[petsc-users] memory corruption when using harmonic extraction with SLEPc

[Dave May]

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On 6 August 2018 at 17:17, Moritz Cygorek <mcygorek at uottawa.ca> wrote:

> Hi,
>
>
> I have found that the memory corruption takes place at the end of the
> first iteration or the beginning of the second iteration, i.e., at a time
> where I expect the harmonic extraction part to do some calculations.
>

Where is the report from valgrind indicating the exact file/function/line
where the problem occurred?



> I've then played around with the command line options and I found that
> harmonic extraction works when -eps_ncv is set to smaller values.
>
> I have the feeling that the memory needs to sustain this number of vectors
> and the eigenvectors for all processes individually. If I run multiple
> processes on a single computer, much more memory is required for storage
> than when I only use a single process, eventually allocating all of the
> available memory
>
>
> Do you know if this behavior of the harmonic extraction routine
> intended/necessary?
>
>
> Regards,
> Moritz
>
>
>
>
>
>
>
> ------------------------------
> *From:* Dave May <dave.mayhem23 at gmail.com>
> *Sent:* Friday, August 3, 2018 12:59:54 AM
> *To:* Moritz Cygorek
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] memory corruption when using harmonic
> extraction with SLEPc
>
> On Thu, 2 Aug 2018 at 21:32, Moritz Cygorek <mcygorek at uottawa.ca> wrote:
>
>> Hi,
>>
>>
>> I want to diagonalize a huge sparse matrix and I'm using the Kryov-Schur
>> method with harmonic extraction (command line option -eps_harmonic )
>> implemented in SLEPc.
>>
>>
>> I manually distribute a sparse matrix across several CPUs and everything
>> works fine when:
>>
>> - I do _not_ use harmonic extraction
>>
>> - I use harmonic extraction on only a single CPU
>>
>>
>> If I try do use harmonic extraction on multiple CPUs, I get a memory
>> corruption.
>>
>> I'm not quite sure where to look at, but somewhere in the output, I find:
>>
>>
>>
>> [1]PETSC ERROR: PetscMallocValidate: error detected at
>> PetscSignalHandlerDefault() line 145 in /home/applications/sources/
>> libraries/petsc-3.9.3/src/sys/error/signal.c
>> [1]PETSC ERROR: Memory [id=0(9072)] at address 0x145bcd0 is corrupted
>> (probably write past end of array)
>> [1]PETSC ERROR: Memory originally allocated in DSAllocateWork_Private()
>> line 74 in /home/applications/sources/libraries/slepc-3.9.2/src/sys/
>> classes/ds/interface/dspriv.c
>>
>>
>> Now, I have the feeling that this might be a bug in SLEPc because, if I
>> had messed up the matrix initialization and distribution, I should also get
>> a memory corruption when I don't use harmonic extraction, right?
>>
>
> Not necessarily
>
>
>> Any suggestions what might be going on?
>>
>
> Run your code through valgrind and make sure that your application code is
> clean. See here
>
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> If errors are detected in your application code, fix them and see if the
> slepc errors go away. If your code is valgrind clean, send through the
> relevant chunk of the valgrind report indicating exactly where the error is
> occurring
>
> Thanks,
>   Dave
>
>
>
>> Regards,
>>
>> Moritz
>>
>>
>>
>>
>>
>>
>>
>>
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