Ruby Memory leak (MRI) - ruby

I must be missing something but every single application I write in Ruby seems like leaking some memory. I use Ruby MRI 2.3 but I see the same behaviour with other versions.
Whenever I write a test application that does something inside a loop it is slowly leaking memory.
while true
#do something
sleep 0.1
end
For instance, I can write to array and then clean it in a loop, or just send http post request.
Here is just one example, but I have many examples like this:
require 'net/http'
require 'json'
require 'openssl'
class Tester
def send_http some_json
begin
#uri = URI('SERVER_URL')
#http = Net::HTTP.new(#uri.host, #uri.port)
#http.use_ssl = true
#http.keep_alive_timeout = 10
#http.verify_mode = OpenSSL::SSL::VERIFY_NONE
#http.read_timeout = 30
#req = Net::HTTP::Post.new(#uri.path, 'Content-Type' => 'application/json')
#req.body = some_json.to_json
res = #http.request(#req)
rescue Exception => e
puts e.message
puts e.backtrace.inspect
end
end
def run
while true
some_json = {"name": "My name"}
send_http(some_json)
sleep 0.1
end
end
end
Tester.new.run
The leak I see is very small, it can be 0.5 mb every hour.
I ran the code with MemoryProfiler and with GC::Profiler.enable and it shows that I have no leaks. So it must be 2 options:
There is a memory leak in C code. This might be possible but I don't use any external gems so I find it hard to believe that Ruby is leaking.
There is no memory leak and this is some sort of Ruby memory management mechanism. The thing is that I can defiantly see the memory growing. Until when will it grow? How much do I need to wait to know if it is a leak or now?
The same code runs perfectly fine with JRuby without any leaks.
I was amazed reading a post:
stack overlflow
from Joe Edgar:
Ruby’s history is mostly as a command line tool for text processing
and therefore it values quick startup and a small memory footprint. It
was not designed for long-running daemon/server processes
If what is written there is true and Ruby doesn't release memory back to OS then... We will always have a leak, right?
For instance:
Ruby asks for memory from OS.
OS provides the memory to Ruby.
Ruby frees the memory but GC still didn't run.
Ruby asks for more memory from OS.
OS provide more memory to Ruby.
Ruby runs GC but it is too late as Ruby already asked twice.
And so on and on.
What am I missing here?

Look Into GC Compaction and (Un)frozen String Literals
"Identical" Strings Aren't Necessarily Identical
Prior to Ruby 2.7.0, mainline Ruby didn't have compacting garbage collection. While I don't fully understand all the internals, the gist is that certain objects couldn't be garbage collected. Since you're using Ruby 2.3, that's something to keep in mind as you work on your memory allocation issues. Other non-YARV VMs may handle their internals differently, which is why you might see variation when using alternative engines like JRuby.
Even with Ruby 3.0.0-preview2, String literals aren't frozen by default, so your current implementation is creating a new String object with a unique object ID every tenth of a second. Consider the following:
3.times.map { 'foo'.__id__ }
#=> [240, 260, 280]
Even though the String objects seem identical, Ruby is actually allocating each one as a unique object in memory. Because a loop iteration is not a scope gate, those String objects can't be collected or compacted by YARV.
Enable Frozen String Literals by Default
You may have other issues as well, but it seems likely that your largest issue is keeping all of those String literals in scope indefinitely within your endless while-loop. You may be able to resolve your garbage collection problem (it's not a memory leak) by using frozen String literals instead. Consider the following:
# run irb with universally-frozen string literals
RUBYOPT="--enable-frozen-string-literal" irb
3.times.map { 'foo'.__id__ }
#=> [240, 240, 240]
You can solve this within your code in other ways as well, but reducing the number of String literals that remain in scope seems like a very sensible place to start.

Related

ruby: Can we survive NoMemoryError?

