<p>Dear Barry:</p><p>I will try to do it according to your advice. I tried to incearse and reduce the processor number, some cases are broken, others aren't. This invalid read problem always exists. If the erros exist, the following is the broken information, </p>
<p>Invalid read can lead to the following errors? thanks.</p><p>"[6]PETSC ERROR: ------------------------------------------------------------------------<br>p2_15964: p4_error: net_recv read: probable EOF on socket: 1<br>
rm_l_2_15965: (354.724282) net_send: could not write to fd=5, errno = 32"<br></p><p>-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</p>
<p>==5821==<br>==5821== Invalid read of size 4<br>==5821== at 0x5143617: MatGetSubMatrix_MPIDense(_p_Mat*, _p_IS*, _p_IS*, int, MatReuse, _p_Mat**) (mpidense.c:251)<br>==5821== by 0x50C2D71: MatGetSubMatrix(_p_Mat*, _p_IS*, _p_IS*, int, MatReuse, _p_Mat**) (matrix.c:5744)<br>
==5821== by 0x805BCE8: mySystem::MakeA(int) (mySystem.C:518)<br>==5821== by 0x80615A6: mySystem::Source(mySystem*, int) (mySystem.C:1927)<br>==5821== by 0x806B5B1: main (myproject.C:293)<br>==5821== Address 0x8f06c64 is 12 bytes after a block of size 472,272 alloc'd<br>
==5821== at 0x401AC01: malloc (vg_replace_malloc.c:207)<br>==5821== by 0x558312D: PetscMallocAlign(unsigned int, int, char const*, char const*, char const*, void**) (mal.c:40)<br>==5821== by 0x558DA83: PetscTrMallocDefault(unsigned int, int, char const*, char const*, char const*, void**) (mtr.c:194)<br>
==5821== by 0x50386A7: MatSeqDenseSetPreallocation_SeqDense (dense.c:1875)<br>==5821== by 0x5038469: MatSeqDenseSetPreallocation(_p_Mat*, double*) (dense.c:1858)<br>==5821== by 0x514BC4B: MatMPIDenseSetPreallocation_MPIDense (mpidense.c:1175)<br>
==5821== by 0x514C889: MatMPIDenseSetPreallocation(_p_Mat*, double*) (mpidense.c:1312)<br>==5821== by 0x514AD8B: MatTranspose_MPIDense(_p_Mat*, _p_Mat**) (mpidense.c:979)<br>==5821== by 0x50B2D85: MatTranspose(_p_Mat*, _p_Mat**) (matrix.c:3603)<br>
==5821== by 0x805BCAA: mySystem::MakeA(int) (mySystem.C:514)<br>==5821== by 0x80615A6: mySystem::Source(mySystem*, int) (mySystem.C:1927)<br>==5821== by 0x806B5B1: main (myproject.C:293)<br></p><p>[6]PETSC ERROR: ------------------------------------------------------------------------<br>
p2_15964: p4_error: net_recv read: probable EOF on socket: 1<br>rm_l_2_15965: (354.724282) net_send: could not write to fd=5, errno = 32<br><br><br>==5821==<br>==5821== Invalid read of size 4<br>==5821== at 0x5143617: MatGetSubMatrix_MPIDense(_p_Mat*, _p_IS*, _p_IS*, int, MatReuse, _p_Mat**) (mpidense.c:251)<br>
==5821== by 0x50C2D71: MatGetSubMatrix(_p_Mat*, _p_IS*, _p_IS*, int, MatReuse, _p_Mat**) (matrix.c:5744)<br>==5821== by 0x805BCE8: mySystem::MakeA(int) (mySystem.C:518)<br>==5821== by 0x80615A6: mySystem::Source(mySystem*, int) (mySystem.C:1927)<br>
==5821== by 0x806B5B1: main (myproject.C:293)<br>==5821== Address 0x8f06c64 is 12 bytes after a block of size 472,272 alloc'd<br>==5821== at 0x401AC01: malloc (vg_replace_malloc.c:207)<br>==5821== by 0x558312D: PetscMallocAlign(unsigned int, int, char const*, char const*, char const*, void**) (mal.c:40)<br>
==5821== by 0x558DA83: PetscTrMallocDefault(unsigned int, int, char const*, char const*, char const*, void**) (mtr.c:194)<br>==5821== by 0x50386A7: MatSeqDenseSetPreallocation_SeqDense (dense.c:1875)<br>==5821== by 0x5038469: MatSeqDenseSetPreallocation(_p_Mat*, double*) (dense.c:1858)<br>
==5821== by 0x514BC4B: MatMPIDenseSetPreallocation_MPIDense (mpidense.c:1175)<br>==5821== by 0x514C889: MatMPIDenseSetPreallocation(_p_Mat*, double*) (mpidense.c:1312)<br>==5821== by 0x514AD8B: MatTranspose_MPIDense(_p_Mat*, _p_Mat**) (mpidense.c:979)<br>
==5821== by 0x50B2D85: MatTranspose(_p_Mat*, _p_Mat**) (matrix.c:3603)<br>==5821== by 0x805BCAA: mySystem::MakeA(int) (mySystem.C:514)<br>==5821== by 0x80615A6: mySystem::Source(mySystem*, int) (mySystem.C:1927)<br>==5821== by 0x806B5B1: main (myproject.C:293)<br>
<br>[6]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range<br>[6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger<br>[6]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[6]PETSC">http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[6]PETSC</a> ERROR: or try <a href="http://valgrind.org">http://valgrind.org</a> on linux or man libgmalloc on Apple to find memory corruption errors<br>
