[petsc-users] Question about memory usage in Multigrid preconditioner
Dave May
dave.mayhem23 at gmail.com
Mon Jul 11 15:18:01 CDT 2016
Hi Frank,
On 11 July 2016 at 19:14, frank <hengjiew at uci.edu> wrote:
> Hi Dave,
>
> I re-run the test using bjacobi as the preconditioner on the coarse mesh
> of telescope. The Grid is 3072*256*768 and process mesh is 96*8*24. The
> petsc option file is attached.
> I still got the "Out Of Memory" error. The error occurred before the
> linear solver finished one step. So I don't have the full info from
> ksp_view. The info from ksp_view_pre is attached.
>
Okay - that is essentially useless (sorry)
>
> It seems to me that the error occurred when the decomposition was going to
> be changed.
>
Based on what information?
Running with -info would give us more clues, but will create a ton of
output.
Please try running the case which failed with -info
> I had another test with a grid of 1536*128*384 and the same process mesh
> as above. There was no error. The ksp_view info is attached for comparison.
> Thank you.
>
[3] Here is my crude estimate of your memory usage.
I'll target the biggest memory hogs only to get an order of magnitude
estimate
* The Fine grid operator contains 4223139840 non-zeros --> 1.8 GB per MPI
rank assuming double precision.
The indices for the AIJ could amount to another 0.3 GB (assuming 32 bit
integers)
* You use 5 levels of coarsening, so the other operators should represent
(collectively)
2.1 / 8 + 2.1/8^2 + 2.1/8^3 + 2.1/8^4 ~ 300 MB per MPI rank on the
communicator with 18432 ranks.
The coarse grid should consume ~ 0.5 MB per MPI rank on the communicator
with 18432 ranks.
* You use a reduction factor of 64, making the new communicator with 288
MPI ranks.
PCTelescope will first gather a temporary matrix associated with your
coarse level operator assuming a comm size of 288 living on the comm with
size 18432.
This matrix will require approximately 0.5 * 64 = 32 MB per core on the 288
ranks.
This matrix is then used to form a new MPIAIJ matrix on the subcomm, thus
require another 32 MB per rank.
The temporary matrix is now destroyed.
* Because a DMDA is detected, a permutation matrix is assembled.
This requires 2 doubles per point in the DMDA.
Your coarse DMDA contains 92 x 16 x 48 points.
Thus the permutation matrix will require < 1 MB per MPI rank on the
sub-comm.
* Lastly, the matrix is permuted. This uses MatPtAP(), but the resulting
operator will have the same memory footprint as the unpermuted matrix (32
MB). At any stage in PCTelescope, only 2 operators of size 32 MB are held
in memory when the DMDA is provided.
>From my rough estimates, the worst case memory foot print for any given
core, given your options is approximately
2100 MB + 300 MB + 32 MB + 32 MB + 1 MB = 2465 MB
This is way below 8 GB.
Note this estimate completely ignores:
(1) the memory required for the restriction operator,
(2) the potential growth in the number of non-zeros per row due to Galerkin
coarsening (I wished -ksp_view_pre reported the output from MatView so we
could see the number of non-zeros required by the coarse level operators)
(3) all temporary vectors required by the CG solver, and those required by
the smoothers.
(4) internal memory allocated by MatPtAP
(5) memory associated with IS's used within PCTelescope
So either I am completely off in my estimates, or you have not carefully
estimated the memory usage of your application code. Hopefully others might
examine/correct my rough estimates
Since I don't have your code I cannot access the latter.
Since I don't have access to the same machine you are running on, I think
we need to take a step back.
[1] What machine are you running on? Send me a URL if its available
[2] What discretization are you using? (I am guessing a scalar 7 point FD
stencil)
If it's a 7 point FD stencil, we should be able to examine the memory usage
of your solver configuration using a standard, light weight existing PETSc
example, run on your machine at the same scale.
This would hopefully enable us to correctly evaluate the actual memory
usage required by the solver configuration you are using.
Thanks,
Dave
>
>
> Frank
>
>
>
>
> On 07/08/2016 10:38 PM, Dave May wrote:
>
>
>
> On Saturday, 9 July 2016, frank <hengjiew at uci.edu> wrote:
>
>> Hi Barry and Dave,
>>
>> Thank both of you for the advice.
>>
>> @Barry
>> I made a mistake in the file names in last email. I attached the correct
>> files this time.
>> For all the three tests, 'Telescope' is used as the coarse preconditioner.
>>
>> == Test1: Grid: 1536*128*384, Process Mesh: 48*4*12
>> Part of the memory usage: Vector 125 124 3971904 0.
>> Matrix 101 101
>> 9462372 0
>>
>> == Test2: Grid: 1536*128*384, Process Mesh: 96*8*24
>> Part of the memory usage: Vector 125 124 681672 0.
>> Matrix 101 101
>> 1462180 0.
>>
>> In theory, the memory usage in Test1 should be 8 times of Test2. In my
>> case, it is about 6 times.
>>
>> == Test3: Grid: 3072*256*768, Process Mesh: 96*8*24. Sub-domain per
>> process: 32*32*32
>> Here I get the out of memory error.
>>
>> I tried to use -mg_coarse jacobi. In this way, I don't need to set
>> -mg_coarse_ksp_type and -mg_coarse_pc_type explicitly, right?
>> The linear solver didn't work in this case. Petsc output some errors.
>>
>> @Dave
>> In test3, I use only one instance of 'Telescope'. On the coarse mesh of
>> 'Telescope', I used LU as the preconditioner instead of SVD.
>> If my set the levels correctly, then on the last coarse mesh of MG where
>> it calls 'Telescope', the sub-domain per process is 2*2*2.
