Hong: thanks for the diagnosis! Marius: how many OpenMP threads are you using per MPI task? In an earlier email, you mentioned the allocation failure at the following line: if ( !(lsum = (doublecomplex*) SUPERLU_MALLOC(sizelsum*num_thread * sizeof(doublecomplex)))) ABORT("Malloc fails for lsum[].");
this is in the solve phase. I think when we do some OpenMP optimization, we allowed several data structures to grow with OpenMP threads. You can try to use 1 thread. The RHS and X memories are easy to compute. However, in order to gauge how much memory is used in the factorization, can you print out the number of nonzeros in the L and U factors? What ordering option are you using? The sparse matrix A looks pretty small. The code can also print out the working storage used during factorization. I am not sure how this printing can be turned on through PETSc. Sherry On Wed, Oct 28, 2020 at 9:43 PM Marius Buerkle <mbuer...@web.de> wrote: > Thanks for the swift reply. > > I also realized if I reduce the number of RHS then it works. But I am > running the code on a cluster with 256GB ram / node. One dense matrix > would be around ~30 Gb so 60 Gb, which is large but does exceed the > memory of even one node and I also get the seg fault if I run it on several > nodes. Moreover, it works well with MUMPS and MKL_CPARDISO solver. The > maxium memory used when using MUMPS is around 150 Gb during the solver > phase but for SuperLU_dist it crashed even before reaching the solver > phase. Could there be such a large difference in memory usage between > SuperLu_dist and MUMPS ? > > > > best, > > marius > > *Gesendet:* Donnerstag, 29. Oktober 2020 um 10:10 Uhr > *Von:* "Zhang, Hong" <hzh...@mcs.anl.gov> > *An:* "Marius Buerkle" <mbuer...@web.de> > *Cc:* "petsc-users@mcs.anl.gov" <petsc-users@mcs.anl.gov>, "Sherry Li" < > xia...@nersc.gov> > *Betreff:* Re: Re: [petsc-users] superlu_dist segfault > Marius, > I tested your code with petsc-release on my mac laptop using np=2 cores. I > first tested a small matrix data file successfully. Then I switch to your > data file and run out of memory, likely due to the dense matrices B and X. > I got an error "Your system has run out of application memory" from my > laptop. > > The sparse matrix A has size 42549 by 42549. Your code creates dense > matrices B and X with the same size -- a huge memory requirement! > By replacing B and X with size 42549 by nrhs (nrhs =< 4000), I had the > code run well with np=2. Note the error message you got > [23]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > The modified code I used is attached. > Hong > > ------------------------------ > *From:* Marius Buerkle <mbuer...@web.de> > *Sent:* Tuesday, October 27, 2020 10:01 PM > *To:* Zhang, Hong <hzh...@mcs.anl.gov> > *Cc:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov>; Sherry Li < > xia...@nersc.gov> > *Subject:* Aw: Re: [petsc-users] superlu_dist segfault > > Hi, > > I recompiled PETSC with debug option, now I get a seg fault at a different > position > > [23]PETSC ERROR: > ------------------------------------------------------------------------ > [23]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [23]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [23]PETSC ERROR: or see > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > [23]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS > X to find memory corruption errors > [23]PETSC ERROR: likely location of problem given in stack below > [23]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [23]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > [23]PETSC ERROR: INSTEAD the line number of the start of the function > [23]PETSC ERROR: is given. > [23]PETSC ERROR: [23] SuperLU_DIST:pzgssvx line 242 > /home/cdfmat_marius/prog/petsc/git/release/petsc/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c > [23]PETSC ERROR: [23] MatMatSolve_SuperLU_DIST line 211 > /home/cdfmat_marius/prog/petsc/git/release/petsc/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c > [23]PETSC ERROR: [23] MatMatSolve line 3466 > /home/cdfmat_marius/prog/petsc/git/release/petsc/src/mat/interface/matrix.c > [23]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [23]PETSC ERROR: Signal received > > I made a small reproducer. The matrix is a bit too big so I cannot attach > it directly to the email, but I put it in the cloud > https://1drv.ms/u/s!AqZsng1oUcKzjYxGMGHojLRG09Sf1A?e=7uHnmw > > Best, > Marius > > > *Gesendet:* Dienstag, 27. Oktober 2020 um 23:11 Uhr > *Von:* "Zhang, Hong" <hzh...@mcs.anl.gov> > *An:* "Marius Buerkle" <mbuer...@web.de>, "petsc-users@mcs.anl.gov" < > petsc-users@mcs.anl.gov>, "Sherry Li" <xia...@nersc.gov> > *Betreff:* Re: [petsc-users] superlu_dist segfault > Marius, > It fails at the line 1075 in file > /home/petsc3.14.release/arch-linux-c-debug/externalpackages/git.superlu_dist/SRC/pzgstrs.c > if ( !(lsum = (doublecomplex*)SUPERLU_MALLOC(sizelsum*num_thread * > sizeof(doublecomplex)))) ABORT("Malloc fails for lsum[]."); > > We do not know what it means. You may use a debugger to check the values > of the variables involved. > I'm cc'ing Sherry (superlu_dist developer), or you may send us a > stand-alone short code that reproduce the error. We can help on its > investigation. > Hong > > > ------------------------------ > *From:* petsc-users <petsc-users-boun...@mcs.anl.gov> on behalf of Marius > Buerkle <mbuer...@web.de> > *Sent:* Tuesday, October 27, 2020 8:46 AM > *To:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject:* [petsc-users] superlu_dist segfault > > Hi, > > When using MatMatSolve with superlu_dist I get a segmentation fault: > > Malloc fails for lsum[]. at line 1075 in file > /home/petsc3.14.release/arch-linux-c-debug/externalpackages/git.superlu_dist/SRC/pzgstrs.c > > The matrix size is not particular big and I am using the petsc release > branch and superlu_dist is v6.3.0 I think. > > Best, > Marius >