[petsc-users] Can't expand MemType 1: jcol 16104

Tue Jul 7 17:08:19 CDT 2015

For superlu_dist failure, this occurs during symbolic factorization.  Since
you are using serial symbolic factorization, it requires the entire graph
of A to be available in the memory of one MPI task. How much memory do you
have for each MPI task?

It won't help even if you use more processes.  You should try to use
parallel symbolic factorization option.

Another point.  You set up process grid as:
       Process grid nprow 32 x npcol 20
For better performance, you show swap the grid dimension. That is, it's
better to use 20 x 32, never gives nprow larger than npcol.

Sherry

On Tue, Jul 7, 2015 at 1:27 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>    I would suggest running a sequence of problems, 101 by 101 111 by 111
> etc and get the memory usage in each case (when you run out of memory you
> can get NO useful information out about memory needs). You can then plot
> memory usage as a function of problem size to get a handle on how much
> memory it is using.  You can also run on more and more processes (which
> have a total of more memory) to see how large a problem you may be able to
> reach.
>
>    MUMPS also has an "out of core" version (which we have never used) that
> could in theory anyways let you get to large problems if you have lots of
> disk space, but you are on your own figuring out how to use it.
>
>   Barry
>
> > On Jul 7, 2015, at 2:37 PM, Anthony Paul Haas <aph at email.arizona.edu>
> wrote:
> >
> > Hi Jose,
> >
> > In my code, I use once PETSc to solve a linear system to get the
> baseflow (without using SLEPc) and then I use SLEPc to do the stability
> analysis of that baseflow. This is why, there are some SLEPc options that
> are not used in test.out-superlu_dist-151x151 (when I am solving for the
> baseflow with PETSc only). I have attached a 101x101 case for which I get
> the eigenvalues. That case works fine. However If i increase to 151x151, I
> get the error that you can see in test.out-superlu_dist-151x151 (similar
> error with mumps: see test.out-mumps-151x151 line 2918 ). If you look a the
> very end of the files test.out-superlu_dist-151x151 and
> test.out-mumps-151x151, you will see that the last info message printed is:
> >
> > On Processor (after EPSSetFromOptions)  0    memory:
> 0.65073152000E+08          =====>  (see line 807 of module_petsc.F90)
> >
> > This means that the memory error probably occurs in the call to EPSSolve
> (see module_petsc.F90 line 810). I would like to evaluate how much memory
> is required by the most memory intensive operation within EPSSolve. Since I
> am solving a generalized EVP, I would imagine that it would be the LU
> decomposition. But is there an accurate way of doing it?
> >
> > Before starting with iterative solvers, I would like to exploit as much
> as I can direct solvers. I tried GMRES with default preconditioner at some
> point but I had convergence problem. What solver/preconditioner would you
> recommend for a generalized non-Hermitian (EPS_GNHEP) EVP?
> >
> > Thanks,
> >
> > Anthony
> >
> > On Tue, Jul 7, 2015 at 12:17 AM, Jose E. Roman <jroman at dsic.upv.es>
> wrote:
> >
> > El 07/07/2015, a las 02:33, Anthony Haas escribió:
> >
> > > Hi,
> > >
> > > I am computing eigenvalues using PETSc/SLEPc and superlu_dist for the
> LU decomposition (my problem is a generalized eigenvalue problem). The code
> runs fine for a grid with 101x101 but when I increase to 151x151, I get the
> following error:
> > >
> > > Can't expand MemType 1: jcol 16104   (and then [NID 00037] 2015-07-06
> 19:19:17 Apid 31025976: OOM killer terminated this process.)
> > >
> > > It seems to be a memory problem. I monitor the memory usage as far as
> I can and it seems that memory usage is pretty low. The most memory
> intensive part of the program is probably the LU decomposition in the
> context of the generalized EVP. Is there a way to evaluate how much memory
> will be required for that step? I am currently running the debug version of
> the code which I would assume would use more memory?
> > >
> > > I have attached the output of the job. Note that the program uses
> twice PETSc: 1) to solve a linear system for which no problem occurs, and,
> 2) to solve the Generalized EVP with SLEPc, where I get the error.
> > >
> > > Thanks
> > >
> > > Anthony
> > > <test.out-superlu_dist-151x151>
> >
> > In the output you are attaching there are no SLEPc objects in the report
> and SLEPc options are not used. It seems that SLEPc calls are skipped?
> >
> > Do you get the same error with MUMPS? Have you tried to solve linear
> systems with a preconditioned iterative solver?
> >
> > Jose
> >
> >
> >
> <module_petsc.F90><test.out-mumps-151x151><test.out_superlu_dist-101x101><test.out-superlu_dist-151x151>
>
>
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