On Thursday, 15 September 2016, frank <hengj...@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? > > 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 <bsm...@mcs.anl.gov > <javascript:_e(%7B%7D,'cvml','bsm...@mcs.anl.gov');>> wrote: > >> >> > On Sep 9, 2016, at 3:11 PM, frank <hengj...@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 <hengj...@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 <hengj...@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 <hengj...@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 <hengj...@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 <hengj...@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 <hengj...@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_options3.txt> >> > >> >> >