[petsc-users] Question about memory usage in Multigrid preconditioner
Hengjie Wang
hengjiew at uci.edu
Fri Sep 9 20:38:38 CDT 2016
Hi Barry,
I checked. On the supercomputer, I had the option "-ksp_view_pre" but it is
not in file I sent you. I am sorry for the confusion.
Regards,
Frank
On Friday, September 9, 2016, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
> > On Sep 9, 2016, at 3:11 PM, frank <hengjiew at uci.edu <javascript:;>>
> wrote:
> >
> > Hi Barry,
> >
> > I think the first KSP view output is from -ksp_view_pre. Before I
> submitted the test, I was not sure whether there would be OOM error or not.
> So I added both -ksp_view_pre and -ksp_view.
>
> But the options file you sent specifically does NOT list the
> -ksp_view_pre so how could it be from that?
>
> Sorry to be pedantic but I've spent too much time in the past trying to
> debug from incorrect information and want to make sure that the information
> I have is correct before thinking. Please recheck exactly what happened.
> Rerun with the exact input file you emailed if that is needed.
>
> Barry
>
> >
> > Frank
> >
> >
> > On 09/09/2016 12:38 PM, Barry Smith wrote:
> >> Why does ksp_view2.txt have two KSP views in it while ksp_view1.txt
> has only one KSPView in it? Did you run two different solves in the 2 case
> but not the one?
> >>
> >> Barry
> >>
> >>
> >>
> >>> On Sep 9, 2016, at 10:56 AM, frank <hengjiew at uci.edu <javascript:;>>
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I want to continue digging into the memory problem here.
> >>> I did find a work around in the past, which is to use less cores per
> node so that each core has 8G memory. However this is deficient and
> expensive. I hope to locate the place that uses the most memory.
> >>>
> >>> Here is a brief summary of the tests I did in past:
> >>>> Test1: Mesh 1536*128*384 | Process Mesh 48*4*12
> >>> Maximum (over computational time) process memory: total
> 7.0727e+08
> >>> Current process memory:
> total 7.0727e+08
> >>> Maximum (over computational time) space PetscMalloc()ed: total
> 6.3908e+11
> >>> Current space PetscMalloc()ed:
> total 1.8275e+09
> >>>
> >>>> Test2: Mesh 1536*128*384 | Process Mesh 96*8*24
> >>> Maximum (over computational time) process memory: total
> 5.9431e+09
> >>> Current process memory:
> total 5.9431e+09
> >>> Maximum (over computational time) space PetscMalloc()ed: total
> 5.3202e+12
> >>> Current space PetscMalloc()ed:
> total 5.4844e+09
> >>>
> >>>> Test3: Mesh 3072*256*768 | Process Mesh 96*8*24
> >>> OOM( Out Of Memory ) killer of the supercomputer terminated the
> job during "KSPSolve".
> >>>
> >>> I attached the output of ksp_view( the third test's output is from
> ksp_view_pre ), memory_view and also the petsc options.
> >>>
> >>> In all the tests, each core can access about 2G memory. In test3,
> there are 4223139840 non-zeros in the matrix. This will consume about
> 1.74M, using double precision. Considering some extra memory used to store
> integer index, 2G memory should still be way enough.
> >>>
> >>> Is there a way to find out which part of KSPSolve uses the most memory?
> >>> Thank you so much.
> >>>
> >>> BTW, there are 4 options remains unused and I don't understand why
> they are omitted:
> >>> -mg_coarse_telescope_mg_coarse_ksp_type value: preonly
> >>> -mg_coarse_telescope_mg_coarse_pc_type value: bjacobi
> >>> -mg_coarse_telescope_mg_levels_ksp_max_it value: 1
> >>> -mg_coarse_telescope_mg_levels_ksp_type value: richardson
> >>>
> >>>
> >>> Regards,
> >>> Frank
> >>>
> >>> On 07/13/2016 05:47 PM, Dave May wrote:
> >>>>
> >>>> On 14 July 2016 at 01:07, frank <hengjiew at uci.edu <javascript:;>>
> wrote:
> >>>> Hi Dave,
> >>>>
> >>>> Sorry for the late reply.
> >>>> Thank you so much for your detailed reply.
> >>>>
> >>>> I have a question about the estimation of the memory usage. There are
> 4223139840 allocated non-zeros and 18432 MPI processes. Double precision is
> used. So the memory per process is:
> >>>> 4223139840 * 8bytes / 18432 / 1024 / 1024 = 1.74M ?
> >>>> Did I do sth wrong here? Because this seems too small.
> >>>>
> >>>> No - I totally f***ed it up. You are correct. That'll teach me for
> fumbling around with my iphone calculator and not using my brain. (Note
> that to convert to MB just divide by 1e6, not 1024^2 - although I
> apparently cannot convert between units correctly....)
> >>>>
> >>>> From the PETSc objects associated with the solver, It looks like it
> _should_ run with 2GB per MPI rank. Sorry for my mistake. Possibilities
> are: somewhere in your usage of PETSc you've introduced a memory leak;
> PETSc is doing a huge over allocation (e.g. as per our discussion of
> MatPtAP); or in your application code there are other objects you have
> forgotten to log the memory for.
> >>>>
> >>>>
> >>>>
> >>>> I am running this job on Bluewater
> >>>> I am using the 7 points FD stencil in 3D.
> >>>>
> >>>> I thought so on both counts.
> >>>>
> >>>> I apologize that I made a stupid mistake in computing the memory per
> core. My settings render each core can access only 2G memory on average
> instead of 8G which I mentioned in previous email. I re-run the job with 8G
> memory per core on average and there is no "Out Of Memory" error. I would
> do more test to see if there is still some memory issue.
> >>>>
> >>>> Ok. I'd still like to know where the memory was being used since my
> estimates were off.
> >>>>
> >>>>
> >>>> Thanks,
> >>>> Dave
> >>>>
> >>>> Regards,
> >>>> Frank
> >>>>
> >>>>
> >>>>
> >>>> On 07/11/2016 01:18 PM, Dave May wrote:
> >>>>> Hi Frank,
> >>>>>
> >>>>>
> >>>>> On 11 July 2016 at 19:14, frank <hengjiew at uci.edu <javascript:;>>
> 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 <javascript:;>>
> 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 <javascript:;>>
> 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 <javascript:;>>
> 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>
> >>>>>>
> >>>>>
> >>>>
> >>> <ksp_view1.txt><ksp_view2.txt><ksp_view3.txt><memory1.txt><
> memory2.txt><petsc_options1.txt><petsc_options2.txt><petsc_options3.txt>
> >
>
>
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