[jsword-devel] Out of Memory Issues Loading repo module lists

Martin Denham mjdenham at gmail.com
Fri Jan 15 08:05:07 MST 2016 

I was also thinking that maybe the default should be to return a full sbmd
and another method or parameter will cause a partial sbmd to be returned.
This would prevent surprises for other JSword users who don't have tight
memory constraints.

Martin

On 15 January 2016 at 14:11, DM Smith <dmsmith at crosswire.org> wrote:

> I’ll do that soon. And get back to you. I hadn’t meant to move
> GatherAllReferences and ReadEverything from tests to examples at this time,
> but later.
>
> — DM
>
> On Jan 15, 2016, at 9:09 AM, Martin Denham <mjdenham at gmail.com> wrote:
>
> Hi DM,
>
> Could you verify that you have checked in the Category fix as I still have
> the problem after fetching the latest commit?  The last commit says 'Fixed
> bug in category' but only includes changes in the examples package.  Also,
> the changes in the examples package, GatherAllReferences and
> ReadEverything, do not compile as they are in the wrong package.
>
> Martin
>
> On 14 January 2016 at 02:16, DM Smith <dmsmith at crosswire.org> wrote:
>
>> Glad it is a good, workable solution.
>>
>> I saw that category problem earlier today and checked in a fix for it. I
>> was addressing a problem with Bible Desktop’s display of a red ? over the
>> cult bibles in the installer. Tried breaking it out into it’s own category.
>> Tried putting it into “Other”. Not satisfied quite yet. But all the others
>> are appropriately classified.
>> — DM
>>
>> On Jan 13, 2016, at 5:30 PM, Martin Denham <mjdenham at gmail.com> wrote:
>>
>> The latest code seems to be running quite smoothly.
>> eBible 680 modules 10Mb ram
>>
>> I could not notice any new major pauses.
>> sbmd.reload works well and AB can show the About dialog.  I can see a
>> slight but insignificant pause as the full attributes are loaded.
>> I have installed various modules from different repositories.
>> The above tests were done on a fairly low spec Android 2.2 AVD with 64Mb
>> heap.
>>
>> The only issue I have noticed is that non-Bibles are appearing in the
>> list of Bibles so I think there may be an issue with Category.  I can see
>> some commentaries and GenBooks in a list that should just contain Bibles.
>> If the problem is not obvious I can investigate further later.
>>
>> Thanks
>> Martin
>>
>> On 12 January 2016 at 13:58, DM Smith <dmsmith at crosswire.org> wrote:
>>
>>> I’m working on transforming the tar.gz to a zip. The zip has much faster
>>> access to files in it. The same amount of time per file. The tar.gz is Tape
>>> ARchive and is fast to get the first and slow to get the last.
>>>
>>> I just did some computations and unpacking the tar.gz is not good for
>>> your app. But you told me that…. :)
>>>
>>> In Him,
>>> DM
>>>
>>> On Jan 12, 2016, at 8:16 AM, Martin Denham <mjdenham at gmail.com> wrote:
>>>
>>> I like this idea: "A file in a jar has an URL that is something like
>>> …/fred.jar!file"
>>>
>>> Martin
>>>
>>> On 11 January 2016 at 23:29, DM Smith <dmsmith at crosswire.org> wrote:
>>>
>>>>
>>>> On Jan 11, 2016, at 6:07 PM, Martin Denham <mjdenham at gmail.com> wrote:
>>>>
>>>> My estimate of file size might be too low because I forgot to take into
>>>> account block size.  Quickly playing around with my android adds about 40%
>>>> making it at least 7Mb for the conf files.
>>>>
>>>>
>>>> Understand.
>>>>
>>>>
>>>> By 'fluff' do you mean extract all the files from mods.d.tar.gz and
>>>> write them all to disk.  I am a little concerned about writing and deleting
>>>> hundreds of small files to the sd card repeatedly.  SD cards are not as
>>>> good at high r/w as normal disks or flash drives.  That is the reason I do
>>>> not store the AB database on the SD card.
>>>>
>>>>
>>>> By fluff, I meant that the conf file would be re-read without a filter,
>>>> thus getting everything.
>>>>
>>>>
>>>> The process described would also make viewing a description (in AB
>>>> right-click About) an unexpectedly expensive operation involving writing
>>>> hundreds of files to the sd card.
>>>>
>>>>
>>>> It would involve re-reading the one file without a filter. It should
>>>> happen fast.
>>>>
>>>>
>>>> I did not know about sbmd.toOSIS() and have not used it.  AB just pops
>>>> up a little dialog with a few fields like About, copyright, licence,
>>>> version, versification.
>>>>
>>>>
>>>> Ok. Then you’ll need to call “fluff” before retreiving those fields.
