call KSPSetOperators(ksp,A,A,SAME_PRECONDITIONER,ierr);CHKERRQ(ierr)<br>
!solve system<br>
call KSPSolve(ksp,b,x,ierr);CHKERRQ(ierr)<br>
call KSPComputeExtremeSingularValues(ksp, smax, smin,
ierr);CHKERRQ(ierr)<br>
<br>
call KSPDestroy(ksp,ierr);CHKERRQ(ierr)<br>
<br>
However it crashes:<br>
<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range<br>
[1]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger<br>
[1]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC" target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC</a>
ERROR: or try <a href="http://valgrind.org" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to find memory corruption
errors<br>
[1]PETSC ERROR: PetscMallocValidate: error detected at
PetscDefaultSignalHandler() line 157 in
/home/lib/petsc-dev1/src/sys/error/signal.c<br>
[1]PETSC ERROR: Memory at address 0x4aa3f00 is corrupted<br>
[1]PETSC ERROR: Probably write past beginning or end of array<br>
[1]PETSC ERROR: Last intact block allocated in
KSPSetUp_GMRES() line 73 in /home/lib/petsc-dev1/src/ksp/ksp/impls/gmres/gmres.c<br>
[1]PETSC ERROR: --------------------- Error Message
------------------------------------<br>
[1]PETSC ERROR: Memory corruption!<br>
[1]PETSC ERROR: !<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: Petsc Development HG revision:
f3c119f7ddbfee243b51907a90acab15127ccb39 HG Date: Sun Apr 29
21:37:29 2012 -0500<br>
[1]PETSC ERROR: See docs/changes/index.html for recent
updates.<br>
[1]PETSC ERROR: See docs/faq.html for hints about trouble
shooting.<br>
[1]PETSC ERROR: See docs/index.html for manual pages.<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: /home/prog on a openmpi-i named node207 by
user Sun May 6 12:58:24 2012<br>
[1]PETSC ERROR: Libraries linked from
/home/lib/petsc-dev1/openmpi-intel-complex-debug-f/lib<br>
[1]PETSC ERROR: Configure run at Mon Apr 30 10:20:49 2012<br>
[1]PETSC ERROR: Configure options --with-blacs-include=/opt/intel/Compiler/11.1/072/mkl/include
--with-blacs-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a
--with-blas-lapack-lib="[/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.a,/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a,/opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.a]"
--with-fortran-interfaces=1 --with-mpi-dir=/opt/mpi/intel/openmpi-1.4.2
--with-petsc-arch=openmpi-intel-complex-debug-f
--with-precision=double --with-scalapack-include=/opt/intel/Compiler/11.1/072/mkl/include
--with-scalapack-lib=/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_scalapack_lp64.a
--with-scalar-type=complex --with-x=0
PETSC_ARCH=openmpi-intel-complex-debug-f<br>
[1]PETSC ERROR: ------------------------------------------------------------------------<br>
[1]PETSC ERROR: PetscMallocValidate() line 138 in
/home/lib/petsc-dev1/src/sys/memory/mtr.c<br>
[1]PETSC ERROR: PetscDefaultSignalHandler() line 157 in
/home/lib/petsc-dev1/src/sys/error/signal.c<br>
<br>
<br>
Call stack from debugger:<br>
<br>
opal_memory_ptmalloc2_int_free, FP=7fffd4765300<br>
opal_memory_ptmalloc2_free_hook, FP=7fffd4765330<br>
PetscFreeAlign, FP=7fffd4765370<br>
PetscTrFreeDefault, FP=7fffd4765520<br>
KSPReset_GMRES, FP=7fffd4765740<br>
KSPReset, FP=7fffd4765840<br>
KSPDestroy, FP=7fffd47659a0<br>
kspdestroy_, FP=7fffd47659d0<br>
<br>
<br>
Any ideas?<br>
<br>
Thanks.<span><font color="#888888"><br>
<br>
-- <br>
Regards,<br>
Alexander<br>
<br>
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<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
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-- <br>
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to
which their experiments lead.<br>
-- Norbert Wiener<br>
</font></span></blockquote><span class="HOEnZb"><font color="#888888">
<br>
<br>
<pre cols="72">--
Regards,
Alexander</pre>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br>