Are you reusing the same KSP the whole time, just making calls to KSPSolve, or are you creating a new KSP object?
Do you make any calls to KSPReset()? Are you doing any MPI_Comm_dup()? Are you attaching any attributes to MPI communicators? Thanks > On Jun 5, 2019, at 1:18 AM, Sanjay Govindjee <s...@berkeley.edu> wrote: > > Junchao, > > Attached is a graph of total RSS from my Mac using openmpi and mpich > (installed with --download-openmpi and --download-mpich). > > The difference is pretty stark! The WaitAll( ) in my part of the code > fixed the run away memory > problem using openmpi but definitely not with mpich. > > Tomorrow I hope to get my linux box set up; unfortunately it needs an OS > update :( > Then I can try to run there and reproduce the same (or find out it is a Mac > quirk, though the > reason I started looking at this was that a use on an HPC system pointed it > out to me). > > -sanjay > > PS: To generate the data, all I did was place a call to > PetscMemoryGetCurrentUsage( ) right after KSPSolve( ), followed by an > MPI_AllReduce( ) to sum across the job (4 processors). > > On 6/4/19 4:27 PM, Zhang, Junchao wrote: >> Hi, Sanjay, >> I managed to use Valgrind massif + MPICH master + PETSc master. I ran ex5 >> 500 time steps with "mpirun -n 4 valgrind --tool=massif --max-snapshots=200 >> --detailed-freq=1 ./ex5 -da_grid_x 512 -da_grid_y 512 -ts_type beuler >> -ts_max_steps 500 -malloc" >> I visualized the output with massif-visualizer. From the attached picture, >> we can see the total heap size keeps constant most of the time and is NOT >> monotonically increasing. We can also see MPI only allocated memory at >> initialization time and kept it. So it is unlikely that MPICH keeps >> allocating memory in each KSPSolve call. >> From graphs you sent, I can only see RSS is randomly increased after >> KSPSolve, but that does not mean heap size keeps increasing. I recommend >> you also profile your code with valgrind massif and visualize it. I failed >> to install massif-visualizer on MacBook and CentOS. But I easily got it >> installed on Ubuntu. >> I want you to confirm that with the MPI_Waitall fix, you still run out of >> memory with MPICH (but not OpenMPI). If needed, I can hack MPICH to get its >> current memory usage so that we can calculate its difference after each >> KSPSolve call. >> >> <massif-ex5.png> >> >> >> --Junchao Zhang >> >> >> On Mon, Jun 3, 2019 at 6:36 PM Sanjay Govindjee <s...@berkeley.edu> wrote: >> Junchao, >> I won't be feasible to share the code but I will run a similar test as you >> have done (large problem); I will >> try with both MPICH and OpenMPI. I also agree that deltas are not ideal as >> there they do not account for latency in the freeing of memory >> etc. But I will note when we have the memory growth issue latency >> associated with free( ) appears not to be in play since the total >> memory footprint grows monotonically. >> >> I'll also have a look at massif. If you figure out the interface, and can >> send me the lines to instrument the code with that will save me >> some time. >> -sanjay >> On 6/3/19 3:17 PM, Zhang, Junchao wrote: >>> Sanjay & Barry, >>> Sorry, I made a mistake that I said I could reproduced Sanjay's >>> experiments. I found 1) to correctly use PetscMallocGetCurrentUsage() when >>> petsc is configured without debugging, I have to add -malloc to run the >>> program. 