>>>> The code for fluff (or whatever we call it) would be something like:
>>>> public void fluff() {
>>>>   if (partiallyLoaded) {
>>>> re-read and process the conf without a filter
>>>> partiallyLoaded = false;
>>>>    }
>>>> }
>>>>
>>>>
>>>> For the 2 reasons above my preference would be to avoid writing
>>>> hundreds of files to the SD card but I can't think of a perfect solution.
>>>> While grappling with this last week I was just trying to get the original
>>>> code to work more efficiently (but failed).  I am not very experienced in
>>>> Memory Analysis but suspected the memory use was higher than it might have
>>>> been.
>>>>
>>>> By design, which files do you write to SD card? If they are only
>>>> written when the mods.d.tar.gz is downloaded, would that help?
>>>>
>>>>
>>>> If the tar.gz was searched each time for the conf it would be more
>>>> expensive to process the tar.gz every time a Description is requested but
>>>> the first time it would be quicker than writing hundreds of .conf files and
>>>> to be honest I think a lot of people do not know about the long-press menu
>>>> in AB so probably just the initial list of modules would be used most of
>>>> the time.
>>>>
>>>>
>>>> I don’t know about the long-press menu. In BibleDesktop, it is easy to
>>>> navigate from one available to the next and each time it shows the full
>>>> conf.
>>>>
>>>>
>>>> Coincidentally my android slowed to a crawl when I tried to copy all of
>>>> eBible's .conf files to it just now - initially fast then 1 file per 3
>>>> secs, after 10 minutes I unplugged it, although that probably is not a
>>>> realistic test and there is probably an explanation for the issue.
>>>>
>>>>
>>>> I’ve nearly got the code written to unpack the conf. Let me zip up the
>>>> files that have changed and send them to you.
>>>>
>>>> Basically, if you delete mods.d.tar.gz, it will fetch a new one
>>>> (current behavior). If you delete mods.d/ it will unpack mods.d.tar.gz into
>>>> it. If you fetch mods.d.tar.gz it will unpack it into mods.d. All of this
>>>> takes place in the folder that mods.d.tar.gz is present.
>>>>
>>>> I tried adding new confs to mods.d that weren’t in mods.d.tar.gz to
>>>> simulate a takedown and that works as well.
>>>>
>>>> If this code is no good for you, I’ve another thought. A file in a jar
>>>> has an URL that is something like …/fred.jar!file. Maybe we can transform
>>>> the mods.d.tar.gz into mods.d.tar and use that addressing mechanism to
>>>> fetch the file? I’ll take a look at how the JRE does that. Maybe, I’ll roll
>>>> the same for JSword over a tar.gz file.
>>>>
>>>> DM
>>>>
>>>>
>>>> Martin
>>>>
>>>> On 11 January 2016 at 19:28, DM Smith <dmsmith at crosswire.org> wrote:
>>>>
>>>>> I have been thinking about this a bit more. I was knew there was a
>>>>> need to prevent stale confs. The time performance is something that I’m not
>>>>> able to test. My machine has an SSD, a fast 4 core CPU and gobs of RAM. So
>>>>> I need you to keep me in line. ;)
>>>>>
>>>>> The easiest way to keep it pristine is to unpack it into a temporary
>>>>> folder, rename the old folder and then rename the new folder. Finally
>>>>> deleting the old folder. By doing it in this order it minimizes the time
>>>>> that mods.d is unavailable. Important for multi-threaded apps and multiple
>>>>> apps that share the same machine simultaneously.
>>>>>
>>>>> Right now the SwordBookMetaData remembers the File for the conf of
>>>>> installed modules and is able to re-read it easily. But it does not store
>>>>> anything about a conf’s location when it is from mods.d.tar.gz. I suppose I
>>>>> could have it remember the location of mods.d.tar.gz and the name of the
>>>>> conf entry and create a method to extract a that conf out of the compressed
>>>>> archive. This would need to be done for each module that the user requests
>>>>> info. To do this is quite expensive as it means inflating the file then
>>>>> iterating over the contents until the desired conf is found.
>>>>>
>>>>> I think that it would be better to see how much time it adds to
>>>>> extract the files and store them on disk. The fluffing of them would only
>>>>> be when the user wants to browse a description of the module.
>>>>>
>>>>> I’d like to modify sbmd.toOSIS to check if the sbmd is partial or full
>>>>> and if not full re-read the conf fully and then continue as before. I think
>>>>> that is how JSword is designed to retreive the conf for presentation to the
>>>>> end user. Does AndBible use that or some other mechanism to get what it
>>>>> wants for presentation?
>>>>>
>>>>> I think I’ll add a “fluff” method to BookMetaData that will do this.
