[petsc-users] Big discrepancy between machines

[Timothée Nicolas]

There is a diference in valgrind indeed between the two. It seems to be
clean on my desktop Mac OS X but not on the cluster. I'll try to see what's
causing this. I still don't understand well what's causing memory leaks in
the case where all PETSc objects are freed correctly (as can pbe checked
with -log_summary).

Also, I have tried running either

valgrind ./my_code -option1 -option2...

or

valgrind mpiexec -n 1 ./my_code -option1 -option2...

It seems the second is the correct way to proceed right ? This gives very
different behaviour for valgrind.

Timothee



2015-12-14 17:38 GMT+09:00 Timothée Nicolas <timothee.nicolas at gmail.com>:

> OK, I'll try that, thx
>
> 2015-12-14 17:38 GMT+09:00 Dave May <dave.mayhem23 at gmail.com>:
>
>> You have the configure line, so it should be relatively straight forward
>> to configure / build petsc in your home directory.
>>
>>
>> On 14 December 2015 at 09:34, Timothée Nicolas <
>> timothee.nicolas at gmail.com> wrote:
>>
>>> OK, The problem is that I don't think I can change this easily as far as
>>> the cluster is concerned. I obtain access to petsc by loading the petsc
>>> module, and even if I have a few choices, I don't see any debug builds...
>>>
>>> 2015-12-14 17:26 GMT+09:00 Dave May <dave.mayhem23 at gmail.com>:
>>>
>>>>
>>>>
>>>> On Monday, 14 December 2015, Timothée Nicolas <
>>>> timothee.nicolas at gmail.com> wrote:
>>>>
>>>>> Hum, OK. I use FORTRAN by the way. Is your comment still valid ?
>>>>>
>>>>
>>>> No. Fortran compilers init variables to zero.
>>>> In this case, I would run a debug build on your OSX machine through
>>>> valgrind and make sure it is clean.
>>>>
>>>> Other obvious thing to check what happens if use exactly the same
>>>> petsc builds on both machines. I see 3.6.1 and 3.6.0 are being used.
>>>>
>>>> For all this type of checking, I would definitely use debug builds on
>>>> both machines. Your cluster build is using the highest level of
>>>> optimization...
>>>>
>>>>
>>>>
>>>>
>>>>> I'll check anyway, but I thought I had been careful about this sort of
>>>>> things.
>>>>>
>>>>> Also, I thought the problem on Mac OS X may have been due to the fact
>>>>> I used the version with debugging on, so I rerun configure with
>>>>> --with-debugging=no, which did not change anything.
>>>>>
>>>>> Thx
>>>>>
>>>>> Timothee
>>>>>
>>>>>
>>>>> 2015-12-14 17:04 GMT+09:00 Dave May <dave.mayhem23 at gmail.com>:
>>>>>
>>>>>> One suggestion is you have some uninitialized variables in your
>>>>>> pcshell. Despite your arch being called "debug", your configure options
>>>>>> indicate you have turned debugging off.
>>>>>>
>>>>>> C standard doesn't prescribe how uninit variables should be treated -
>>>>>> the behavior is labelled as undefined. As a result, different compilers on
>>>>>> different archs with the same optimization flags can and will treat uninit
>>>>>> variables differently. I find OSX c compilers tend to set them to zero.
>>>>>>
>>>>>> I suggest compiling a debug build on both machines and trying your
>>>>>> test again. Also, consider running the debug builds through valgrind.
>>>>>>
>>>>>> Thanks,
>>>>>>   Dave
>>>>>>
>>>>>> On Monday, 14 December 2015, Timothée Nicolas <
>>>>>> timothee.nicolas at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I have noticed I have a VERY big difference in behaviour between two
>>>>>>> machines in my problem, solved with SNES. I can't explain it, because I
>>>>>>> have tested my operators which give the same result. I also checked that
>>>>>>> the vectors fed to the SNES are the same. The problem happens only with my
>>>>>>> shell preconditioner. When I don't use it, and simply solve using -snes_mf,
>>>>>>> I don't see anymore than the usual 3-4 changing digits at the end of the
>>>>>>> residuals. However, when I use my pcshell, the results are completely
>>>>>>> different between the two machines.
>>>>>>>
>>>>>>> I have attached output_SuperComputer.txt and
>>>>>>> output_DesktopComputer.txt, which correspond to the output from the exact
>>>>>>> same code and options (and of course same input data file !). More precisely
>>>>>>>
>>>>>>> output_SuperComputer.txt : output on a supercomputer called Helios,
>>>>>>> sorry I don't know the exact specs.
>>>>>>> In this case, the SNES norms are reduced successively:
>>>>>>> 0 SNES Function norm 4.867111712420e-03
>>>>>>> 1 SNES Function norm 5.632325929998e-08
>>>>>>> 2 SNES Function norm 7.427800084502e-15
>>>>>>>
>>>>>>> output_DesktopComputer.txt : output on a Mac OS X Yosemite 3.4 GHz
>>>>>>> Intel Core i5 16GB 1600 MHz DDr3. (the same happens on an other laptop with
>>>>>>> Mac OS X Mavericks).
>>>>>>> In this case, I obtain the following for the SNES norms,
>>>>>>> while in the other, I obtain
>>>>>>> 0 SNES Function norm 4.867111713544e-03
>>>>>>> 1 SNES Function norm 1.560094052222e-03
>>>>>>> 2 SNES Function norm 1.552118650943e-03
>>>>>>> 3 SNES Function norm 1.552106297094e-03
>>>>>>> 4 SNES Function norm 1.552106277949e-03
>>>>>>> which I can't explain, because otherwise the KSP residual (with the
>>>>>>> same operator, which I checked) behave well.
>>>>>>>
>>>>>>> As you can see, the first time the preconditioner is applied (DB_,
>>>>>>> DP_, Drho_ and PS_ solves), the two outputs coincide (except for the few
>>>>>>> last digits, up to 9 actually, which is more than I would expect), and
>>>>>>> everything starts to diverge at the first print of the main KSP (the one
>>>>>>> stemming from the SNES) residual norms.
>>>>>>>
>>>>>>> Do you have an idea what may cause such a strange behaviour ?
>>>>>>>
>>>>>>> Best
>>>>>>>
>>>>>>> Timothee
>>>>>>>
>>>>>>
>>>>>
>>>
>>
>
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