[6]PETSC ERROR: likely location of problem given in stack below<br>[6]PETSC ERROR: --------------------- Stack Frames ------------------------------------<br>[6]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,<br>
[6]PETSC ERROR: INSTEAD the line number of the start of the function<br>[6]PETSC ERROR: is given.<br>[6]PETSC ERROR: [6] MatGetSubMatrix_MPIDense line 218 src/mat/impls/dense/mpi/mpidense.c<br>[6]PETSC ERROR: [6] MatGetSubMatrix line 5721 src/mat/interface/matrix.c<br>
[6]PETSC ERROR: --------------------- Error Message ------------------------------------<br>[6]PETSC ERROR: Signal received!<br>[6]PETSC ERROR: ------------------------------------------------------------------------<br>[6]PETSC ERROR: Petsc Release Version 2.3.3, Patch 8, Fri Nov 16 17:03:40 CST 2007 HG revision: 414581156e67e55c761739b0deb119f7590d0f4b<br>
[6]PETSC ERROR: See docs/changes/index.html for recent updates.<br>[6]PETSC ERROR: See docs/faq.html for hints about trouble shooting.<br>[6]PETSC ERROR: See docs/index.html for manual pages.<br>[6]PETSC ERROR: ------------------------------------------------------------------------<br>
[6]PETSC ERROR: /data4/ylu/codes/new/examples/myproj/myproj-dbg on a linux named <a href="http://wolf29.cluster1.isl.org">wolf29.cluster1.isl.org</a> by yujie Tue Jan 6 16:20:55 2009<br>[6]PETSC ERROR: Libraries linked from /home/yujie/codes/petsc-2.3.3-p8/lib/linux<br>
[6]PETSC ERROR: Configure run at Fri Apr 11 17:24:03 2008<br>[6]PETSC ERROR: Configure options --with-mpi-dir=/home/yujie/mpich127/ --with-clanguage=C++ --with-debugging=1 --with-shared=1 --with-hypre=1 --with-spooles=1 --download-spooles=1 --with-superlu_dist=1 --download-superlu_dist=1<br>
[6]PETSC ERROR: ------------------------------------------------------------------------<br>[6]PETSC ERROR: User provided function() line 0 in unknown directory unknown file<br>p6_11637: p4_error: : 59<br>rm_l_6_11638: (333.669678) net_send: could not write to fd=5, errno = 32<br>
<br></p><br><div class="gmail_quote">On Tue, Jan 6, 2009 at 5:52 PM, Barry Smith <span dir="ltr"><<a href="mailto:bsmith@mcs.anl.gov">bsmith@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Looks like this is some old version of PETSc. The line numbers don't match PETSc 3.0.0<br>
Please switch to 3.0.0 and see if the problem occurs and send the valgrind output again<br>
<br>
Please switch to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a> for this.<br>
<br>
Barry<br>
<br>
I don't see a problem with the MatTranspose_ but there is a bad read in the MatGetSubMatrix<div><div class="Wj3C7c"><br>
<br>
On Jan 6, 2009, at 6:53 PM, Yujie wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
According to Barry's advice, I use Valgrind to check my codes. I find there is an problem in MatTranspose_MPIDense(). It breaks my codes. The following is the information. could you give me some advice? thanks a lot<br>
==5821==<br>
==5821== Invalid read of size 4<br>
==5821== at 0x5143617: MatGetSubMatrix_MPIDense(_p_Mat*, _p_IS*, _p_IS*, int, MatReuse, _p_Mat**) (mpidense.c:251)<br>
==5821== by 0x50C2D71: MatGetSubMatrix(_p_Mat*, _p_IS*, _p_IS*, int, MatReuse, _p_Mat**) (matrix.c:5744)<br>
==5821== by 0x805BCE8: mySystem::MakeA(int) (mySystem.C:518)<br>
==5821== by 0x80615A6: mySystem::Source(mySystem*, int) (mySystem.C:1927)<br>
==5821== by 0x806B5B1: main (myproject.C:293)<br>
==5821== Address 0x8f06c64 is 12 bytes after a block of size 472,272 alloc'd<br>
==5821== at 0x401AC01: malloc (vg_replace_malloc.c:207)<br>
==5821== by 0x558312D: PetscMallocAlign(unsigned int, int, char const*, char const*, char const*, void**) (mal.c:40)<br>
==5821== by 0x558DA83: PetscTrMallocDefault(unsigned int, int, char const*, char const*, char const*, void**) (mtr.c:194)<br>
==5821== by 0x50386A7: MatSeqDenseSetPreallocation_SeqDense (dense.c:1875)<br>
==5821== by 0x5038469: MatSeqDenseSetPreallocation(_p_Mat*, double*) (dense.c:1858)<br>
==5821== by 0x514BC4B: MatMPIDenseSetPreallocation_MPIDense (mpidense.c:1175)<br>
==5821== by 0x514C889: MatMPIDenseSetPreallocation(_p_Mat*, double*) (mpidense.c:1312)<br>
==5821== by 0x514AD8B: MatTranspose_MPIDense(_p_Mat*, _p_Mat**) (mpidense.c:979)<br>
==5821== by 0x50B2D85: MatTranspose(_p_Mat*, _p_Mat**) (matrix.c:3603)<br>
==5821== by 0x805BCAA: mySystem::MakeA(int) (mySystem.C:514)<br>
==5821== by 0x80615A6: mySystem::Source(mySystem*, int) (mySystem.C:1927)<br>
==5821== by 0x806B5B1: main (myproject.C:293)<br>
<br>
Regards,<br>
Yujie<br>
<br>
</blockquote>
<br>
</div></div></blockquote></div><br>