Why this XML parsing Ruby code runs slower with GC disabled? - ruby

I've got a piece of code parsing 500 MB XML file using libxml-ruby gem. What is surprising to me, this code runs slower with GC disabled, which seems counter-intuitive. What might be the reason? I've go plenty of memory available and the system is not swapping.
require 'xml'
#GC.disable
#reader = XML::Reader.file('books.xml', :options => XML::Parser::Options::NOBLANKS)
#reader.read
#reader.read
while #reader.name == 'book'
book_id = #reader.get_attribute('id')
#reader.read
until #reader.name == 'book' && #reader.node_type == XML::Reader::TYPE_END_ELEMENT
case #reader.name
when 'author'
author = #reader.read_string
when 'title'
title = #reader.read_string
when 'genre'
genre = #reader.read_string
when 'price'
price = #reader.read_string
when 'publish_date'
publish_date = #reader.read_string
when 'description'
description = #reader.read_string
end
#reader.next
end
#reader.read
end
#reader.close
Here are the results I got:
ruby gc on gc off
2.2.0 16.93s 18.81s
2.1.5 16.22s 18.58s
2.0.0 17.63s 17.99s
Why disable the garbage collector? I've read in Ruby Performance Optimization book that Ruby is slow mostly because programmers don't think about memory consumption, which makes garbage collector use a lot of execution time. Thus turning off the GC should instantly speed things up (at the cost of memory usage of course), as long as the system is not swapping.
I wanted to see if my XML parsing module can be improved, so I started experimenting with it by disabling the GC, which brought me to this problem. I expected a significant speed-up with GC disabled, but instead I got the opposite. I know that differences are not huge, but still this is strange to me.
libxml-ruby gem uses a native C LibXML implementation under the hood - can it be the reason?
The file that I used is manually multiplicated books.xml sample downloaded from some Microsoft documentation:
<catalog>
<book id="bk101">
<author>John Doe</author>
<title>XML for dummies</title>
<genre>Computer</genre>
<price>44.95</price>
<publish_date>2000-10-01</publish_date>
<description>Some description</description>
</book>
....
</catalog>
My setup: OS X Yosemite, Intel Core i5 2.6 GHz, 16GB of RAM.
Thanks for any suggestions.

You are forgetting the operating system - you've disabled GC in your MRI process but you have no control over the linux/unix kernel and how it allocates memory to your MRI application.
In fact, I believe that by disabling GC you have significantly hamstrung the behaviour of your application, making it likely that your program will need to continuously request more RAM from the kernel. This will likely involve some form of overhead in the kernel as it allocates swap or memory to you.
Your source data is a 500 mb xml file that you are reading, node by node, into your MRI program's memory footprint. It's likely your MRI process consumes several GB of data by the time it is done processing; and none of the values in your main reading block are discarded after each iteration - they simply hang around in memory, and are only finally cleaned up when your application exits and the memory is handed back to the operating system.
GC is in place to manage this; it is intended to prevent your application from requesting additional memory from the kernel unless it absolutely needs it, and to allow your application to run "well enough" within the memory allocated to it within reason.
So I'm not honestly surprised you see a slowdown with GC disabled. What would be telling is the load average and swap usage of your box during your benchmarks.