When ruby runs out of memory for it's internal allocations, it raises NoMemoryError.
We can catch this, and even do simple operations, but it seems that if we try to continue on, even after garbage collection, we will eventually hit a fatal memory allocation problem, which on my Linux box looks like:
[FATAL] failed to allocate memory
I suspect at this point this is my OS complaining about ruby running out of memory, instead of ruby catching it.
What I don't understand is that there are many cases where we should be able to continue after we rescue a NoMemoryError (and hence give up on the allocation that caused the failure) but it seems that ruby never cleans up the mess. A simple example is to cause (and rescue) a NoMemoryError by shifting too big of a number. For example:
begin
a = 1<<10000000000000
puts "Calculated answer somehow"
rescue NoMemoryError => e
puts "RESCUE: out of memory"
end
puts "Finished first begin/rescue/end"
GC.start # This is in vain
begin
a = 1<<10000000000000
puts "Calculated answer somehow"
rescue NoMemoryError => e
puts "RESCUE: out of memory"
end
puts "Finished second begin/rescue/end"
We catch the first one, which it seems should regain the memory from what I presume to be a BigNum overflow, but that memory never comes back, not even courtesy the garbage collection. So the next time we try to start allocating a bunch of memory (in this case with the same problem) we actually hit a fatal error. The full output:
RESCUE: out of memory
Finished begin/rescue/end
[FATAL] failed to allocate memory
Is there some way to fixup the state after Ruby has hit NoMemoryError if we rescue (and hence abort) the operation that took too much memory?
It feels like this might be a problem with the Garbage Collector, possibly not properly marking memory as no longer in use when we do a rescue, which makes me think there might be a GC bug that this is revealing.

Memory leak after algorithm in Rails?

I wrote an algorithm inspired by the merge part of the merge sort.
def self.merge(arr)
if arr.length == 1
return arr
end
groups = []
(0...-(-arr.length/2)).each do |i|
groups << []
if !arr[2*i+1].nil?
arr[2*i].each do |cal1|
arr[2*i+1].each do |cal2|
mergecal = func(cal1,cal2)
if mergecal
groups[i] << mergecal
else
mergecal = nil
end
end
end
else
groups[i] = arr[2*i]
end
end
arr = nil
return merge(groups)
end
After the page using this algorithm is rendered, Task Manager reported around 500MB of RAM usage. Then by refreshing the same page again, memory usage have now reached 1GB. I tried adding GC.start(full_mark: true) to the controller just after the function call, but nothing seems to have changed. I'm not sure whether the memory leak has to code with my code or Ruby itself.
Ruby garbage collection doesn't immediately reduce the amount of memory your ruby program has allocated. Memory allocation is expensive so even if the objects you create are immediately collected by GC the memory is slowly released back to the OS. If you think this function has a memory leak you should try running it in a non-rails process where you have more control over object lifecycles. You can use GC.stat to get information about the number of live and free objects before and after you run the GC. It's also worth reading up on how ruby GC works I like this article.

How to deal with Ruby 2.1.2 memory leaks?