>>>>> This could be called to get it to fluff at another time.
>>>>>
>>>>> DM
>>>>>
>>>>> On Jan 11, 2016, at 1:00 PM, Martin Denham <mjdenham at gmail.com> wrote:
>>>>>
>>>>> My rough estimates have the total size of conf files in all repos at
>>>>> about 5Mb which is not too different to the size of a module like ESV so
>>>>> the impact should not be significant and it should not be a problem if this
>>>>> is required.
>>>>>
>>>>> Other things to consider that come to mind i) would need to remove
>>>>> conf files no longer in mods.d.tar.gz or delete and re-extract everything
>>>>> after a refresh ii) Time taken to save files - loading the list is already
>>>>> slow.
>>>>>
>>>>> I can't think of any major reason not to do as you describe.
>>>>>
>>>>> However, would an easier approach be to find files in the zip a bit
>>>>> like this
>>>>> <http://stackoverflow.com/questions/11123528/finding-a-file-in-zipentry-java>.
>>>>> Speed would not be an issue because it would only be done once or twice
>>>>> after fetching the list e.g. to view About or to actually download.  The
>>>>> mod.conf file name/path could be saved in SBMD if required.
>>>>>
>>>>> Martin
>>>>>
>>>>>
>>>>> On 11 January 2016 at 01:39, DM Smith <dmsmith at crosswire.org> wrote:
>>>>>
>>>>>> I’m trying to figure out how to reload a conf from a remote source
>>>>>> (to go from a partial load to a full load).  The problem is that the
>>>>>> AbstractSwordInstaller sits over top of mods.d.tar.gz, which it does not
>>>>>> unpack. Instead, it iterates over all the entries in that binary file and
>>>>>> handles each entry (i.e. a conf) in core. It doesn’t hit the disk. I’m
>>>>>> wondering whether it would be alright to unpack the file in the same
>>>>>> folder? That would allow a SwordBookMetaData to reload the file. It would
>>>>>> also mean that SwordBookMetaData would only need one means of reading a
>>>>>> conf as it’d be a file and not a byte array.
>>>>>>
>>>>>> It isn’t a problem with desktop or server apps, but it might be for
>>>>>> AndBible.
>>>>>>
>>>>>> — DM
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jan 10, 2016, at 3:31 PM, DM Smith <dmsmith at crosswire.org> wrote:
>>>>>>
>>>>>> The problem you encountered was 2 bugs:
>>>>>> When the module is not UTF-8 the remote repository’s conf is re-read,
>>>>>> but the filter wasn’t passed.
>>>>>> Not intended, but IniSection required a filter, rather than saying a
>>>>>> null filter meant everything passed.
>>>>>>
>>>>>> I’ve checked in that fix. Still trying to make the memory less….
>>>>>>
>>>>>> — DM
>>>>>>
>>>>>> On Jan 10, 2016, at 1:18 PM, DM Smith <dmsmith at crosswire.org> wrote:
>>>>>>
>>>>>> The “Partial load of conf file.’ was to load all of the things in a
>>>>>> conf that the JSword engine needs to work with a module. I don’t know why
>>>>>> the CrossWire repo is working for me but not for you. I’ll keep working on
>>>>>> it today. The problem with the previous commit was fixed with the last
>>>>>> commit. I wasn’t “adjusting” the module after loading to fill in things
>>>>>> like BookDriver and BookCategory.
>>>>>>
>>>>>> I’m wondering whether getting the list of Books from the installer
>>>>>> creates a deep rather than a shallow copy of them.
>>>>>>
>>>>>> Today I hope to make SwordBookMetaData even more lazy. It has a
>>>>>> BookDriver and validates its storage when the repo is loaded. I plan to
>>>>>> break one of my modules by renaming one of the files and see the impact.
>>>>>> Chris and I have noticed that the FileState objects are not fully released.
>>>>>> This actually is part of the design.
>>>>>>
>>>>>> Anyway, I think it is going in the right direction. Reducing the
>>>>>> memory 4x is a  good thing. The data structures within the IniSection may
>>>>>> be too heavy. I may relax the requirement that it maintains the SWORD confs
>>>>>> order. The idea was to be able to modify the provided conf, retaining its
>>>>>> order. However, now we never modify that conf.
>>>>>>
>>>>>> configAll was a deep clone of configSword. configAll adds in the
>>>>>> contents of configJSword and then configFrontend. These last two are
>>>>>> created even if not needed. We could make them lazy as well.
>>>>>>
>>>>>> DM
>>>>>>
>>>>>> On Jan 10, 2016, at 11:07 AM, Martin Denham <mjdenham at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Thanks for the quick response.  I have had a brief look at the new
>>>>>> commits.
