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

Martin Denham mjdenham at gmail.com
Fri Jan 15 14:15:07 MST 2016 

Wow, just tried Reduced the footprint of IniSection, used by
SwordBookMetaData.
<https://github.com/crosswire/jsword/commit/24343c32bfd25586a3b85a32df454525890ed51f>
and
it uses even less memory than my experiments: 3Mb for eBible and 4.5Mb for
all repos.

There seems to be a minor dependency error in Ini.java as a result of
changes in IniSection.  I just changed List to Collection to make it
compile.
    public List<String> getKeys()

Martin

On 15 January 2016 at 18:36, DM Smith <dmsmith at crosswire.org> wrote:

> I haven’t had a moment to look at the internal data structures. One of the
> natures of IniSection is that it is a multi-map. That means a key can be
> repeated one or more times. Though the typical case is that it is not
> repeated.
>
> So get(String key, int index) is needed.
>
> The order of values for a repeated key needs to be retained. So for a
> given key that has n values, they can be logically accessed as 0 .. n-1.
> Being able to iterate over the list to get them is just fine. It doesn’t
> need to be indexed access. Aside: The reason for keeping them ordered is
> that a SWORD app expects GlobalOptionFilter to be executed in the order it
> occurs. It is not readily obvious but each of the values for a
> GlobalOptionFilter is the name of a C++ class. The collection of them forms
> a chain of modification on the raw text from a module. While we are
> independent of SWORD apps and library, we try to coexist and support the
> same underlying abilities.
> So HashMap<String, HashSet<String>> doesn’t retain the order of the values.
>
> The current implementation has the keys being ordered by insertion order.
> (TreeMap and List). This is no longer necessary. We’ve added the ability to
> request the keys in a particular order. SWORD treats the conf file as a
> database of key, value pairs where order (other than for repeated keys) is
> unimportant.
>
> If a key/value is repeated, it is ignored. The code does this by using a
> set. But it could have used a list and call contains on it. It is a
> time/space trade-off.
>
> Couple of options:
> 1) Have two data structures:
> One to hold key, value pairs.
> Another to hold key, value lists.
> The invariant is that a stored key can be in at most one of these.
> The trick is that when adding a key,value pair an entry may need to
> migrate from the one data structure to the other.
> Also, removing a key/value means looking at both data structures and
> possibly migrating from one to the other.
> The old code did something like this, but I opted for something simpler.
> 2) Use lighterweight data structures that meet the minimum requirements of
> order.
>
> I’ll give it a go.
>
> — DM
>
> On Jan 15, 2016, at 12:35 PM, Martin Denham <mjdenham at gmail.com> wrote:
>
> I have done a few experiments using different data structures in
> IniSection and they seem to occupy a lot less memory but some IniSection
> functions are no longer well supported e.g. get(String key, int index), so
> I am not sure if this is worth pursuing.
>
> HashMap<String, String> 3Mb for all repos (forgot to check just eBible)
> HashMap<String, HashSet<String>> 3.6Mb for eBible and 5Mb for all repos
>
> This compares to 10Mb just for eBible with the original data structure.
>
> Martin
>
> On 15 January 2016 at 15:05, Martin Denham <mjdenham at gmail.com> wrote:
>
>> 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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