I have a couple of database management tasks that need to go through every record in the database. It was my understanding that with the CakePHP 3.x ORM, I could do something like this, and it would only ever have one record in memory at a time:
$records = TableRegistry::get('Whatever')->find();
foreach ($records as $record) {
// do some processing
}
However, this is eventually crashing with an "out of memory" exception. I've added a bit of logging of memory_get_peak_usage, and it's increasing with every iteration, even if there is nothing other than the logging happening inside the foreach loop. The delta is around 12K every time through the loop.
I'm running 3.2.7, and results are similar whether I have debugging and/or SQL logging enabled or not. Adding frequent calls to gc_collect_cycles() only slows the process down, it doesn't help with the memory usage.
Is this expected, or a bug? If the former, is there anything I can do differently in this code to prevent it? (Obviously, I could process it in smaller batches, but that's not an elegant solution.)
CakePHP 3.x ORM has built in query caching for the ResultSet object. When you iterator over the result set the entities are stored in an internal array. This is done so that you can rewind the iterator and loop again.
If you are going to iterate over a large result set only once, and you want to reduce memory usage then you have to disable result buffering.
$records = TableRegistry::get('Whatever')->find()->bufferResults(false);
foreach ($records as $record) {
// do some processing
}
With buffering turned off the entity is fetched from the result set and there should be no references to it afterwards.
Documentation for this feature is available in the CakePHP book: https://book.cakephp.org/3.0/en/orm/retrieving-data-and-resultsets.html#working-with-result-sets
Here's the API reference: https://api.cakephp.org/3.6/class-Cake.Database.Query.html#_bufferResults
From my understanding it is the expected behaviour, as you execute the query build with the ORM when you start iterating over the object($records). Thus all the data is loaded into memory, and you then iterate over each entry one by one.
If you want to limit the memory usage I would suggest you look into limit and offset. With these you can extract subsets to work on, thus limiting memory usage.
Related
I have few m of records in db, and need to process it from time to time. However this operation takes all memory on my server. I'm running this operation using sidekiq. So while this task using all memory, my rails app becomes very slow.
In general(no logic included) my code looks like
Model.each do |m|
//do some logic code here
end
How do i make garbage collector to run after some amount of records(for ex. 10k records) so i wouldn't face out of memory situations. Will splitting it in chunks help me?
You should always use find_each when dealing with potentially large tables.
That way, models will be retrieved from the database and loaded in memory batch by batch (the default size is 1000 but you can customize it to your needs).
Just be aware that sorting by arbitrary columns doesn't play well with find_each, as it implicitly sorts records by ID so that it has a way to fetch records by batches.
You can force the garbage collector to run with GC.start, but if you are doing
Model.all.each do |m|
end
then garbage collection cannot free the already processed records - they are still referenced by the array that each is iterating over, so running the garbage collector explicitly won't do anything.
Instead use find_each (or its close relative, find_in_batches) which fetches records and processes them in batches (you can control the batch size - I think it is 1000 by default). This way the entire result set is never in memory and previously processed batches are not referenced by anything and so can be disposed of.
How do I improve performance when writing to neo4j. I currently have neo4j set up on a server and I am currently running it in embedded more. I believe my configurations are storing all the content of my graph database in memory based upon configurations I've found online
neostore.nodestore.db.mapped_memory=0
neostore.relationship.db.mapped_memory=0
neostore.propertystore.db.mapped_memory=0
neostore.propertystore.db.strings.mapped_memory=0
neostore.propertystore.db.arrays.mapped_memory=0
neostore.propertystore.db.index.keys.mapped_memory=0
neostore.propertystore.db.index.mapped_memory=0
node_auto_indexing=true
node_keys_indexable=type,id
cache_type=strong
use_memory_mapped_buffers=false
node_cache_size=12G
relationship_cache_size=12G
node_cache_array_fraction=10
relationship_cache_array_fraction=10
Please let me know if this is incorrect. The problem that I am encountering is that when I try to persist information to the graph database. It appears that those times are not very quick in comparison to our MYSQL times of the samething(ex. to add 250 items would take about 3sec and in MYSQL it takes 1sec) . I read online that when you have multiple indexes that that can slow down performance on persisting data so I am working on that right now to see if that is my culprit. But, I just wanted to make sure that my configurations seem to be inline when it comes to running your graph database in memory.
Second question to this topic. Okay, if my configurations are good and my database is indeed in memory, then is there a way to optimize persisting data just in case this isn't the silver bullet. If we ran one thread against our test that executes this functionality, oppose to 10 threads, its seems like the times for execution bubbles up
ex.( thread 1 finishes 1s, thread 2 finishes 2s, thread 3 finishes 3s,etc). Is there some special multithreaded configuration that I am missing to improve the performance when mulitple threads are hitting it at one time.
