[MOAB-dev] Fwd: Re: Job exiting early [ThermHydraX]
kanaev at ibrae.ac.ru
kanaev at ibrae.ac.ru
Tue May 20 03:40:03 CDT 2014
Please disregard that, the global_id space for Quads was
incontinuous in my mesh file
Will check back with correct mesh
Anton
On Mon, 19 May 2014 15:17:14 -0400, wrote:
Hello MOAB dev,
I've attached a simplified version of my program that crashes
presumably after particular numbers calls of exchange_tags
I ran it couple of times on Mira on 1024 cores (64 nodes in --mode
c16)
It performs around 524378 iterations and then crushes (error file
attached)
Can you please take a look at what Scott Parker from ALCF suggests
about it:
-------- Original Message --------
SUBJECT:
Re: Job exiting early [ThermHydraX]
DATE:
Fri, 9 May 2014 18:48:25 -0500
FROM:
Scott Parker
TO:
Anton-
I took a look at the core files and from the stack trace it appears
that the code is failing in an MPI_Isend call
that is called from moab.ParallelComm::recv_buffer which is called
from moab::ParallelComm::exchange_tags
called from main(). The stack
looks like:
main
moab::ParallelComm::exchange_tags
moab.ParallelComm::recv_buffer
MPI_Isend
I've been able to get the same failure and error message you are
seeing by having an MPI process call MPI_Isend
when there are no matching receives. After 2 million Isends the
program exits with the error you are seeing. So
I'm pretty sure your ending up with a large number of outstanding
requests and the program is failing because
it can't allocate space for new MPI_Request objects.
I'd suggest looking at how Moab is calling MPI and how many requests
might be outstanding at any one time.
Since the code is running for 5 hours and looks to be executing
hundreds of thousands of iterations I wonder
if there is some sort of send-receive mismatch that is letting
requests accumulate. I think your best bet is to
talk to the Moab folks and see if they have any ideas about why this
might be happening.
One possibility is a load imbalance between processes - if you
don't
have any MPI_Barriers or other collectives in
your code you could try adding a barrier to synchronize the
processes.
If the Moab guys can't help you and adding a barrier doesn't help I
can work with you to instrument the code to
collect more information on how MPI is being called and we could
possibly pin down the source of the problem
that way.
Scott
On 5/2/14, 11:14 PM, kanaev at ibrae.ac.ru [1] wrote:
Hello Scott
The dir is cd /gpfs/mira-fs0/projects/ThermHydraX/kanaev/pinit The
run produced core files is 253035 I took another run with the
line MPI_Allreduce(&r,&rmax,1,MPI_REAL8,MPI_MAX,MPI_COMM_WORLD);
commented and it stopped the same very time iteration #524378, just
passed some more lines I use MOAB library and its function of
exchanging data between processors so i think i cannot really count
MPI requests Anton
On Mon, 28 Apr 2014 16:45:41 -0500, Scott Parker wrote:
Can you point me to the directory where your binary and core
files
are?
The stack trace you sent shows a call to MPI_Waitany, do you know
how many MPI requests
the code generally has outstanding at any time?
-Scott
On 4/28/14, 4:30 PM, kanaev at ibrae.ac.ru [1] wrote:
Hello Scott,
I took rerun with the mentioned keys. The code was freshly compiled
with makefile attached just in case.
I've got 1024 core files. Two of them are attached.
I run bgq_stack for core.0 and here's what i got:
[akanaev at miralac1 pinit]$bgq_stack pinit core.0
------------------------------------------------------------------------
Program : /gpfs/mira-fs0/projects/ThermHydraX/kanaev/pinit/pinit
------------------------------------------------------------------------
+++ID Rank: 0, TGID: 1, Core: 0, HWTID:0 TID: 1 State: RUN
00000000018334c0
_ZN4PAMI6Device2MU7Factory12advance_implEPNS1_7ContextEmm
/bgsys/source/srcV1R2M1.17463/comm/sys/buildtools/pami/components/devices/bgq/mu2/Factory.h:269
000000000170da28
PAMI_Context_trylock_advancev
/bgsys/source/srcV1R2M1.17463/comm/sys/buildtools/pami/api/c/pami.cc:554
000000000155d0dc
PMPI_Waitany
/bgsys/source/srcV1R2M1.17463/comm/lib/dev/mpich2/src/mpid/pamid/include/../src/mpid_progress.h:239
00000000010e84e4
00000072.long_branch_r2off.H5Dget_space+0
:0
0000000001042be0
00000012.long_branch_r2off._ZNSt14basic_ifstreamIcSt11char_traitsIcEEC1EPKcSt13_Ios_Openmode+0
:0
00000000019de058
generic_start_main
/bgsys/drivers/V1R2M1/ppc64/toolchain/gnu/glibc-2.12.2/csu/../csu/libc-start.c:226
00000000019de354
__libc_start_main
/bgsys/drivers/V1R2M1/ppc64/toolchain/gnu/glibc-2.12.2/csu/../sysdeps/unix/sysv/linux/powerpc/libc-start.c:194
0000000000000000
??