>> On the last coarse mesh of 'Telescope', there is only one grid point per
>> process.
>> I still got the OOM error. The detailed petsc option file is attached.
>
>
> Do you understand the expected memory usage for the particular parallel
> LU implementation you are using? I don't (seriously). Replace LU with
> bjacobi and re-run this test. My point about solver debugging is still
> valid.
>
> And please send the result of KSPView so we can see what is actually used
> in the computations
>
> Thanks
> Dave
>
>
>>
>>
>> Thank you so much.
>>
>> Frank
>>
>>
>>
>> On 07/06/2016 02:51 PM, Barry Smith wrote:
>>
>>> On Jul 6, 2016, at 4:19 PM, frank <hengjiew at uci.edu> wrote:
>>>>
>>>> Hi Barry,
>>>>
>>>> Thank you for you advice.
>>>> I tried three test. In the 1st test, the grid is 3072*256*768 and the
>>>> process mesh is 96*8*24.
>>>> The linear solver is 'cg' the preconditioner is 'mg' and 'telescope' is
>>>> used as the preconditioner at the coarse mesh.
>>>> The system gives me the "Out of Memory" error before the linear system
>>>> is completely solved.
>>>> The info from '-ksp_view_pre' is attached. I seems to me that the error
>>>> occurs when it reaches the coarse mesh.
>>>>
>>>> The 2nd test uses a grid of 1536*128*384 and process mesh is 96*8*24.
>>>> The 3rd test uses the same grid but a different process mesh 48*4*12.
>>>>
>>> Are you sure this is right? The total matrix and vector memory usage
>>> goes from 2nd test
>>> Vector 384 383 8,193,712 0.
>>> Matrix 103 103 11,508,688 0.
>>> to 3rd test
>>> Vector 384 383 1,590,520 0.
>>> Matrix 103 103 3,508,664 0.
>>> that is the memory usage got smaller but if you have only 1/8th the
>>> processes and the same grid it should have gotten about 8 times bigger. Did
>>> you maybe cut the grid by a factor of 8 also? If so that still doesn't
>>> explain it because the memory usage changed by a factor of 5 something for
>>> the vectors and 3 something for the matrices.
>>>
>>>
>>> The linear solver and petsc options in 2nd and 3rd tests are the same in
>>>> 1st test. The linear solver works fine in both test.
>>>> I attached the memory usage of the 2nd and 3rd tests. The memory info
>>>> is from the option '-log_summary'. I tried to use '-momery_info' as you
>>>> suggested, but in my case petsc treated it as an unused option. It output
>>>> nothing about the memory. Do I need to add sth to my code so I can use
>>>> '-memory_info'?
>>>>
>>> Sorry, my mistake the option is -memory_view
>>>
>>> Can you run the one case with -memory_view and -mg_coarse jacobi
>>> -ksp_max_it 1 (just so it doesn't iterate forever) to see how much memory
>>> is used without the telescope? Also run case 2 the same way.
>>>
>>> Barry
>>>
>>>
>>>
>>> In both tests the memory usage is not large.
>>>>
>>>> It seems to me that it might be the 'telescope' preconditioner that
>>>> allocated a lot of memory and caused the error in the 1st test.
>>>> Is there is a way to show how much memory it allocated?
>>>>
>>>> Frank
>>>>
>>>> On 07/05/2016 03:37 PM, Barry Smith wrote:
>>>>
>>>>> Frank,
>>>>>
>>>>> You can run with -ksp_view_pre to have it "view" the KSP before
>>>>> the solve so hopefully it gets that far.
>>>>>
>>>>> Please run the problem that does fit with -memory_info when the
>>>>> problem completes it will show the "high water mark" for PETSc allocated
>>>>> memory and total memory used. We first want to look at these numbers to see
>>>>> if it is using more memory than you expect. You could also run with say
>>>>> half the grid spacing to see how the memory usage scaled with the increase
>>>>> in grid points. Make the runs also with -log_view and send all the output
>>>>> from these options.
>>>>>
>>>>> Barry
>>>>>
>>>>> On Jul 5, 2016, at 5:23 PM, frank <hengjiew at uci.edu> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I am using the CG ksp solver and Multigrid preconditioner to solve a
>>>>>> linear system in parallel.
>>>>>> I chose to use the 'Telescope' as the preconditioner on the coarse
>>>>>> mesh for its good performance.
>>>>>> The petsc options file is attached.
>>>>>>
>>>>>> The domain is a 3d box.
>>>>>> It works well when the grid is 1536*128*384 and the process mesh is
>>>>>> 96*8*24. When I double the size of grid and keep the same process mesh and
>>>>>> petsc options, I get an "out of memory" error from the super-cluster I am
>>>>>> using.
>>>>>> Each process has access to at least 8G memory, which should be more
>>>>>> than enough for my application. I am sure that all the other parts of my
>>>>>> code( except the linear solver ) do not use much memory. So I doubt if
>>>>>> there is something wrong with the linear solver.
>>>>>> The error occurs before the linear system is completely solved so I
>>>>>> don't have the info from ksp view. I am not able to re-produce the error
>>>>>> with a smaller problem either.
>>>>>> In addition, I tried to use the block jacobi as the preconditioner
>>>>>> with the same grid and same decomposition. The linear solver runs extremely
>>>>>> slow but there is no memory error.
>>>>>>
>>>>>> How can I diagnose what exactly cause the error?
>>>>>> Thank you so much.
>>>>>>
>>>>>> Frank
>>>>>> <petsc_options.txt>
>>>>>>
>>>>>
>>>> <ksp_view_pre.txt><memory_test2.txt><memory_test3.txt><petsc_options.txt>
>>>>
>>>
>>
>
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