Neo4J version
1.9.1-enterprise
My Jvm configs are
-Xms25G -Xmx25G -XX:+UseNUMA -XX:+UseSerialGC
My Machine Specs:
File system type ext3
You cache arguments are invalid.
node_cache_size=12G
relationship_cache_size=12G
node_cache_array_fraction=10
relationship_cache_array_fraction=10
These can only be used with the GCR cache. Setting the cache isn't going to put everything in memory for you at start up, you will have to write code to do this for you. Something like this:
GlobalGraphOperations ggo = GlobalGraphOperations.at(graphDatabaseFactory);
for (Node n : ggo.getAllNodes()) {
for (String propertyKey : n.getPropertyKeys()) {
n.getProperty(propertyKey);
}
for (Relationship relationship : n.getRelationships()) {
}
}
Beware with the strong cache, if you have a lot of nodes/relationships, eventually your cache will become large and performing GC against it will cause long pauses in your system.
My recommendation would be to use the memory mapped files, as this is an OS handled and will be outside of heap space. It doesn't provide near the speed of caching, but it will provide a speed up if you have to read from the neo store.
I use Delphi XE2 along with DISQLite v3 (which is basically a port of SQLite3). I love everything about SQLite3, except the lack of concurrent writing, especially that I extensively rely on multi-threading in this project :(
My profiler made it clear I needed to do something about it, so I decided to use this approach:
Whenever I need to insert a record in DB, Instead of doing an INSERT, I write the SQL query in a special foler, ie.
WriteToFile_Inline(SPECIAL_FOLDER_PATH + '\' + GUID, FileName + '|' + IntToStr(ID) + '|' + Hash + '|' + FloatToStr(ModifDate) + '|' + ...);
I added a timer (in the main app thread) that fires every minute, parse these files and then INSERT the queries using a transaction.
Delete those temporary files at the end.
The result is I have like 500% performance gain. Plus this technique is ACID, as I can always scan the SPECIAL_FOLDER_PATH after a power failure and execute the INSERTs I find.
Despite the good results, I'm not very happy with the method used (hackish to say the least), I keep thinking that if I could have a generics-like with fast lookup access, thread-safe, ACID list, this would be much cleaner (and possibly faster?)
So my question is: do you know anything like that for Delphi XE2?
PS. I trust many of you reading the code above be in shock and will start insulting me at this point! Please be my guest, but if you know a better (ie. faster) ACID approach, please share your thoughts!
Your idea of sending the inserts to a queue, which will rearrange the inserts, and join them via prepared statements is very good. Using a timer in the main thread or a separated thread is up to you. It will avoid any locking.
Do not forget to use a transaction, then commit it every 100/1000 inserts for instance.
About high performance using SQLite3, see e.g. this blog article (and graphic below):
In this graphic, best performance (file off) comes from:
PRAGMA synchronous = OFF
Using prepared statements
Inside a transaction
In WAL mode (especially in concurrency mode)
You may also change the page size, or the journal size, but settings above are the best. See https://stackoverflow.com/search?q=sqlite3+performance
If you do not want to use a background thread, ensure WAL is ON, prepare your statements, use batchs, and regroup your process to release the SQLite3 lock as soon as possible.
The best performance will be achieved by adding a Client-Server layer, just as we did for mORMot.
With files you organized an asynchronous job queue with persistance. It allows you to avoid one-by-one and use batch (records group) approach to insert the records. Comparing one-by-one and batch:
first works in auto-commit mode (probably) for each record, second wraps a batch into a single transaction and gives greatest performance gain.
first prepares an INSERT command each time when you need to insert a record (probably), second once per batch and gives second by value gain.
I dont think, that SQLite concurrency is a problem in your case (at least not the main issue). Because in SQLite a single insert is comparably fast and concurrency performance issues you will get with high workload. Probably similar results you will get with other DBMS, like Oracle.
To improve your batch approach, consider the following:
consider to set journal_mode to WAL and disable shared cache mode.
use a background thread to process your queue. Instead of a fixed time interval (1 min), check SPECIAL_FOLDER_PATH more often. And if the queue has more than X Kb of data, then start processing. Or use a count of queued records and event to notify the thread, that the queue should start processing.
use multy-record prepared INSERT instead of single-record INSERT. You can build an INSERT for 100 records and process your queue data in a single batch, but by 100 record chanks.
consider to write / read a binary field values instead of a text values.
consider to use a set of files with preallocated size.
etc
sqlite3_busy_timeout is pretty inefficient because it doesn't return immediately when the table it's waiting on is unlocked.
I would try creating a critical section (TCriticalSection?) to protect each table. If you enter the critical section before inserting a row and exit it immediately thereafter, you will create better table locks than SQLite provides.
Without knowing your access patterns, though, it's hard to say if this will be faster than batching up a minute's worth of inserts into single transactions.
