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<div class="moz-cite-prefix">Hi Barry,<br>
<br>
As I mentioned earlier, the code works fine in PETSc debug mode
but fails in non-debug mode.<br>
<br>
I have attached my code.<br>
<br>
<pre class="moz-signature" cols="72">Thank you
Yours sincerely,
TAY wee-beng</pre>
On 15/4/2014 2:26 AM, Barry Smith wrote:<br>
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<blockquote
cite="mid:909E1CF9-F3A2-43E2-8F25-405070CFB192@mcs.anl.gov"
type="cite">
<pre wrap=""> Please send the code that creates da_w and the declarations of w_array
Barry
On Apr 14, 2014, at 9:40 AM, TAY wee-beng <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:zonexo@gmail.com"><zonexo@gmail.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Barry,
I'm not too sure how to do it. I'm running mpi. So I run:
mpirun -n 4 ./a.out -start_in_debugger
I got the msg below. Before the gdb windows appear (thru x11), the program aborts.
Also I tried running in another cluster and it worked. Also tried in the current cluster in debug mode and it worked too.
mpirun -n 4 ./a.out -start_in_debugger
--------------------------------------------------------------------------
An MPI process has executed an operation involving a call to the
"fork()" system call to create a child process. Open MPI is currently
operating in a condition that could result in memory corruption or
other system errors; your MPI job may hang, crash, or produce silent
data corruption. The use of fork() (or system() or other calls that
create child processes) is strongly discouraged.
The process that invoked fork was:
Local host: n12-76 (PID 20235)
MPI_COMM_WORLD rank: 2
If you are *absolutely sure* that your application will successfully
and correctly survive a call to fork(), you may disable this warning
by setting the mpi_warn_on_fork MCA parameter to 0.
--------------------------------------------------------------------------
[2]PETSC ERROR: PETSC: Attaching gdb to ./a.out of pid 20235 on display localhost:50.0 on machine n12-76
[0]PETSC ERROR: PETSC: Attaching gdb to ./a.out of pid 20233 on display localhost:50.0 on machine n12-76
[1]PETSC ERROR: PETSC: Attaching gdb to ./a.out of pid 20234 on display localhost:50.0 on machine n12-76
[3]PETSC ERROR: PETSC: Attaching gdb to ./a.out of pid 20236 on display localhost:50.0 on machine n12-76
[n12-76:20232] 3 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
[n12-76:20232] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
....
1
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[1]PETSC ERROR: or try <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://valgrind.org">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors
[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[1]PETSC ERROR: to get more information on the crash.
[1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file (null)
[3]PETSC ERROR: ------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[3]PETSC ERROR: or see <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[3]PETSC ERROR: or try <a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://valgrind.org">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors
[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[3]PETSC ERROR: to get more information on the crash.
[3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file (null)
...
Thank you.
Yours sincerely,
TAY wee-beng
On 14/4/2014 9:05 PM, Barry Smith wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> Because IO doesn’t always get flushed immediately it may not be hanging at this point. It is better to use the option -start_in_debugger then type cont in each debugger window and then when you think it is “hanging” do a control C in each debugger window and type where to see where each process is you can also look around in the debugger at variables to see why it is “hanging” at that point.
Barry
This routines don’t have any parallel communication in them so are unlikely to hang.
On Apr 14, 2014, at 6:52 AM, TAY wee-beng
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:zonexo@gmail.com"><zonexo@gmail.com></a>
wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi,
My code hangs and I added in mpi_barrier and print to catch the bug. I found that it hangs after printing "7". Is it because I'm doing something wrong? I need to access the u,v,w array so I use DMDAVecGetArrayF90. After access, I use DMDAVecRestoreArrayF90.
call DMDAVecGetArrayF90(da_u,u_local,u_array,ierr)
call MPI_Barrier(MPI_COMM_WORLD,ierr); if (myid==0) print *,"3"
call DMDAVecGetArrayF90(da_v,v_local,v_array,ierr)
call MPI_Barrier(MPI_COMM_WORLD,ierr); if (myid==0) print *,"4"
call DMDAVecGetArrayF90(da_w,w_local,w_array,ierr)
call MPI_Barrier(MPI_COMM_WORLD,ierr); if (myid==0) print *,"5"
call I_IIB_uv_initial_1st_dm(I_cell_no_u1,I_cell_no_v1,I_cell_no_w1,I_cell_u1,I_cell_v1,I_cell_w1,u_array,v_array,w_array)
call MPI_Barrier(MPI_COMM_WORLD,ierr); if (myid==0) print *,"6"
call DMDAVecRestoreArrayF90(da_w,w_local,w_array,ierr) !must be in reverse order
call MPI_Barrier(MPI_COMM_WORLD,ierr); if (myid==0) print *,"7"
call DMDAVecRestoreArrayF90(da_v,v_local,v_array,ierr)
call MPI_Barrier(MPI_COMM_WORLD,ierr); if (myid==0) print *,"8"
call DMDAVecRestoreArrayF90(da_u,u_local,u_array,ierr)
--
Thank you.
Yours sincerely,
TAY wee-beng
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