<div dir="ltr"><br><br><div class="gmail_quote">On Sun, May 13, 2012 at 5:30 PM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Sun, May 13, 2012 at 7:33 PM, Mohammad Mirzadeh <span dir="ltr"><<a href="mailto:mirzadeh@gmail.com" target="_blank">mirzadeh@gmail.com</a>></span> wrote:<br></div><div class="gmail_quote"><div class="im">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><br><br><div class="gmail_quote">On Sat, May 12, 2012 at 3:16 AM, Matthew Knepley <span dir="ltr"><<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On Sat, May 12, 2012 at 4:33 AM, Mohammad Mirzadeh <span dir="ltr"><<a href="mailto:mirzadeh@gmail.com" target="_blank">mirzadeh@gmail.com</a>></span> wrote:<br></div><div class="gmail_quote"><div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi guys,<div><br></div><div>I'm having a really weird issue here! My code seg faults for certain problem size and after using gdb I have been able to pinpoint the problem to a VecGetArray call. Here's a series of things I have tried so far</div>
<div><br></div><div>1) -on_error_attach_debugger -----> unsuccessful; does not launch debugger </div><div>2) -start_in_debugger -------> unsuccessful; does not start debugger</div></div></blockquote><div><br></div>
</div><div>Run with -log_summary. It will tell you what options the program got. Also, are there errors relating to X? Send</div><div>all output to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a></div>
<div><div>
</div></div></div></blockquote><div><br></div><div>Matt, -log_summary also does not generate any output! I was eventually able to start_in_debugger using xterm. Previously I was trying to start in kdbg. Even with xterm, -on_error_attach_debugger does not start the debugger. In either case, starting the debugger in xterm using -start_in_debugger or attaching the debugger myself manually, I get a segfault at VecGetArray and then the program terminates without any further output. </div>
</div></div></blockquote><div><br></div></div><div>You SEGV before it can evidently.</div><div class="im"><div> </div></div></div></blockquote><div><br></div><div>sigh ... Just found it. You are right! I was, and I don't know why!, allocating a large array on the stack and for certain size I was having a stack overflow problem. Thanks for the help anyways.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="gmail_quote"><div class="im"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div dir="ltr"><div>3) attaching debugger myself -----> code runs in debugger and seg faults when calling VecGetArray</div>
</div></blockquote><div><br></div></div><div>Is this a debug build? What dereference is causing the SEGV? Is the Vec a valid object? It sounds like</div><div>it has been corrupted.</div><div><div> </div></div>
</div></blockquote><div><br></div><div>Yes; with the -g option. How can I check if Vec is "valid"? </div></div></div></blockquote><div><br></div></div><div>PetscValidHeaderSpecific(v,VEC_CLASSID,1);</div><div class="im">
<div> </div>
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<div>4) using ierr=VecGetArray;CHKERRQ(ierr) ------> PETSc does not produce error messages; the code simply seg faults and terminates</div><div>5) checking the values of ierr inside the debugger ---------> They are all 0 up untill the code terminates; I think this means petsc does not generate error?</div>
<div>6) checking for memory leak with valgrind -----------> All I get are leaks from OpenMPI and PetscInitialize and PetscFinalize; I think these are just routine and safe?</div></div></blockquote><div><br></div></div>
</div></blockquote><div><br></div><div>Should I attach the whole valgrind output here or send it to petsc-maint? I just repeast these two a couple of times!:</div></div></div></blockquote><div><br></div></div><div>None of this output about lost memory matters. Send the entire output to petsc-maint</div>
<div><br></div><div> Matt</div><div><div class="h5"><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_quote"><div><div>==4508== 320 (288 direct, 32 indirect) bytes in 1 blocks are definitely lost in loss record 2,644 of 2,665</div>
<div>==4508== at 0x4C2815C: malloc (vg_replace_malloc.c:236)</div><div>==4508== by 0x86417ED: ???</div><div>==4508== by 0x5D4D099: orte_rml_base_comm_start (in /usr/lib/openmpi/lib/libopen-rte.so.0.0.0)</div><div>
==4508== by 0x8640AD1: ???</div><div>==4508== by 0x5D3AFE6: orte_ess_base_app_setup (in /usr/lib/openmpi/lib/libopen-rte.so.0.0.0)</div><div>==4508== by 0x8846E41: ???</div><div>==4508== by 0x5D23A52: orte_init (in /usr/lib/openmpi/lib/libopen-rte.so.0.0.0)</div>
<div>==4508== by 0x5A9E806: ??? (in /usr/lib/openmpi/lib/libmpi.so.0.0.1)</div><div>==4508== by 0x5ABFD7F: PMPI_Init (in /usr/lib/openmpi/lib/libmpi.so.0.0.1)</div><div>==4508== by 0x530A90: PetscInitialize(int*, char***, char const*, char const*) (pinit.c:668)</div>
<div>==4508== by 0x4A4955: PetscSession::PetscSession(int*, char***, char const*, char const*) (utilities.h:17)</div><div>==4508== by 0x4A1DA5: main (main_Test2.cpp:49)</div></div><div><br></div><div>==4508== 74 bytes in 1 blocks are definitely lost in loss record 2,411 of 2,665</div>
<div><div>==4508== at 0x4C2815C: malloc (vg_replace_malloc.c:236)</div><div>==4508== by 0x6F2DDA1: strdup (strdup.c:43)</div><div>==4508== by 0x5F85117: ??? (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0)</div><div>
==4508== by 0x5F85359: mca_base_param_lookup_string (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0)</div><div>==4508== by 0xB301869: ???</div><div>==4508== by 0xB2F5126: ???</div><div>==4508== by 0x5F82E17: mca_base_components_open (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0)</div>
<div>==4508== by 0x5ADA6BA: mca_btl_base_open (in /usr/lib/openmpi/lib/libmpi.so.0.0.1)</div><div>==4508== by 0xA6A9B93: ???</div><div>==4508== by 0x5F82E17: mca_base_components_open (in /usr/lib/openmpi/lib/libopen-pal.so.0.0.0)</div>
<div>==4508== by 0x5AE3C88: mca_pml_base_open (in /usr/lib/openmpi/lib/libmpi.so.0.0.1)</div><div>==4508== by 0x5A9E9E0: ??? (in /usr/lib/openmpi/lib/libmpi.so.0.0.1)</div></div><div><br></div><div><br></div><div>but eventually I get:</div>
<div><br></div><div><div>==4508== LEAK SUMMARY:</div><div>==4508== definitely lost: 5,949 bytes in 55 blocks</div><div>==4508== indirectly lost: 3,562 bytes in 32 blocks</div><div>==4508== possibly lost: 0 bytes in 0 blocks</div>
<div>==4508== still reachable: 181,516 bytes in 2,660 blocks</div><div>==4508== suppressed: 0 bytes in 0 blocks</div><div>==4508== Reachable blocks (those to which a pointer was found) are not shown.</div><div>
==4508== To see them, rerun with: --leak-check=full --show-reachable=y</div></div><div><br></div><div>which seems considerable!</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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How can we say anything without the valgrind output?</div><div><br></div><div> Matt</div><div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div><br></div><div>What else can I try to find the problem? Any recommendation is really appreciated!</div>
<div><br></div><div>Thanks,</div><div>Mohammad</div></div>
</blockquote></div></div><span><font color="#888888"><br><br clear="all"><span><font color="#888888"><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>
</font></span></font></span></blockquote></div><br></div>
</blockquote></div></div></div><div class="HOEnZb"><div class="h5"><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>
</div></div></blockquote></div><br></div>