I have a worker process which spawns up to 50 threads and do some async operations (most of which are http calls). When I start up the process, it starts with some 35MB of used memory, and quickly grows to 250MB. From that point it grows further more and the problem is that the memory never stops growing (even though the growing phase decreases over time). After several days, process just outgrows the available memory and crashes.
I did a lot of analysis and profiling and can't seem to find what is wrong. Process memory is constantly growing, even though the heap size is pretty much constant. I've collected GC.stat output into spreadsheet that you can access here:
https://docs.google.com/spreadsheets/d/17TohDNXQ_MXM31CeAmR2ptHFYfvOeF3dB6WCBkBS_Bc/edit?usp=sharing
Even though it seems that the process memory has finally stabilized at 415MB, it will continue to grow over next couple of days until it reaches 512MB limit and crashes.
I've also tried tracking objects with objectspace, but the sum of memory of tracked objects never crosses 70-80MB which perfectly aligns with GC reports. Where are the remaining 300MB+ (and growing) spent.. i have no clue.
How to deal with these kinds of problems? Are there any tools that could give me clearer insight on how the memory is being consumed?
UPDATE: Gems and OS
I'm using following gems:
gem "require_all", "~> 1.3"
gem "thread", "~> 0.1"
gem "equalizer", "~> 0.0.9"
gem "digest-murmurhash", "~> 0.3", require: "digest/murmurhash"
gem "google-api-client", "~> 0.7", require: "google/api_client"
gem "aws-sdk", "~> 1.44"
The application is deployed on heroku, though memory leak is noticable when running it locally on Mac OS X 10.9.4.
UPDATE: Leaks
I've upgraded stringbuffer and analyzed everything like #mtm suggested and now there are no memory leaks identified by leak tool, no increases in ruby heap size over time, and yet, the process memory is still growing. Originally I thought that it stopped growing at some point, but several hours later it outgrew the limit and process crashed.
From your GC logs it appears the issue is not a ruby object reference leak as the heap_live_slot value is not increasing significantly. That would suggest the problem is one of:
Data being stored outside the heap (Strings, Arrays etc)
A leak in a gem that uses native code
A leak in the Ruby interpreter itself (least likely)
It's interesting to note that the problem exhibits on both OSX and Heroku (Ubuntu Linux).
Object data and the "heap"
Ruby 2.1 garbage collection uses the reported "heap" only for Objects that contain a tiny amount of data. When the data contained in an Object goes over a certain limit, the data is moved and allocated to an area outside of the heap. You can get the overall size of each data type with ObjectSpace:
require 'objspace'
ObjectSpace.count_objects_size({})
Collecting this along with your GC stats might indicate where memory is being allocated outside the heap. If you find a particular type, say :T_ARRAY increasing a lot more than the others you might need to look for an array you are forever appending to.
You can use pry-byebug to drop into a console to troll around specific objects, or even looking at all objects from the root:
ObjectSpace.memsize_of(some_object)
ObjectSpace.reachable_objects_from_root
There's a bit more detail on one of the ruby developers blog and also in this SO answer. I like their JRuby/VisualVM profiling idea.
Testing native gems
Use bundle to install your gems into a local path:
bundle install --path=.gems/
Then you can find those that include native code:
find .gems/ -name "*.c"
Which gives you: (in my order of suspiciousness)
digest-stringbuffer-0.0.2
digest-murmurhash-0.3.0
nokogiri-1.6.3.1
json-1.8.1
OSX has a useful dev tool called leaks that can tell you if it finds unreferenced memory in a running process. Not very useful for identifying where the memory comes from in Ruby but will help to identify when it is occurring.
First to be tested is digest-stringbuffer. Grab the example from the Readme and add in some GC logging with gc_tracer
require "digest/stringbuffer"
require "gc_tracer"
GC::Tracer.start_logging "gclog.txt"
module Digest
class Prime31 < StringBuffer
def initialize
#prime = 31
end
def finish
result = 0
buffer.unpack("C*").each do |c|
result += (c * #prime)
end
[result & 0xffffffff].pack("N")
end
end
end
And make it run lots
while true do
a=[]
500.times do |i|
a.push Digest::Prime31.hexdigest( "abc" * (1000 + i) )
end
sleep 1
end
Run the example:
bundle exec ruby ./stringbuffertest.rb &
pid=$!
Monitor the resident and virtual memory sizes of the ruby process, and the count of leaks identified:
while true; do
ps=$(ps -o rss,vsz -p $pid | tail +2)
leaks=$(leaks $pid | grep -c Leak)
echo "$(date) m[$ps] l[$leaks]"
sleep 15
done
And it looks like we've found something already:
Tue 26 Aug 2014 18:22:36 BST m[104776 2538288] l[8229]
Tue 26 Aug 2014 18:22:51 BST m[110524 2547504] l[13657]
Tue 26 Aug 2014 18:23:07 BST m[113716 2547504] l[19656]
Tue 26 Aug 2014 18:23:22 BST m[113924 2547504] l[25454]
Tue 26 Aug 2014 18:23:38 BST m[113988 2547504] l[30722]
Resident memory is increasing and the leaks tool is finding more and more unreferenced memory. Confirm the GC heap size, and object count looks stable still
tail -f gclog.txt | awk '{ print $1, $3, $4, $7, $13 }
1581853040832 468 183 39171 3247996
1581859846164 468 183 33190 3247996
1584677954974 469 183 39088 3254580
1584678531598 469 183 39088 3254580
1584687986226 469 183 33824 3254580
1587512759786 470 183 39643 3261058
1587513449256 470 183 39643 3261058
1587521726010 470 183 34470 3261058
Then report the issue.
It appears to my very untrained C eye that they allocate both a pointer and a buffer but only clean up the buffer.
Looking at digest-murmurhash, it seems to only provide functions that rely on StringBuffer so the leak might be fine once stringbuffer is fixed.
When they have patched it, test again and move onto the next gem. It's probably best to use snippets of code from your implementation for each gem test rather than a generic example.
Testing MRI
First step would be to prove the issue on multiple machines under the same MRI to rule out anything local, which you've already done.
Then try the same Ruby version on a different OS, which you've done too.
Try the code on JRuby or Rubinius if possible. Does the same issue occur?
Try the same code on 2.0 or 1.9 if possible, see if the same problem exists.
Try the head development version from github and see if that makes any difference.
If nothing becomes apparent, submit a bug to Ruby detailing the issue and all the things you have eliminated. Wait for a dev to help out and provide whatever they need. They will most likely want to reproduce the issue so if you can get the most concise/minimal example of the issue set up. Doing that will often help you identify what the issue is anyway.
I fix memory leak and release digest/stringbuffer v0.0.3.
https://rubygems.org/gems/digest-stringbuffer
You can try again by v0.0.3.
I'm author of digest/murmurhash and digest/stringbuffer gems.
Indeed, It seems like have leaks in digest/stringbuffer.
I'll fix it later.
Can you explain more code?
I recommend using singleton methods like this.
Digest::MurmurHash1.hexdigest(some_data)
Maybe, It's not leak since singleton methods are not using digest/stringbuffer.

