Re: [vcap-dev] Java OOM debugging


Lari Hotari <Lari@...>
 

fyi. Tomcat 8.0.20 might be consuming more memory than 8.0.18:
https://github.com/cloudfoundry/java-buildpack/issues/166#issuecomment-94517568

Other things we’ve tried:

- We set verbose garbage collection to verify there was no
memory size issues within the JVM. There wasn’t.

- We tried setting minimum memory for native, it had no
effect. The container still gets killed

- We tried adjusting the ‘memory heuristics’ so that they
added up to 80 rather than 100. This had the effect of causing a delay
in the container being killed. However it still was killed.
I think adjusting memory heuristics so that they add up to 80 doesn't
make a difference because the values aren't percentages.
The values are proportional weighting values used in the memory
calculation:
https://github.com/grails-samples/java-buildpack/blob/b4abf89/docs/jre-oracle_jre.md#memory-calculation

I found out that the only way to reserve "unused" memory is to set a
high value for the native memory lower bound in the memory_sizes.native
setting of config/open_jdk_jre.yml .
Example:
https://github.com/grails-samples/java-buildpack/blob/22e0f6a/config/open_jdk_jre.yml#L25



This seems like classic memory leak behaviour to me.
In my case it wasn't a classical Java memory leak, since the Java
application wasn't leaking memory. I was able to confirm this by getting
some heap dumps with the HeapDumpServlet
(https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/HeapDumpServlet.groovy)
and analyzing them.

In my case the JVM's RSS memory size is slowly growing. It probably is
some kind of memory leak since one process I've been monitoring now is
very close to the memory limit. The uptime is now almost 3 weeks.

Here is the latest diff of the meminfo report.
https://gist.github.com/lhotari/ee77decc2585f56cf3ad#file-meminfo_diff_example2-txt

From a Java perspective this isn't classical. The JVM heap isn't filling
up. The problem is that RSS size is slowly growing and will eventually
cause the Java process to cross the memory boundary so that the process
gets kill by the Linux kernel cgroups OOM killer.

RSS size might be growing because of many reasons. I have been able to
slow down the growth by doing the various MALLOC_ and JVM parameter
tuning (-XX:MinMetaspaceExpansion=1M -XX:CodeCacheExpansionSize=1M). I'm
able to get a longer uptime, but the problem isn't solved.

Lari


On 15-05-11 06:41 AM, Head-Rapson, David wrote:

Thanks for the continued advice.



We’ve hit on a key discovery after yet another a soak test this weekend.

- When we deploy using Tomcat 8.0.18 we don’t see the issue

- When we deploy using Tomcat 8.0.20 (same app version, same
CF space, same services bound, same JBP code version, same JRE
version, running at the same time), we see the crashes occurring after
just a couple of hours.



Ideally we’d go ahead with the memory calculations you mentioned
however we’re stuck on lucid64 because we’re using Pivotal CF 1.3.x &
we’re having upgrade issues to 1.4.x.

So we’re not able to adjust MALLOC_ARENA_MAX, nor are we able to view
RSS in pmap as you describe



Other things we’ve tried:

- We set verbose garbage collection to verify there was no
memory size issues within the JVM. There wasn’t.

- We tried setting minimum memory for native, it had no
effect. The container still gets killed

- We tried adjusting the ‘memory heuristics’ so that they
added up to 80 rather than 100. This had the effect of causing a delay
in the container being killed. However it still was killed.



This seems like classic memory leak behaviour to me.



*From:*Lari Hotari [mailto:lari.hotari(a)sagire.fi] *On Behalf Of *Lari
Hotari
*Sent:* 08 May 2015 16:25
*To:* Daniel Jones; Head-Rapson, David
*Cc:* cf-dev(a)lists.cloudfoundry.org
*Subject:* Re: [Cf-dev] [vcap-dev] Java OOM debugging




For my case, it turned out to be essential to reserve enough memory
for "native" in the JBP. For the 2GB total memory, I set the minimum
to 330M. With that setting I have been able to get over 2 weeks up
time by now.

I mentioned this in my previous email:

The workaround for that in my case was to add a native key under
memory_sizes in open_jdk_jre.yml and set the minimum to 330M (that is
for a 2GB total memory).
see example
https://github.com/grails-samples/java-buildpack/blob/22e0f6a/config/open_jdk_jre.yml#L25
that was how I got the app I'm running on CF to stay within the memory
bounds. I'm sure there is now also a way to get the keys without
forking the buildpack. I could have also adjusted the percentage
portions, but I wanted to set a hard minimum for this case.