Related

Julia 1.1 with JLD HDF5 package and memory release in Windows

I'm using Julia 1.1 with JLD and HDF5 to save a file onto the disk, where I met a couple of question about the memory usage.
Issue 1:
First, I defined a 4 GB matrix A.
A = zeros(ComplexF64,(243,243,4000));
When I type the command and look at windows task manager:
A=nothing
It took several minutes for Julia to release those memory back to me. Most of the time, (In Task manager) Julia just doesn't release the memory usage at all, even though the command returned results saying that A occupied 0 bytes instantly.
varinfo()
name size summary
–––––––––––––––– ––––––––––– –––––––
A 0 bytes Nothing
Base Module
Core Module
InteractiveUtils 162.930 KiB Module
Main Module
ans 0 bytes Nothing
Issue 2:
Further, when I tried to use JLD and HDF5 to save file onto the disk. This time, the task manager told me that, when using the save("test.jld", "A", A) command, an extra 4GB memory was used.
using JLD,HDF5
A = zeros(ComplexF64,(243,243,4000));
save("test.jld", "A", A)
Further, after I typed
A=nothing
Julia won't release the 8 GB memory back to me.
Finding 3:
An interesting thing I found was that, if I retype the command
A = zeros(ComplexF64,(243,243,4000));
The task manager would told me the cashed memory was released, and the total memory usage was again only 4GB.
Question 1:
What's going on with memory management in Julia? Was it just a mistake by Windows, or some command in Julia? How to check the Julia memory usage instantly?
Question 2:
How to tell the Julia to instantly release the memory usage?
Question 3:
Is there a way to tell JLD package not use those extra 4GB meomory?
(Better, could someone tell me how to create A directly on the disk without even creating it in the memory? I knew there's memory mapped I/O in JLD package. I have tried it, but it seemed to require me to create matrix A in the memory and save A onto the disk first, before I could recall the memory mapped A again. )
This is a long question, so thanks ahead!
Julia uses garbage collector to de-alocate the memory. Usually a garbage collector does not run after every line of code but only when needed.
Try to force garbage collection by running the command:
GC.gc()
This releases memory space for unreferenced Julia objects. In this way you can check whether the memory actually has been released.
Side note: JLD used to be somewhat not-always-working (I do not know the current status). Hence you first consideration for non-cross-platform object persistence always should be the serialize function from the in-built Serialization package - check the documentation at https://docs.julialang.org/en/v1/stdlib/Serialization/index.html#Serialization.serialize

MRI duplicates memory allocation when Thread.new

It seems that MRI makes duplication of memory allocation for every new thread.
I use Ubuntu x64, ruby-2.2.4 (rvm), and this what i get:
Just started irb:
I see pmap -d 1656 59760K (allocated memory, or '[ stack ]' for the program stack [man pmap(1)]) memory usage:
And when creating a thread:
I see pmap -d 1656 127352K memory usage:
So, I see duplication 59760K -> 127352K of memory allocation.
Such behavior is similar to result of the fork() call, which being used for creation a new process, makes a copy of its calling process data ('copy-on-write' is out this context) for new process.
But Thread is created in the same process and shares its data, and it looks strange...
In practice, it means that Thread in Ruby has similar to Process restriction in memory usage: new thread creation fails when allocated memory getting closer to physical memory size.
I am curious, WHY?
UPDATE
It's not duplication memory but additional allocation for ~50K for each thread.
Thanks #tadman for suggestion that it's an overhead and not something like copying memory in the fork()'s way.

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.

Why 'Total MB' in golang heap profile is less than 'RES' in top?

I have a service written in go that takes 6-7G memory at runtime (RES in top). So I used the pprof tool trying to figure out where the problem is.
go tool pprof --pdf http://<service>/debug/pprof/heap > heap_prof.pdf
But there are only about 1-2G memory in result ('Total MB' in pdf). Where's the rest ?
And I've tried profile my service with GOGC=off, as a result the 'Total MB' is exactly the same as 'RES' in top. It seems that memory is GCed but haven't been return to kernel won't be profiled.
Any idea?
P.S, I've tested in both 1.0.3 and 1.1rc3.
This is because Go currently does not give memory of GC-ed objects back to the operating system, to be precise, only for objects smaller then predefined limit (32KB). Instead memory is cached to speed up future allocations Go:malloc. Also, it seems that this is going to be fixed in the future TODO.
Edit:
New GC behavior: If the memory is not used for a while (about 5 min), runtime will advise the kernel to remove the physical mappings from the unused virtual ranges. This process can be forced by calling runtime.FreeOSMemory()

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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