Thanks for letting us know, now we can rest easy.
> On Jun 5, 2019, at 1:00 PM, Zhang, Junchao <jczh...@mcs.anl.gov> wrote: > > OK, I see. I mistakenly read PetscMemoryGetCurrentUsage as > PetscMallocGetCurrentUsage. You should also do PetscMallocGetCurrentUsage(), > so that we know whether the increased memory is allocated by PETSc. > > On Wed, Jun 5, 2019, 9:58 AM Sanjay GOVINDJEE <s...@berkeley.edu> wrote: > PetscMemoryGetCurrentUsage( ) is just a cover for rgetusage( ), so the use of > the function is unrelated to Petsc. The only difference here is mpich versus > openmpi. > Notwithstanding, I can make a plot of the sum of the deltas around kspsolve. > > Sent from my iPad > > On Jun 5, 2019, at 7:22 AM, Zhang, Junchao <jczh...@mcs.anl.gov> wrote: > >> Sanjay, >> It sounds like the memory is allocated by PETSc, since you call >> PetscMemoryGetCurrentUsage(). Make sure you use the latest PETSc version. >> You can also do an experiment that puts two PetscMemoryGetCurrentUsage() >> before & after KSPSolve(), calculates the delta, and then sums over >> processes, so we know whether the memory is allocated in KSPSolve(). >> >> --Junchao Zhang >> >> >> On Wed, Jun 5, 2019 at 1:19 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> >>>> >>> >>