Is it possible to ensure that threaded code doesn't have side effects in Ruby?

Data safety and GIL removal mentions that if you don't have the Giant Interpreter Lock in place, you increase the risk of race conditions. The blog post gave the following example:
# As noted in the blog post, this'll work correctly in MRI Ruby (1.8 or 1.9)
# but may or may not work correctly in Rubinius 2.0 or JRuby
#array, threads = [], []
4.times do
threads << Thread.new { (1..100_000).each {|n| #array << n} }
end
threads.each{|t| t.join }
puts #array.size
One approach I'd take to making the code thread safe is to do functional programming and not have code within the thread modify objects/variables that weren't created within the thread:
threads = 4.times.map do
Thread.new do
sub_array = []
# Modifying sub_array is fine, because it was created by this thread
(1..100_000).each {|n| sub_array << n}
sub_array
end
end
puts threads.map(&:value).flatten(1).size
# Or (and don't forget nil!)
# array = threads.map(&:value).flatten(1) ; nil
# puts array.size
Is it possible to specify that a thread isn't allowed to modify objects/variables that don't "belong" to it, and raise a warning or exception if it does?
Assume that the threaded code doesn't do anything spectacularly pathological like calling ObjectSpace.each_object.
I don't know of a way to limit Ruby's access to things in any capacity other than the long-standing tradition of forking out a new process that is independent. Most languages are like this with very few exceptions, with strictly functional languages being in that set as you point out.
The most responsible approach here is to either use Mutex locking, or to create classes that are thread-safe by keeping data isolated and independent. This requires careful design, but if done right your threaded application is nearly as simple as a standard one.