2) I have to instrument the code outside of KSPSolve(). In my >>> case, it is in SNESSolve_NEWTONLS. In old experiments, I did it inside >>> KSPSolve. Since KSPSolve can recursively call KSPSolve, the old results >>> were misleading. >>> With these fixes, I measured differences of RSS and Petsc malloc >>> before/after KSPSolve. I did experiments on MacBook using >>> src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c with commands >>> like mpirun -n 4 ./ex5 -da_grid_x 64 -da_grid_y 64 -ts_type beuler >>> -ts_max_steps 500 -malloc. >>> I find if the grid size is small, I can see a non-zero RSS-delta randomly, >>> either with one mpi rank or multiple ranks, with MPICH or OpenMPI. If I >>> increase grid sizes, e.g., -da_grid_x 256 -da_grid_y 256, I only see >>> non-zero RSS-delta randomly at the first few iterations (with MPICH or >>> OpenMPI). When the computer workload is high by simultaneously running >>> ex5-openmpi and ex5-mpich, the MPICH one pops up much more non-zero >>> RSS-delta. But "Malloc Delta" behavior is stable across all runs. There is >>> only one nonzero malloc delta value in the first KSPSolve call. All >>> remaining are zero. Something like this: >>> mpirun -n 4 ./ex5-mpich -da_grid_x 256 -da_grid_y 256 -ts_type beuler >>> -ts_max_steps 500 -malloc >>> RSS Delta= 32489472, Malloc Delta= 26290304, RSS End= >>> 136114176 >>> RSS Delta= 32768, Malloc Delta= 0, RSS End= >>> 138510336 >>> RSS Delta= 0, Malloc Delta= 0, RSS End= >>> 138522624 >>> RSS Delta= 0, Malloc Delta= 0, RSS End= >>> 138539008 >>> So I think I can conclude there is no unfreed memory in KSPSolve() >>> allocated by PETSc. Has MPICH allocated unfreed memory in KSPSolve? That >>> is possible and I am trying to find a way like PetscMallocGetCurrentUsage() >>> to measure that. Also, I think RSS delta is not a good way to measure >>> memory allocation. It is dynamic and depends on state of the computer >>> (swap, shared libraries loaded etc) when running the code. We should focus >>> on malloc instead. If there was a valgrind tool, like performance >>> profiling tools, that can let users measure memory allocated but not freed >>> in a user specified code segment, that would be very helpful in this case. >>> But I have not found one. >>> >>> Sanjay, did you say currently you could run with OpenMPI without out of >>> memory, but with MPICH, you ran out of memory? Is it feasible to share >>> your code so that I can test with? Thanks. >>> >>> --Junchao Zhang >>> >>> On Sat, Jun 1, 2019 at 3:21 AM Sanjay Govindjee <s...@berkeley.edu> wrote: >>> Barry, >>> >>> If you look at the graphs I generated (on my Mac), you will see that >>> OpenMPI and MPICH have very different values (along with the fact that >>> MPICH does not seem to adhere >>> to the standard (for releasing MPI_ISend resources following and MPI_Wait). >>> >>> -sanjay >>> >>> PS: I agree with Barry's assessment; this is really not that acceptable. >>> >>> On 6/1/19 1:00 AM, Smith, Barry F. wrote: >>> > Junchao, >>> > >>> > This is insane. Either the OpenMPI library or something in the OS >>> > underneath related to sockets and interprocess communication is grabbing >>> > additional space for each round of MPI communication! Does MPICH have >>> > the same values or different values than OpenMP? When you run on Linux do >>> > you get the same values as Apple or different. --- Same values seem to >>> > indicate the issue is inside OpenMPI/MPICH different values indicates >>> > problem is more likely at the OS level. Does this happen only with the >>> > default VecScatter that uses blocking MPI, what happens with PetscSF >>> > under Vec? Is it somehow related to PETSc's use of nonblocking sends and >>> > receives? One could presumably use valgrind to see exactly what lines in >>> > what code are causing these increases. I don't think we can just shrug >>> > and say this is the way it is, we need to track down and understand the >>> > cause (and if possible fix). >>> > >>> > Barry >>> > >>> > >>> >> On May 31, 2019, at 2:53 PM, Zhang, Junchao <jczh...