??:0
> Have these sort of runs succeeded in the past using the same
code base with no changes and similar input data?
That is the first time i'm trying to run this code for that long
time
Thanks
Anton
On Thu, 24 Apr 2014 15:45:49 -0500, Scott Parker wrote:
Anton-
Thanks, it's aborting because of a runtime error that appears to be
in the mpich layer.
Can you rerun with "--env
BG_COREDUMPONEXIT=1:BG_COREDUMPONERROR=1" added to your qsub line -
that should
generate some core files on which you can run bgq_stack.
The system software (driver) on Mira was updated this week and I'd
like to get a clearer picture of
whether that could be related to you problem, so
Has your code been recompiled since Monday? If not can you
recompile and try running again
Have these sort of runs succeeded in the past using the same code
base with no changes and similar input data?
-Scott
On 4/24/14, 2:59 PM, kanaev at ibrae.ac.ru [1] wrote:
Sorry about the attached files, here the are
There's no core files after exiting, looks like stopping because of
time requested expires but you can see from cobaltlog it's about 5
hours passed (10 hours was requested) before exit
Anton
On Thu, 24 Apr 2014 14:07:07 -0500, Scott Parker wrote:
Anton-
Please send these emails to support at alcf.anl.gov [2] as I may not
always be available to investigate.
I don't see the cobalt or error files attached, so I can't really
say anything about why your job may be
failing. Do you get core files when the job crashed? If so I'd
recommend using 'bgq_stack '
to try and get the file and line number where the failure occurred.
Knowing the line may be enough
to let you figure it out, if not you'll need to dump the values of
the variables at the time of the crash
to get a clearer picture of what is going on.
Scott
On 4/24/14, 1:36 PM, kanaev at ibrae.ac.ru [1] wrote:
Hello Scott,
I've tried twice to run 10 hours 1024 cores job on Mira in mode c16
with
qsub -n 64 -t 10:00:00 --mode c16 -A ThermHydraX pinit
Lid_128x128x1p1024.h5m
Both times job exited earlier than expected on the same iteration
after the same error during executing the following
section (it's
between two couts):
...
//LOOP OVER OWNED CELLS
double r = 0;
for (moab::Range::iterator it = owned_ents.begin(); it !=
owned_ents.end(); it++) {
EntityHandle ent = *it;
int cellid = mb->id_from_handle(ent);
double Vol_;
double u_;
double v_;
double w_;
double r1,r2,r3;
double tmp;
result = mb->tag_get_data(u, &ent, 1, &u_);
PRINT_LAST_ERROR;
result = mb->tag_get_data(v, &ent, 1, &v_);
PRINT_LAST_ERROR;
result = mb->tag_get_data(w, &ent, 1, &w_);
PRINT_LAST_ERROR;
double result;
SCALAR_PRODUCT(result,u_,v_,w_,CG[cellid][2].lx,CG[cellid][2].ly,CG[cellid][2].lz);
r1 = (sound + fabs(result))/CG[cellid][2].length;
SCALAR_PRODUCT(result,u_,v_,w_,CG[cellid][3].lx,CG[cellid][3].ly,CG[cellid][3].lz);
r2 = (sound + fabs(result))/CG[cellid][3].length;
SCALAR_PRODUCT(result,u_,v_,w_,CG[cellid][5].lx,CG[cellid][5].ly,CG[cellid][5].lz);
r3 = (sound + fabs(result))/CG[cellid][5].length;
tmp = MAX3(r1,r2,r3);
r = MAX(tmp,r);
}
double rmax;
MPI_Allreduce(&r,&rmax,1,MPI_REAL8,MPI_MAX,MPI_COMM_WORLD);
tau = CFL/rmax;
ttime+=tau;
...
So it may be Allreduce
I've attached cobaltlog and error files of both runs
Can you please take a look and suggest a further debugging
Thanks
Anton
Links:
------
[1] mailto:kanaev at ibrae.ac.ru
[2] mailto:support at alcf.anl.gov
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