[petsc-users] KSPSolve errors on blues

Fri Jun 10 11:43:32 CDT 2016

I found that this was caused by using -fieldsplit_0_pc_type hypre, which
ate a lot of memory during the KSPSolve().
Does hypre use BoomerAMG as the default pc type? I am curious why it uses
such a huge memory. PETSs allocated mem is about 22G, but the total process
memory is up to 100G. So it looks like the additional 70+G is associated
with hypre, which is more than 3 times of Petsc matrices and vectors!

-Xujun

On Wed, Jun 8, 2016 at 4:29 PM, Xujun Zhao <xzhao99 at gmail.com> wrote:

> OK, this makes sense.
> Now my libMesh code use SerialMesh, which keeps a copy on each processor,
> although the operation is parallelized. So it requires more memory if
> multiple CPUs are used. This may be a potential culprit. But I suppose the
> 60x60x60 mesh data(all second order) shouldn't be so large.... there may be
> some other bugs
>
> On Wed, Jun 8, 2016 at 4:18 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> > On Jun 8, 2016, at 4:08 PM, Xujun Zhao <xzhao99 at gmail.com> wrote:
>> >
>> > Barry,
>> >
>> > Thank you. I am testing on the blues.
>> > btw, what do they mean for the different types of memory usage? for
>> example, below is the summary of mem usage for 60x60x60(with 2.9M dofs).
>> The max process memory is 3 times as the max space PetscMalloc()ed.
>>
>>    PetscMalloced is basically the PETSc data structures; Process memory
>> is size of the program plus PETSc malloced space plus space allocated by
>> any other library, in this case libMesh. It looks like libMesh is requiring
>> a lot of space?
>>
>>   Barry
>>
>> >
>> > Summary of Memory Usage in PETSc
>> > Maximum (over computational time) process memory:        total
>> 1.0930e+11 max 5.6928e+10 min 5.2376e+10
>> > Current process memory:
>>      total 3.1762e+09 max 2.8804e+09 min 2.9583e+08
>> > Maximum (over computational time) space PetscMalloc()ed: total
>> 3.0071e+10 max 1.5286e+10 min 1.4785e+10
>> > Current space PetscMalloc()ed:
>>  total 1.5453e+05 max 7.7264e+04 min 7.7264e+04
>> >
>> >
>> >
>> > On Wed, Jun 8, 2016 at 1:40 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>> >
>> > > On Jun 8, 2016, at 1:30 PM, Xujun Zhao <xzhao99 at gmail.com> wrote:
>> > >
>> > > A quick test of a smaller system on my laptop with 25x25x25 mesh
>> gives the following info.
>> > > The memory used keeps increasing from 1 to 3 CPUs, but slightly
>> decreases with 4 CPUs.
>> >
>> >    yes this does not look problematic
>> >
>> > > On the other hand, 60x60x60 mesh (2.9M dofs) is also not a big
>> system...
>> >
>> >   True.
>> >
>> >    I think you need to run the 60 60 60 system also on 1 2 4 and 8
>> processes to see how the memory trends. I don't think we should eliminate
>> memory as the culprit yet.
>> >
>> >
>> >   Barry
>> >
>> > >
>> > >
>> > > ------------------------------------------------- 1 CPU
>> -------------------------------------------------
>> > > Summary of Memory Usage in PETSc
>> > > Maximum (over computational time) process memory:        total
>> 4.7054e+09 max 4.7054e+09 min 4.7054e+09
>> > > Current process memory:
>>        total 4.7054e+09 max 4.7054e+09 min 4.7054e+09
>> > > Maximum (over computational time) space PetscMalloc()ed: total
>> 1.6151e+09 max 1.6151e+09 min 1.6151e+09
>> > > Current space PetscMalloc()ed:
>>    total 7.7232e+04 max 7.7232e+04 min 7.7232e+04
>> > >
>> > > ------------------------------------------------- 2 CPU
>> -------------------------------------------------
>> > > Summary of Memory Usage in PETSc
>> > > Maximum (over computational time) process memory:        total
>> 6.2389e+09 max 3.1275e+09 min 3.1113e+09
>> > > Current process memory:
>>        total 6.2389e+09 max 3.1275e+09 min 3.1113e+09
>> > > Maximum (over computational time) space PetscMalloc()ed: total
>> 2.1589e+09 max 1.1193e+09 min 1.0397e+09
>> > > Current space PetscMalloc()ed:
>>    total 1.5446e+05 max 7.7232e+04 min 7.7232e+04
>> > >
>> > > ------------------------------------------------- 3 CPU
>> -------------------------------------------------
>> > > Summary of Memory Usage in PETSc
>> > > Maximum (over computational time) process memory:        total
>> 7.7116e+09 max 1.9572e+09 min 1.8715e+09
>> > > Current process memory:
>>        total 7.7116e+09 max 1.9572e+09 min 1.8715e+09
>> > > Maximum (over computational time) space PetscMalloc()ed: total
>> 2.1754e+09 max 5.8450e+08 min 5.0516e+08
>> > > Current space PetscMalloc()ed:
>>    total 3.0893e+05 max 7.7232e+04 min 7.7232e+04
>> > >
>> > > ------------------------------------------------- 4 CPU
>> -------------------------------------------------
>> > > Summary of Memory Usage in PETSc
>> > > Maximum (over computational time) process memory:        total
>> 7.1188e+09 max 2.4651e+09 min 2.2909e+09
>> > > Current process memory:
>>        total 7.1188e+09 max 2.4651e+09 min 2.2909e+09
>> > > Maximum (over computational time) space PetscMalloc()ed: total
>> 2.1750e+09 max 7.6982e+08 min 6.5289e+08
>> > > Current space PetscMalloc()ed:
>>    total 2.3170e+05 max 7.7232e+04 min 7.7232e+04
>> > >
>> > >
>> > > On Wed, Jun 8, 2016 at 11:51 AM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> > >
>> > >    Signal 9 SIGKILL on batch systems usually means the process was
>> killed because it ran out of time or ran out of memory.
>> > >
>> > >     Perhaps there is something in the code that is unscalable and
>> requires more more memory with more processes. You can run on 1 2 and 3
>> processes and measure the memory usage to see if it goes up with the number
>> of processes using for example -memory_view
>> > >
>> > >   Barry
>> > >
>> > >
>> > >
>> > > > On Jun 8, 2016, at 11:41 AM, Xujun Zhao <xzhao99 at gmail.com> wrote:
>> > > >
>> > > > Hi all,
>> > > >
>> > > > I am running a FE Stokes Solver with schur complement type PC on
>> blues. The program runs well when mesh is 40X40X40 (0.88M dofs), but when I
>> use 60X60X60 mesh, the program crashes and gives out some errors, which
>> looks like a segmentation fault. The "strange" thing is that it runs well
>> with 1CPU, 2CPUs, but fails on 4 or 8 CPUs. The log files are also
>> attached. It seems like the global matrix and vector are assembled well,
>> and errors come out before calling the KSPSolve().
>> > > >
>> > > > btw, I use the recent PETSc 3.7 dbg version. for libMesh I use both
>> dbg and opt version, but none of those can give useful information. Has
>> anyone met such situations before? Many thinks.
>> > > > <ex01_validation_test.o1386940><ex01_validation_test.o1387007>
>> > >
>> > >
>> >
>> >
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20160610/8dd64a53/attachment-0001.html>