Ruby Memory Management

I have been using Ruby for a while now and I find, for bigger projects, it can take up a fair amount of memory. What are some best practices for reducing memory usage in Ruby?
Please, let each answer have one "best practice" and let the community vote it up.
When working with huge arrays of ActiveRecord objects be very careful... When processing those objects in a loop if on each iteration you are loading their related objects using ActiveRecord's has_many, belongs_to, etc. - the memory usage grows a lot because each object that belongs to an array grows...
The following technique helped us a lot (simplified example):
students.each do |student|
cloned_student = student.clone
...
cloned_student.books.detect {...}
ca_teachers = cloned_student.teachers.detect {|teacher| teacher.address.state == 'CA'}
ca_teachers.blah_blah
...
# Not sure if the following is necessary, but we have it just in case...
cloned_student = nil
end
In the code above "cloned_student" is the object that grows, but since it is "nullified" at the end of each iteration this is not a problem for huge array of students. If we didn't do "clone", the loop variable "student" would have grown, but since it belongs to an array - the memory used by it is never released as long as array object exists.
Different approach works too:
students.each do |student|
loop_student = Student.find(student.id) # just re-find the record into local variable.
...
loop_student.books.detect {...}
ca_teachers = loop_student.teachers.detect {|teacher| teacher.address.state == 'CA'}
ca_teachers.blah_blah
...
end
In our production environment we had a background process that failed to finish once because 8Gb of RAM wasn't enough for it. After this small change it uses less than 1Gb to process the same amount of data...
Don't abuse symbols.
Each time you create a symbol, ruby puts an entry in it's symbol table. The symbol table is a global hash which never gets emptied.
This is not technically a memory leak, but it behaves like one. Symbols don't take up much memory so you don't need to be too paranoid, but it pays to be aware of this.
A general guideline: If you've actually typed the symbol in code, it's fine (you only have a finite amount of code after all), but don't call to_sym on dynamically generated or user-input strings, as this opens the door to a potentially ever-increasing number
Don't do this:
def method(x)
x.split( doesn't matter what the args are )
end
or this:
def method(x)
x.gsub( doesn't matter what the args are )
end
Both will permanently leak memory in ruby 1.8.5 and 1.8.6. (not sure about 1.8.7 as I haven't tried it, but I really hope it's fixed.) The workaround is stupid and involves creating a local variable. You don't have to use the local, just create one...
Things like this are why I have lots of love for the ruby language, but no respect for MRI
Beware of C extensions which allocate large chunks of memory themselves.
As an example, when you load an image using RMagick, the entire bitmap gets loaded into memory inside the ruby process. This may be 30 meg or so depending on the size of the image.
However, most of this memory has been allocated by RMagick itself. All ruby knows about is a wrapper object, which is tiny(1).
Ruby only thinks it's holding onto a tiny amount of memory, so it won't bother running the GC. In actual fact it's holding onto 30 meg.
If you loop over a say 10 images, you can run yourself out of memory really fast.
The preferred solution is to manually tell the C library to clean up the memory itself - RMagick has a destroy! method which does this. If your library doesn't however, you may need to forcibly run the GC yourself, even though this is generally discouraged.
(1): Ruby C extensions have callbacks which will get run when the ruby runtime decides to free them, so the memory will eventually be successfully freed at some point, just perhaps not soon enough.
Measure and detect which parts of your code are creating objects that cause memory usage to go up. Improve and modify your code then measure again. Sometimes, you're using gems or libraries that use up a lot of memory and creating a lot of objects as well.
There are many tools out there such as busy-administrator that allow you to check the memory size of objects (including those inside hashes and arrays).
$ gem install busy-administrator
Example # 1: MemorySize.of
require 'busy-administrator'
data = BusyAdministrator::ExampleGenerator.generate_string_with_specified_memory_size(10.mebibytes)
puts BusyAdministrator::MemorySize.of(data)
# => 10 MiB
Example # 2: MemoryUtils.profile
Code
require 'busy-administrator'
results = BusyAdministrator::MemoryUtils.profile(gc_enabled: false) do |analyzer|
BusyAdministrator::ExampleGenerator.generate_string_with_specified_memory_size(10.mebibytes)
end
BusyAdministrator::Display.debug(results)
Output:
{
memory_usage:
{
before: 12 MiB
after: 22 MiB
diff: 10 MiB
}
total_time: 0.406452
gc:
{
count: 0
enabled: false
}
specific:
{
}
object_count: 151
general:
{
String: 10 MiB
Hash: 8 KiB
BusyAdministrator::MemorySize: 0 Bytes
Process::Status: 0 Bytes
IO: 432 Bytes
Array: 326 KiB
Proc: 72 Bytes
RubyVM::Env: 96 Bytes
Time: 176 Bytes
Enumerator: 80 Bytes
}
}
You can also try ruby-prof and memory_profiler. It is better if you test and experiment different versions of your code so you can measure the memory usage and performance of each version. This will allow you to check if your optimization really worked or not. You usually use these tools in development / testing mode and turn them off in production.

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