@mcs.anl.gov> wrote: >>> >> >>> >> Sanjay, >>> >> I tried petsc with MPICH and OpenMPI on my Macbook. I inserted >>> >> PetscMemoryGetCurrentUsage/PetscMallocGetCurrentUsage at the beginning >>> >> and end of KSPSolve and then computed the delta and summed over >>> >> processes. Then I tested with >>> >> src/ts/examples/tutorials/advection-diffusion-reaction/ex5.c >>> >> With OpenMPI, >>> >> mpirun -n 4 ./ex5 -da_grid_x 128 -da_grid_y 128 -ts_type beuler >>> >> -ts_max_steps 500 > 128.log >>> >> grep -n -v "RSS Delta= 0, Malloc Delta= 0" 128.log >>> >> 1:RSS Delta= 69632, Malloc Delta= 0 >>> >> 2:RSS Delta= 69632, Malloc Delta= 0 >>> >> 3:RSS Delta= 69632, Malloc Delta= 0 >>> >> 4:RSS Delta= 69632, Malloc Delta= 0 >>> >> 9:RSS Delta=9.25286e+06, Malloc Delta= 0 >>> >> 22:RSS Delta= 49152, Malloc Delta= 0 >>> >> 44:RSS Delta= 20480, Malloc Delta= 0 >>> >> 53:RSS Delta= 49152, Malloc Delta= 0 >>> >> 66:RSS Delta= 4096, Malloc Delta= 0 >>> >> 97:RSS Delta= 16384, Malloc Delta= 0 >>> >> 119:RSS Delta= 20480, Malloc Delta= 0 >>> >> 141:RSS Delta= 53248, Malloc Delta= 0 >>> >> 176:RSS Delta= 16384, Malloc Delta= 0 >>> >> 308:RSS Delta= 16384, Malloc Delta= 0 >>> >> 352:RSS Delta= 16384, Malloc Delta= 0 >>> >> 550:RSS Delta= 16384, Malloc Delta= 0 >>> >> 572:RSS Delta= 16384, Malloc Delta= 0 >>> >> 669:RSS Delta= 40960, Malloc Delta= 0 >>> >> 924:RSS Delta= 32768, Malloc Delta= 0 >>> >> 1694:RSS Delta= 20480, Malloc Delta= 0 >>> >> 2099:RSS Delta= 16384, Malloc Delta= 0 >>> >> 2244:RSS Delta= 20480, Malloc Delta= 0 >>> >> 3001:RSS Delta= 16384, Malloc Delta= 0 >>> >> 5883:RSS Delta= 16384, Malloc Delta= 0 >>> >> >>> >> If I increased the grid >>> >> mpirun -n 4 ./ex5 -da_grid_x 512 -da_grid_y 512 -ts_type beuler >>> >> -ts_max_steps 500 -malloc_test >512.log >>> >> grep -n -v "RSS Delta= 0, Malloc Delta= 0" 512.log >>> >> 1:RSS Delta=1.05267e+06, Malloc Delta= 0 >>> >> 2:RSS Delta=1.05267e+06, Malloc Delta= 0 >>> >> 3:RSS Delta=1.05267e+06, Malloc Delta= 0 >>> >> 4:RSS Delta=1.05267e+06, Malloc Delta= 0 >>> >> 13:RSS Delta=1.24932e+08, Malloc Delta= 0 >>> >> >>> >> So we did see RSS increase in 4k-page sizes after KSPSolve. As long as >>> >> no memory leaks, why do you care about it? Is it because you run out of >>> >> memory? >>> >> >>> >> On Thu, May 30, 2019 at 1:59 PM Smith, Barry F. <bsm...@mcs.anl.gov> >>> >> wrote: >>> >> >>> >> Thanks for the update. So the current conclusions are that using the >>> >> Waitall in your code >>> >> >>> >> 1) solves the memory issue with OpenMPI in your code >>> >> >>> >> 2) does not solve the memory issue with PETSc KSPSolve >>> >> >>> >> 3) MPICH has memory issues both for your code and PETSc KSPSolve >>> >> (despite) the wait all fix? >>> >> >>> >> If you literately just comment out the call to KSPSolve() with OpenMPI >>> >> is there no growth in memory usage? >>> >> >>> >> >>> >> Both 2 and 3 are concerning, indicate possible memory leak bugs in MPICH >>> >> and not freeing all MPI resources in KSPSolve() >>> >> >>> >> Junchao, can you please investigate 2 and 3 with, for example, a TS >>> >> example that uses the linear solver (like with -ts_type beuler)? Thanks >>> >> >>> >> >>> >> Barry >>> >> >>> >> >>> >> >>> >>> On May 30, 2019, at 1:47 PM, Sanjay Govindjee <s...