>>>>>>
>>>>>> A lot of the attributes aren't being returned now so it is tricky to
>>>>>> test and there are various errors but running the current tip 'Partial
>>>>>> load of conf file.
>>>>>> <https://github.com/crosswire/jsword/commit/80020f51c6a762d458ce8ae70007b78eadee1fb3>'
>>>>>> the SBMD for eBible is now only a quarter of the original size at 10Mb
>>>>>> which is fine but I still don't understand why it is so large for the
>>>>>> minimal attribute set now being returned.
>>>>>>
>>>>>> I get a lot of errors like:
>>>>>> SwordBookMetaData(492): Book not supported: malformed conf file for
>>>>>> [BBE] no ModDrv found.
>>>>>> SwordBookMetaData(492): Malformed conf file: missing
>>>>>> [BBE]Description=. Using BBE
>>>>>>
>>>>>> and peculiarly the eBible repo seems to be the only repo I can use
>>>>>> because all the others error.
>>>>>>
>>>>>> I also tried the previous commit Cut the memory requirements of a
>>>>>> SwordBookMetaData in half.
>>>>>> <https://github.com/crosswire/jsword/commit/cc32ba8f1bb245932a747390d03874b2be70e9a1> but
>>>>>> it did not work because basic attributes like language were not being
>>>>>> returned.
>>>>>>
>>>>>> I still don't understand why removing configSword should reduce
>>>>>> memory by half because it should just be removing references to data that
>>>>>> is also referenced from configAll, so it would reduce memory slightly but
>>>>>> not much.
>>>>>>
>>>>>> Martin
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 10 January 2016 at 04:14, DM Smith <dmsmith at crosswire.org> wrote:
>>>>>>
>>>>>>> OK. That’s done. Also accidentally introduced a bug with the last
>>>>>>> commit. It is noticeably fast.
>>>>>>>
>>>>>>> Next up, allow for *a* SwordBookMetaData to be reloaded fully. This
>>>>>>> is needed to bring in all the other elements which are information only,
>>>>>>> such as About, in order to display info to the end user. Since the user
>>>>>>> will only look at one modules info at a time, it will load that one. You
>>>>>>> may need to change your code (hope not) to force that one to reload.
>>>>>>>
>>>>>>> Give the code a try to see if it solves your out of memory error.
>>>>>>>
>>>>>>> DM
>>>>>>>
>>>>>>>
>>>>>>> On Jan 9, 2016, at 9:06 PM, DM Smith <dmsmith at crosswire.org> wrote:
>>>>>>>
>>>>>>> I’ll be adding a filter to IniSection. Something like:
>>>>>>> if  (filter.test(key)) {
>>>>>>> use the key
>>>>>>> } else {
>>>>>>> do nothing
>>>>>>> }
>>>>>>>
>>>>>>> SwordBookMetaData will be responsible for building the filter. At
>>>>>>> least for a first go around. A single object should do.
>>>>>>>
>>>>>>> DM
>>>>>>>
>>>>>>> On Jan 9, 2016, at 6:29 PM, DM Smith <dmsmith at crosswire.org> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Yes, like you I have thought of streamlining conf loading for repo
>>>>>>> lists.  One idea I had was to enable specification of a filter to
>>>>>>> SwordBookMetaData to limit the conf values that are stored.
>>>>>>>
>>>>>>>
>>>>>>> I was thinking of something similar. My ideas aren’t good enough to
>>>>>>> be put into practice, but some kind of flag indicating empty, partially or
>>>>>>> fully loaded. Empty would mean that it hasn’t gone to disk to get the conf.
>>>>>>> Partial means that it read everything, but threw away most as not
>>>>>>> interesting (since the conf does not have order you have to read and parse
>>>>>>> it all). Full would mean that nothing was pitched.
>>>>>>> SwordBookMetaData.getProperty would need to be changed to determine whether
>>>>>>> the key is in memory or might be on disk and do the right thing. Or we
>>>>>>> could keep getProperty as it is and if you want one of the fields that is
>>>>>>> not stored (e.g. About) you have to call reload().
>>>>>>>
>>>>>>> Maybe we could also cache that info into a separate file(s)? When
>>>>>>> mods.d.tar.gz is updated then the cache would be recomputed. In doing the
>>>>>>> computation, each conf would be read then pitched. Basically, the storage
>>>>>>> would be o.c.c.utils.Ini, if one file or IniSection, if many files.
>>>>>>>
>>>>>>> What do you think?
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> jsword-devel mailing list
>>>>>>> jsword-devel at crosswire.org
>>>>>>> http://www.crosswire.org/mailman/listinfo/jsword-devel
>>>>>>>
>>>>>>>
>>>>>>>
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