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

[Barry Smith]

  -malloc_log is not helpful because it can only record PETSc memory usage; most of the memory usage with direct solvers will be from SuperLU_Dist


> On Jul 8, 2015, at 5:41 PM, Anthony Haas <aph at email.arizona.edu> wrote:
> 
> Hi Barry,
> 
> For the sequence of problems, will -memory_info and -malloc_log also provide useful information about memory when Superlu_dist or Slepc routines are called?
> 
> Thanks
> 
> Anthony
> 
> 
> 
> On 07/07/2015 01:27 PM, Barry Smith 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>
>