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

Wed Jul 8 08:46:33 CDT 2015

Did you find out how to change option to use parallel symbolic
factorization?  Perhaps PETSc team can help.

Sherry

On Tue, Jul 7, 2015 at 3:58 PM, Xiaoye S. Li <xsli at lbl.gov> wrote:

> Is there an inquiry function that tells you all the available options?
>
> Sherry
>
> On Tue, Jul 7, 2015 at 3:25 PM, Anthony Paul Haas <aph at email.arizona.edu>
> wrote:
>
>> Hi Sherry,
>>
>> Thanks for your message. I have used superlu_dist default options. I did
>> not realize that I was doing serial symbolic factorization. That is
>> probably the cause of my problem.
>> Each node on Garnet has 60GB usable memory and I can run with 1,2,4,8,16
>> or 32 core per node.
>>
>> So I should use:
>>
>> -mat_superlu_dist_r 20
>> -mat_superlu_dist_c 32
>>
>> How do you specify the parallel symbolic factorization option? is it
>> -mat_superlu_dist_matinput 1
>>
>> Thanks,
>>
>> Anthony
>>
>>
>> On Tue, Jul 7, 2015 at 3:08 PM, Xiaoye S. Li <xsli at lbl.gov> wrote:
>>
>>> 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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