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<div class="moz-cite-prefix">On 14/4/2014 10:44 PM, Matthew Knepley
wrote:<br>
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<blockquote
cite="mid:CAMYG4GnNmBbo4rMevHF-s_jqWux5cEV-Ztd377K8KSbt-bH_ig@mail.gmail.com"
type="cite">
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<div class="gmail_quote">On Mon, Apr 14, 2014 at 9:40 AM, TAY
wee-beng <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:zonexo@gmail.com" target="_blank">zonexo@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
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<div>Hi Barry,<br>
<br>
I'm not too sure how to do it. I'm running mpi. So I
run:<br>
<br>
mpirun -n 4 ./a.out -start_in_debugger<br>
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<div><br>
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<div> add -debugger_pause 10</div>
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<br>
It seems that I need to use a value of 60. It gives a segmentation
fault after the location I debug earlier:<br>
<br>
#0 0x00002b672cdee78a in f90array3daccessscalar_ ()<br>
from /home/wtay/Lib/petsc-3.4.4_shared_rel/lib/libpetsc.so<br>
#1 0x00002b672cdedcae in F90Array3dAccess ()<br>
from /home/wtay/Lib/petsc-3.4.4_shared_rel/lib/libpetsc.so<br>
#2 0x00002b672d2ad044 in dmdavecrestorearrayf903_ ()<br>
from /home/wtay/Lib/petsc-3.4.4_shared_rel/lib/libpetsc.so<br>
#3 0x00000000008a1d8d in fractional_initial_mp_initial_ ()<br>
#4 0x0000000000539289 in MAIN__ ()<br>
#5 0x000000000043c04c in main ()<br>
<br>
What;'s that supposed to mean?<br>
<blockquote
cite="mid:CAMYG4GnNmBbo4rMevHF-s_jqWux5cEV-Ztd377K8KSbt-bH_ig@mail.gmail.com"
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<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0
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<div> I got the msg below. Before the gdb windows appear
(thru x11), the program aborts.<br>
<br>
Also I tried running in another cluster and it worked.
Also tried in the current cluster in debug mode and it
worked too.<br>
<br>
<i><u><b>mpirun -n 4 ./a.out -start_in_debugger</b></u></i><i><u><b><br>
</b></u></i><i><u><b>--------------------------------------------------------------------------</b></u></i><i><u><b><br>
</b></u></i><i><u><b>An MPI process has executed
an operation involving a call to the</b></u></i><i><u><b><br>
</b></u></i><i><u><b>"fork()" system call to
create a child process. Open MPI is currently</b></u></i><i><u><b><br>
</b></u></i><i><u><b>operating in a condition that
could result in memory corruption or</b></u></i><i><u><b><br>
</b></u></i><i><u><b>other system errors; your MPI
job may hang, crash, or produce silent</b></u></i><i><u><b><br>
</b></u></i><i><u><b>data corruption. The use of
fork() (or system() or other calls that</b></u></i><i><u><b><br>
</b></u></i><i><u><b>create child processes) is
strongly discouraged. </b></u></i><i><u><b><br>
</b></u></i><i><u><b><br>
</b></u></i><i><u><b>The process that invoked fork
was:</b></u></i><i><u><b><br>
</b></u></i><i><u><b><br>
</b></u></i><i><u><b> Local host: n12-76
(PID 20235)</b></u></i><i><u><b><br>
</b></u></i><i><u><b> MPI_COMM_WORLD rank: 2</b></u></i><i><u><b><br>
</b></u></i><i><u><b><br>
</b></u></i><i><u><b>If you are *absolutely sure*
that your application will successfully</b></u></i><i><u><b><br>
</b></u></i><i><u><b>and correctly survive a call
to fork(), you may disable this warning</b></u></i><i><u><b><br>
</b></u></i><i><u><b>by setting the
mpi_warn_on_fork MCA parameter to 0.</b></u></i><i><u><b><br>
</b></u></i><i><u><b>--------------------------------------------------------------------------</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[2]PETSC ERROR: PETSC:
Attaching gdb to ./a.out of pid 20235 on display
localhost:50.0 on machine n12-76</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[0]PETSC ERROR: PETSC:
Attaching gdb to ./a.out of pid 20233 on display
localhost:50.0 on machine n12-76</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: PETSC:
Attaching gdb to ./a.out of pid 20234 on display
localhost:50.0 on machine n12-76</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: PETSC:
Attaching gdb to ./a.out of pid 20236 on display
localhost:50.0 on machine n12-76</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[n12-76:20232] 3 more
processes have sent help message
help-mpi-runtime.txt / mpi_init:warn-fork</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[n12-76:20232] Set MCA
parameter "orte_base_help_aggregate" to 0 to see
all help / error messages</b></u></i><i><u><b><br>
</b></u></i><i><u><b><br>
</b></u></i><i><u><b>....</b></u></i><i><u><b><br>
</b></u></i><i><u><b><br>
</b></u></i><i><u><b> 1</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR:
------------------------------------------------------------------------</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: Caught signal
number 11 SEGV: Segmentation Violation, probably
memory access out of range</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: Try option
-start_in_debugger or -on_error_attach_debugger</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: or see <a
moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[1]PETSC
ERROR: or try <a moz-do-not-send="true"
href="http://valgrind.org" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to find memory
corruption errors</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: configure
using --with-debugging=yes, recompile, link, and
run </b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: to get more
information on the crash.</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[1]PETSC ERROR: User provided
function() line 0 in unknown directory unknown
file (null)</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR:
------------------------------------------------------------------------</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: Caught signal
number 11 SEGV: Segmentation Violation, probably
memory access out of range</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: Try option
-start_in_debugger or -on_error_attach_debugger</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: or see <a
moz-do-not-send="true"
href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind"
target="_blank">http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a>[3]PETSC
ERROR: or try <a moz-do-not-send="true"
href="http://valgrind.org" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to find memory
corruption errors</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: configure
using --with-debugging=yes, recompile, link, and
run </b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: to get more
information on the crash.</b></u></i><i><u><b><br>
</b></u></i><i><u><b>[3]PETSC ERROR: User provided
function() line 0 in unknown directory unknown
file (null)</b></u></i><br>
<br>
...<br>
<pre cols="72">Thank you.
Yours sincerely,
TAY wee-beng</pre>
On 14/4/2014 9:05 PM, Barry Smith wrote:<br>
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<blockquote type="cite">
<pre> 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" href="mailto:zonexo@gmail.com" target="_blank"><zonexo@gmail.com></a> wrote:
</pre>
<blockquote type="cite">
<pre>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
</pre>
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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
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