[petsc-users] Performance of the Telescope Multigrid Preconditioner
Matthew Knepley
knepley at gmail.com
Tue Oct 4 15:20:33 CDT 2016
On Tue, Oct 4, 2016 at 3:09 PM, frank <hengjiew at uci.edu> wrote:
> Hi Dave,
>
> Thank you for the reply.
> What do you mean by the "nested calls to KSPSolve"?
>
KSPSolve is called again after redistributing the computation.
> I tried to call KSPSolve twice, but the the second solve converged in 0
> iteration. KSPSolve seems to remember the solution. How can I force both
> solves start from the same initial guess?
>
Did you zero the solution vector between solves? VecSet(x, 0.0);
Matt
> Thank you.
>
> Frank
>
>
>
> On 10/04/2016 12:56 PM, Dave May wrote:
>
>
>
> On Tuesday, 4 October 2016, frank <hengjiew at uci.edu> wrote:
>
>> Hi,
>> This question is follow-up of the thread "Question about memory usage in
>> Multigrid preconditioner".
>> I used to have the "Out of Memory(OOM)" problem when using the
>> CG+Telescope MG solver with 32768 cores. Adding the "-matrap 0;
>> -matptap_scalable" option did solve that problem.
>>
>> Then I test the scalability by solving a 3d poisson eqn for 1 step. I
>> used one sub-communicator in all the tests. The difference between the
>> petsc options in those tests are: 1 the pc_telescope_reduction_factor; 2
>> the number of multigrid levels in the up/down solver. The function
>> "ksp_solve" is timed. It is kind of slow and doesn't scale at all.
>>
>> Test1: 512^3 grid points
>> Core# telescope_reduction_factor MG levels# for up/down
>> solver Time for KSPSolve (s)
>> 512 8 4 /
>> 3 6.2466
>> 4096 64 5 /
>> 3 0.9361
>> 32768 64 4 /
>> 3 4.8914
>>
>> Test2: 1024^3 grid points
>> Core# telescope_reduction_factor MG levels# for up/down
>> solver Time for KSPSolve (s)
>> 4096 64 5 / 4
>> 3.4139
>> 8192 128 5 /
>> 4 2.4196
>> 16384 32 5 / 3
>> 5.4150
>> 32768 64 5 /
>> 3 5.6067
>> 65536 128 5 /
>> 3 6.5219
>>
>
> You have to be very careful how you interpret these numbers. Your solver
> contains nested calls to KSPSolve, and unfortunately as a result the
> numbers you report include setup time. This will remain true even if you
> call KSPSetUp on the outermost KSP.
>
> Your email concerns scalability of the silver application, so let's focus
> on that issue.
>
> The only way to clearly separate setup from solve time is to perform two
> identical solves. The second solve will not require any setup. You should
> monitor the second solve via a new PetscStage.
>
> This was what I did in the telescope paper. It was the only way to
> understand the setup cost (and scaling) cf the solve time (and scaling).
>
> Thanks
> Dave
>
>
>
>> I guess I didn't set the MG levels properly. What would be the efficient
>> way to arrange the MG levels?
>> Also which preconditionr at the coarse mesh of the 2nd communicator
>> should I use to improve the performance?
>>
>> I attached the test code and the petsc options file for the 1024^3 cube
>> with 32768 cores.
>>
>> Thank you.
>>
>> Regards,
>> Frank
>>
>>
>>
>>
>>
>>
>> On 09/15/2016 03:35 AM, Dave May wrote:
>>
>> HI all,
>>
>> I the only unexpected memory usage I can see is associated with the call
>> to MatPtAP().
>> Here is something you can try immediately.
>> Run your code with the additional options
>> -matrap 0 -matptap_scalable
>>
>> I didn't realize this before, but the default behaviour of MatPtAP in
>> parallel is actually to to explicitly form the transpose of P (e.g.
>> assemble R = P^T) and then compute R.A.P.
>> You don't want to do this. The option -matrap 0 resolves this issue.
>>
>> The implementation of P^T.A.P has two variants.
>> The scalable implementation (with respect to memory usage) is selected
>> via the second option -matptap_scalable.
>>
>> Try it out - I see a significant memory reduction using these options for
>> particular mesh sizes / partitions.
>>
>> I've attached a cleaned up version of the code you sent me.
>> There were a number of memory leaks and other issues.
>> The main points being
>> * You should call DMDAVecGetArrayF90() before VecAssembly{Begin,End}
>> * You should call PetscFinalize(), otherwise the option -log_summary
>> (-log_view) will not display anything once the program has completed.
>>
>>
>> Thanks,
>> Dave
>>
>>
>> On 15 September 2016 at 08:03, Hengjie Wang <hengjiew at uci.edu> wrote:
>>
>>> Hi Dave,
>>>
>>> Sorry, I should have put more comment to explain the code.
>>> The number of process in each dimension is the same: Px = Py=Pz=P. So is
>>> the domain size.
>>> So if the you want to run the code for a 512^3 grid points on 16^3
>>> cores, you need to set "-N 512 -P 16" in the command line.
>>> I add more comments and also fix an error in the attached code. ( The
>>> error only effects the accuracy of solution but not the memory usage. )
>>>
>>> Thank you.
>>> Frank
>>>
>>>
>>> On 9/14/2016 9:05 PM, Dave May wrote:
>>>
>>>
>>>
>>> On Thursday, 15 September 2016, Dave May <dave.mayhem23 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Thursday, 15 September 2016, frank <hengjiew at uci.edu> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I write a simple code to re-produce the error. I hope this can help to
>>>>> diagnose the problem.
>>>>> The code just solves a 3d poisson equation.
>>>>>
>>>>
>>>> Why is the stencil width a runtime parameter?? And why is the default
>>>> value 2? For 7-pnt FD Laplace, you only need a stencil width of 1.
>>>>
>>>> Was this choice made to mimic something in the real application code?
>>>>
>>>
>>> Please ignore - I misunderstood your usage of the param set by -P
>>>
>>>
>>>>
>>>>
>>>>>
>>>>> I run the code on a 1024^3 mesh. The process partition is 32 * 32 *
>>>>> 32. That's when I re-produce the OOM error. Each core has about 2G memory.
>>>>> I also run the code on a 512^3 mesh with 16 * 16 * 16 processes. The
>>>>> ksp solver works fine.
>>>>> I attached the code, ksp_view_pre's output and my petsc option file.
>>>>>
>>>>> Thank you.
>>>>> Frank
>>>>>
>>>>> On 09/09/2016 06:38 PM, Hengjie Wang wrote:
>>>>>
>>>>> 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> 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> 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> 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> 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>
>>>>>> >>>>>>
>>>>>> >>>>>
>>>>>> >>>>
>>>>>> >>> <ksp_view1.txt><ksp_view2.txt><ksp_view3.txt><memory1.txt><m
>>>>>> emory2.txt><petsc_options1.txt><petsc_options2.txt><petsc_op
>>>>>> tions3.txt>
>>>>>> >
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>
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--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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