@berkeley.edu> wrote: >>> >>> >>> >>> Lawrence, >>> >>> Thanks for taking a look! This is what I had been wondering about -- >>> >>> my knowledge of MPI is pretty minimal and >>> >>> this origins of the routine were from a programmer we hired a decade+ >>> >>> back from NERSC. I'll have to look into >>> >>> VecScatter. It will be great to dispense with our roll-your-own >>> >>> routines (we even have our own reduceALL scattered around the code). >>> >>> >>> >>> Interestingly, the MPI_WaitALL has solved the problem when using >>> >>> OpenMPI but it still persists with MPICH. Graphs attached. >>> >>> I'm going to run with openmpi for now (but I guess I really still need >>> >>> to figure out what is wrong with MPICH and WaitALL; >>> >>> I'll try Barry's suggestion of >>> >>> --download-mpich-configure-arguments="--enable-error-messages=all >>> >>> --enable-g" later today and report back). >>> >>> >>> >>> Regarding MPI_Barrier, it was put in due a problem that some processes >>> >>> were finishing up sending and receiving and exiting the subroutine >>> >>> before the receiving processes had completed (which resulted in data >>> >>> loss as the buffers are freed after the call to the routine). >>> >>> MPI_Barrier was the solution proposed >>> >>> to us. I don't think I can dispense with it, but will think about some >>> >>> more. >>> >>> >>> >>> I'm not so sure about using MPI_IRecv as it will require a bit of >>> >>> rewriting since right now I process the received >>> >>> data sequentially after each blocking MPI_Recv -- clearly slower but >>> >>> easier to code. >>> >>> >>> >>> Thanks again for the help. >>> >>> >>> >>> -sanjay >>> >>> >>> >>> On 5/30/19 4:48 AM, Lawrence Mitchell wrote: >>> >>>> Hi Sanjay, >>> >>>> >>> >>>>> On 30 May 2019, at 08:58, Sanjay Govindjee via petsc-users >>> >>>>> <petsc-users@mcs.anl.gov> wrote: >>> >>>>> >>> >>>>> The problem seems to persist but with a different signature. Graphs >>> >>>>> attached as before. >>> >>>>> >>> >>>>> Totals with MPICH (NB: single run) >>> >>>>> >>> >>>>> For the CG/Jacobi data_exchange_total = 41,385,984; >>> >>>>> kspsolve_total = 38,289,408 >>> >>>>> For the GMRES/BJACOBI data_exchange_total = 41,324,544; >>> >>>>> kspsolve_total = 41,324,544 >>> >>>>> >>> >>>>> Just reading the MPI docs I am wondering if I need some sort of >>> >>>>> MPI_Wait/MPI_Waitall before my MPI_Barrier in the data exchange >>> >>>>> routine? >>> >>>>> I would have thought that with the blocking receives and the >>> >>>>> MPI_Barrier that everything will have fully completed and cleaned up >>> >>>>> before >>> >>>>> all processes exited the routine, but perhaps I am wrong on that. >>> >>>> Skimming the fortran code you sent you do: >>> >>>> >>> >>>> for i in ...: >>> >>>> call MPI_Isend(..., req, ierr) >>> >>>> >>> >>>> for i in ...: >>> >>>> call MPI_Recv(..., ierr) >>> >>>> >>> >>>> But you never call MPI_Wait on the request you got back from the >>> >>>> Isend. So the MPI library will never free the data structures it >>> >>>> created. >>> >>>> >>> >>>> The usual pattern for these non-blocking communications is to allocate >>> >>>> an array for the requests of length nsend+nrecv and then do: >>> >>>> >>> >>>> for i in nsend: >>> >>>> call MPI_Isend(..., req[i], ierr) >>> >>>> for j in nrecv: >>> >>>> call MPI_Irecv(..., req[nsend+j], ierr) >>> >>>> >>> >>>> call MPI_Waitall(req, ..., ierr) >>> >>>> >>> >>>> I note also there's no need for the Barrier at the end of the routine, >>> >>>> this kind of communication does neighbourwise synchronisation, no need >>> >>>> to add (unnecessary) global synchronisation too. >>> >>>> >>> >>>> As an aside, is there a reason you don't use PETSc's VecScatter to >>> >>>> manage this global to local exchange? >>> >>>> >>> >>>> Cheers, >>> >>>> >>> >>>> Lawrence >>> >>> <cg_mpichwall.png><cg_wall.png><gmres_mpichwall.png><gmres_wall.png> >>> >> > > <mac-mpich-openmpi.png>