I am using ActiveRecord to bulk migrate some data from a table in one database to a different table in another database. About 4 million rows.
I am using find_each to fetch in batches. Then I do a little bit of logic to each record fetched, and write it to a different db. I have tried both directly writing one-by-one, and using the nice activerecord-import gem to batch write.
However, in either case, my ruby process memory usage is growing quite a bit throughout the life of the export/import. I would think that using find_each, I'm getting batches of 1000, there should only be 1000 of them in memory at a time... but no, each record I fetch seems to be consuming memory forever, until the process is over.
Any ideas? Is ActiveRecord caching something somewhere that I can turn off?
update 17 Jan 2012
I think I'm going to give up on this. I have tried:
* Making sure everything is wrapped in a ActiveRecord::Base.uncached do
* Adding ActiveRecord::IdentityMap.enabled = false (I think that should turn off the identity map for the current thread, although it's not clearly documented, and I think the identity map isn't on by default in current Rails anyhow)
Neither of those seem to have much effect, memory is still leaking.
I then added a periodic explicit:
GC.start
That seems to slow down the rate of memory leak, but the memory leak still happens (eventually exhausting all memory and bombing).
So I think I'm giving up, and deciding it is not currently possible to use AR to read millions of rows from one db and insert them into another. Perhaps there is a memory leak in MySQL-specific code being used (that's my db), or somewhere else in AR, or who knows.
I would suggest queueing each unit of work into a Resque queue . I have found that ruby has some quirks when iterating over large arrays like these.
Have one main thread that queue's up the work by ID, then have multiple resque workers hitting that queue to get the work done.
I have used this method on approx 300k records, so it would most likely scale to millions.
Change line #86 to bulk_queue = [] since bulk_queue.clear only sets the length of the arrya to 0 makeing it impossible for the GC to clear it.
I have a MVC application which returns 2 types of Json responses from 2 controller methods; AnyRemindersExist() and GetAllUserReminders(). The first returns a boolean, 2nd returns an array, both wrapped as Json.
I have a JavaScript timer checking for calendar reminders against a user. It makes the first call (AnyRemindersExist) to check whether reminders exist and whether the client should then make the 2nd call.
For example, if the result of the Json response is false from the Any() query, it doesn't then make the 2nd controller action which makes a LINQ select call. If there are reminders that exist, it then goes further and then requests them (making use of the LINQ SELECT).
Imagine a system ramped up where 100-1000s users use the system and on the client, every 30-60 seconds a request comes in to load in the reminders. Does this Any() call help in anyway in reducing load on the server?
If you're always going to get the actual values afterwards, then no - it would make more sense to have fewer requests, and just always give the full results. I very much doubt that returning no results is slower than returning an indication that there are no results.
EDIT: tvanfosson's latest comment (at the time of this writing) is worth promoting:
You can really only tell by measuring and I'd only resort to it IFF the performance of the select only option didn't meet the requirements.
That's the most important thing about performance: the value of a guess is much less than the value of test data.
I would say that it depends on how the underlying queries are translated. If the any call is translated into an indexed lookup when the select (perhaps due to a join to get related data) must do some sort of table scan, then it will save some work in the case when there are no reminders to be found. It will cause a little extra work when there are reminders. It might be useful if the majority of the calls don't result in any results.
In the general case, though, I would just select the data and only try to optimize IF that turns out to not be fast enough. The conditions under which it will actually save effort on the server are pretty narrow and might only apply if you hand-craft the SQL rather than depend on your ORM.
Any only checks to see if there is at least one item in the Collection that is being returned. Versus using something like Count > 0 which counts the total amount of items in the collection then yes this is more optimal.
If your AnyRemindersExist method is operating on a similar principle then not calling a second call to the server would reduce your load.
So you are asking if not doing work the application doesn't need to do would reduce the workload on the server?
Of course. How would this answer every be "yes, doing extra work for no reason won't effect the server load".
It ultimately depends on how much faster the Any check is compared to getting the results and how often it will be false.
If the Any call takes near as long as the select then it pretty
much never makes sense.
If the Any call is much faster than the select but 90% of the
time it's true, then it probably isn't worth it (best case you
get 10% improvement, worst case it's actually more work).
If the Any call is much faster than the select and 90% of the
time it's false, then it probably makes sense to check if there
are any before actually getting results.
So the answer is it depends on your specific scenario. Ultimately you're going to need to measure both the relative performance (on different typical loads, maybe some queries are more intensive than others) as well as the frequency that there are no results to return.
Actually it should almost never make sense to check Any in this case.
If Any returns false then you don't need to grab the results.
However this means it would have returned no results anyway, so
unless your Any check is significantly faster than a select
returning 0 results, there's no added benefit here.
On the other hand, if Any returns true, then you'll need to get the
results anyway, so in this case Any is purely additional work done.