I've been trying to get some insight by diffing the reports gathered
from the meminfo servlet
https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/MemoryInfoServlet.groovy


Here is such an example of a diff:
https://gist.github.com/lhotari/ee77decc2585f56cf3ad#file-meminfo_diff_example-txt

meminfo has pmap output included to get the report of the memory map
of the process. I have just noticed that most of the memory has
already been mmap:ed from the OS and it's just growing in RSS size.
For example:
< 00000000a7600000 1471488 1469556 1469556 rw--- [ anon ]
00000000a7600000 1471744 1470444 1470444 rw--- [ anon ]
The pmap output from lucid64 didn't include the RSS size, so you have
to use cflinuxfs2 for this. It's also better because of other reasons.
The glibc in lucid64 is old and has some bugs around the MALLOC_ARENA_MAX.

I was manually able to estimate the maximum size of the RSS size of
what the Java process will consume by simply picking the large
anon-blocks from the pmap report and calculating those blocks by the
allocated virtual size (VSS).
Based on this calculation, I picked the minimum of 330M for "native"
in open_jdk_jre.yml as I mentioned before.

It looks like these rows are for the Heap size:
< 00000000a7600000 1471488 1469556 1469556 rw--- [ anon ]
00000000a7600000 1471744 1470444 1470444 rw--- [ anon ]
It looks like the JVM doesn't fully allocate that block in RSS
initially and most of the growth of RSS size comes from that in my
case. In your case, it might be something different.

I also added a servlet for getting glibc malloc_info statistics in XML
format (). I haven't really analysed that information because of time
constraints and because I don't have a pressing problem any more. btw.
The malloc_info XML report is missing some key elements, that has been
added in later glibc versions
(https://github.com/bminor/glibc/commit/4d653a59ffeae0f46f76a40230e2cfa9587b7e7e).

If killjava.sh never fires and the app crashed with Warden out of
memory errors, then I believe it's the kernel's cgroups OOM killer
that has killed the container processes. I have found this location
where Warden oom notifier gets the OOM notification event:
https://github.com/cloudfoundry/warden/blob/ad18bff/warden/lib/warden/container/features/mem_limit.rb#L70
This is the oom.c source code:
https://github.com/cloudfoundry/warden/blob/ad18bff7dc56acbc55ff10bcc6045ebdf0b20c97/warden/src/oom/oom.c
. It reads the cgroups control files and receives events from the
kernel that way.

I'd suggest that you use pmap for the Java process after it has
started and calculate the maximum RSS size by calculating the VSS size
of the large anon blocks instead of RSS for the blocks that the Java
process has reserved for it's different memory areas (I think you
shouldn't . You should discard adding VSS for the
CompressedClassSpaceSize block.
After this calculation, add enough memory to the "native" parameter in
JBP until the RSS size calculated this way stays under the limit.
That's the only "method" I have come up by now.

It might be required to have some RSS space allocated for any zip/jar
files read by the Java process. I think that Java uses mmap files for
zip file reading by default and that might go on top of all other limits.
To test this theory, I'd suggest testing by adding
-Dsun.zip.disableMemoryMapping=true system property setting to
JAVA_OPTS. That disables the native mmap for zip/jar file reading. I
haven't had time to test this assumption.

I guess the only way to understand how Java allocates memory is to
look at the source code.
from http://openjdk.java.net/projects/jdk8u/ , the instructions to get
the source code of JDK 8:
hg clone http://hg.openjdk.java.net/jdk8u/jdk8u;cd jdk8u;sh get_source.sh
This tool is really good for grepping and searching the source code:
http://geoff.greer.fm/ag/ <http://geoff.greer.fm/ag/>
On Ubuntu it's in silversearcher-ag package, "apt-get install
silversearcher-ag" and on MacOSX brew it's "brew install
the_silver_searcher".
This alias is pretty useful:
alias codegrep='ag --color --group --pager less -C 5'
Then you just search for the correct location in code by starting with
the tokens you know about:
codegrep MaxMetaspaceSize
this gives pretty good starting points in looking how the JDK
allocates memory.

So the JDK source code is only a few commands away.

It would be interesting to hear more about this if someone has the
time to dig in to this. This is about how far I got and I hope sharing
this information helps someone continue. :)


Lari
github/twitter: lhotari

On 15-05-08 10:02 AM, Daniel Jones wrote:

Hi Lari et al,



Thanks for your help Lari.



David and I are pairing on this issue, and we're yet to resolve
it. We're in the process of creating a repeatable test case (our
most crashy app makes calls to external services that need
mocking), but in the meantime, here's what we've seen.



Between Java Buildpack commit e89e546 and 17162df, we see apps
crashing with Warden out of memory errors. killjava.sh never
fires, and this has led us to believe that the kernel is shooting
a cgroup process in the head after the cgroup oversteps its memory
limit. We cannot find any evidence of the OOM killer firing in any
logs, but we may not be looking in the right place.



