[FLASH-USERS] larger FLASH hdf5 files in visit

[Philipp Moesta]

Hi Jacob, Sean,

just to add another more non-solution comment to this. I have the same 
problem with VisIt for non-flash (Cactus/Carpet) hdf5 data files, adding 
more support to the idea that this likely is an issue in VisIt itself 
and not in the respective hdf5 readers.

Philipp

On 7/8/16 7:55 AM, Sean Couch wrote:
> Hi Jacob,
>
> I don’t have a solution, but I will chime in and say that you’re not
> crazy and not doing anything wrong. I’ve seen exactly this type of
> behavior with VisIt many times.  It’s like each process allocates enough
> memory for the entire dataset…  What’s more is that there are clearly
> memory leaks to boot.  For example, when making movies of a series of
> large FLASH plot files, I would see memory crashes after roughly the
> same number of frame creations.  Then restarting the movie making from
> where it left off would work fine, until the magic number of frames had
> again been made…
>
> As far as file size go, VisIt should have no problem with ~16 Gb files.
>  I routinely visualize plot files that are 100s of Gb in size.  But
> doing it in parallel is always a pain…
>
> I’ve looked briefly into the FLASH reader for VisIt and I don’t think
> the bug is there.  The reader is extremely simple.  I think the bug must
> be in the VisIt source itself.  And it’s been there for a very long time…
>
> Sorry, this is not helpful but I don’t have a good solution.  Except to
> switch to yt as John suggests (but in my experience that’s no panacea,
> either…).
>
> Cheers,
> Sean
>
>
> ----------------------------------------------------------------------------------------------------------
> Sean M. Couch
> Assistant Professor
> Department of Physics and Astronomy
> Department of Computational Mathematics, Science, and Engineering
> National Superconducting Cyclotron Laboratory/Facility for Rare Isotope
> Beams
> Michigan State University
> 567 Wilson Rd, 3250 BPS
> East Lansing, MI  48824
> (517) 884-5035    ——    couch at pa.msu.edu <mailto:couch at pa.msu.edu>    ——
>    www.pa.msu.edu/~couch <http://www.pa.msu.edu/~couch>
>
>
>
>
>
>> On Jul 8, 2016, at 10:02 AM, John ZuHone <jzuhone at space.mit.edu
>> <mailto:jzuhone at space.mit.edu>> wrote:
>>
>> Hi Jacob,
>>
>> I know this question is about VisIt, but I should point out that FLASH
>> support for VisIt has lingered for quite some time now.
>>
>> yt is a pretty powerful package for dealing with FLASH data—it’s one
>> of the data types that has the fullest support in yt, and you can do a
>> lot more than you can in VisIt.
>>
>> Find out more at http://yt-project.org <http://yt-project.org/>, or
>> ping me off-list at john.zuhone at cfa.harvard.edu
>> <mailto:john.zuhone at cfa.harvard.edu> if you have more questions.
>>
>> Best,
>>
>> John Z
>>
>>> On Jul 8, 2016, at 9:59 AM, McFarland, Jacob A.
>>> <mcfarlandja at missouri.edu <mailto:mcfarlandja at missouri.edu>> wrote:
>>>
>>> All,
>>>
>>> I just wanted to ping the community one more time to see if anyone
>>> has any suggestions on this issue. I have not received any feedback
>>> yet but I have received emails from some other users with this issue.
>>>
>>> Thanks for any help you can provide.
>>>
>>> - Jacob
>>> ------------------------------------------------------------------------
>>> *From:* flash-users-bounces at flash.uchicago.edu
>>> <mailto:flash-users-bounces at flash.uchicago.edu> [flash-users-bounces at flash.uchicago.edu
>>> <mailto:flash-users-bounces at flash.uchicago.edu>] on behalf of
>>> McFarland, Jacob A.
>>> *Sent:* Tuesday, July 05, 2016 9:00 AM
>>> *To:* flash-users at flash.uchicago.edu
>>> <mailto:flash-users at flash.uchicago.edu>
>>> *Subject:* [FLASH-USERS] larger FLASH hdf5 files in visit
>>>
>>> Hello all,
>>>
>>> I emailed the visit users group with this issue but I have not
>>> received any info back yet. As this is a problem many of you may have
>>> encountered with FLASH data I thought the FLASH users group might
>>> have some advice as well.
>>>
>>> I am having a problem with Visit consuming a lot of memory when
>>> opening FLASH hdf5 files. I have simulations with about 50E6 nodes on
>>> the fluid mesh and about 20k particles. The hdf5 files are written
>>> with parallel hdf5 (I ran the setup with +hdf5TypeIO). The chk files
>>> are 5-16gb or so in size, getting larger in time as there are more
>>> nodes at later times.
>>>
>>> When I open the files with Visit each processor seems to consume
>>> enough memory to open the whole chk file no matter how many processor
>>> I throw at it. This means I end up memory limited and have to rune
>>> with very few processor on each computer node.
>>>
>>> I expected visit would be able to break up the hdf5 files so that
>>> each processor would not need the whole file in memory. This is the
>>> behavior I have seen when using other codes with data in the silo
>>> format.
>>>
>>> Is this the normal behavior for visit with large FLASH data files?
>>>
>>> If not, any suggestions on what I am doing wrong?
>>>
>>> If so, any suggestions on how to mitigate this memory problem?
>>>
>>> Thanks,
>>> Jacob
>>
>

-- 
Philipp