The JBP is setting heap to be 70%, metaspace to be 15% (with max
set to the same as initial), 5% for "stack", 5% for "normalised
stack" and 10% for "native". We do not understand why this adds up
to 105%, but haven't looked into the JBP algorithm yet. Any
pointers on what "normalised stack" is would be much appreciated,
as this doesn't appear in the list of heuristics supplied via app env.



Other team members tried applying the same settings that you
suggested - thanks for this. Apps still crash with these settings,
albeit less frequently.



After reading the blog you linked to
(http://java.dzone.com/articles/java-8-permgen-metaspace) we
wondered whether the increased /reserved /metaspace claimed after
metaspace GC might be causing a problem; however we reused the
test code to create a metaspace leak in a CF app and saw metaspace
GCs occur correctly, and memory usage never grow over
MaxMetaspaceSize. This figures, as the committed metaspace is
still less than MaxMetaspaceSize, and the reserved appears to be
whatever RAM is free across the whole DEA.



We noted that an Oracle blog
(https://blogs.oracle.com/poonam/entry/about_g1_garbage_collector_permanent)
mentions that the metaspace size parameters are approximate. We're
currently wondering if native allocations by Tomcat (APR, NIO) are
taking up more container memory, and so when the metaspace fills,
it's creeping slightly over the limit and triggering the kernel's
OOM killer.



Any suggestions would be much appreciated. We've tried to resist
tweaking heuristics blindly, but are running out of options as
we're struggling to figure out how the Java process is using
/committed/ memory. pmap seems to show virtual memory, and so it's
hard to see if things like the metaspace or NIO ByteBuffers are
nabbing too much and trigger the kernel's OOM killer.



Thanks for all your help,



Daniel Jones & David Head-Rapson



On Wed, Apr 29, 2015 at 8:07 PM, Lari Hotari <Lari(a)hotari.net
<mailto:Lari(a)hotari.net>> wrote:

Hi,

I created a few tools to debug OOM problems since the application
I was responsible for running on CF was failing constantly because
of OOM problems. The problems I had, turned out not to be actual
memory leaks in the Java application.

In the "cf events appname" log I would get entries like this:
2015-xx-xxTxx:xx:xx.00-0400 app.crash appname
index: 1, reason: CRASHED, exit_description: out of memory,
exit_status: 255

These type of entries are produced when the container goes over
it's memory resource limits. It doesn't mean that there is a
memory leak in the Java application. The container gets killed by
the Linux kernel oom killer
(https://github.com/cloudfoundry/warden/blob/master/warden/README.md#limit-handle-mem-value)
based on the resource limits set to the warden container.

The memory limit is specified in number of bytes. It is enforced
using the control group associated with the container. When a
container exceeds this limit, one or more of its processes will be
killed by the kernel. Additionally, the Warden will be notified
that an OOM happened and it subsequently tears down the container.

In my case it never got killed by the killjava.sh script that gets
called in the java-buildpack when an OOM happens in Java.

This is the tool I built to debug the problems:
https://github.com/lhotari/java-buildpack-diagnostics-app
I deployed that app as part of the forked buildpack I'm using.
Please read the readme about what it's limitations are. It worked
for me, but it might not work for you. It's opensource and you can
fork it. :)

There is a solution in my toolcase for creating a heapdump and
uploading that to S3:
https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/HeapDumpServlet.groovy
The readme explains how to setup Amazon S3 keys for this:
https://github.com/lhotari/java-buildpack-diagnostics-app#amazon-s3-setup
Once you get a dump, you can then analyse the dump in a java
profiler tool like YourKit.

I also have a solution that forks the java-buildpack modifies
killjava.sh and adds a script that uploads the heapdump to S3 in
the case of OOM:
https://github.com/lhotari/java-buildpack/commit/2d654b80f3bf1a0e0f1bae4f29cb85f56f5f8c46

In java-buildpack-diagnostics-app I have also other tools for
getting Linux operation system specific memory information, for
example:

https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/MemoryInfoServlet.groovy
https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/MemorySmapServlet.groovy
https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/MallocInfoServlet.groovy

These tools are handy for looking at details of the Java process
RSS memory usage growth.

There is also a solution for getting ssh shell access inside your
application with tmate.io <http://tmate.io>:
https://github.com/lhotari/java-buildpack-diagnostics-app/blob/master/src/main/groovy/io/github/lhotari/jbpdiagnostics/TmateSshServlet.groovy
(this version is only compatible with the new "cflinuxfs2" stack)

It looks like there are serious problems on CloudFoundry with the
memory sizing calculation. An application that doesn't have a OOM
problem will get killed by the oom killer because the Java process
will go over the memory limits.
I filed this issue:
https://github.com/cloudfoundry/java-buildpack/issues/157 , but
that might not cover everything.

The workaround for that in my case was to add a native key under
memory_sizes in open_jdk_jre.yml and set the minimum to 330M (that
is for a 2GB total memory).
see example
https://github.com/grails-samples/java-buildpack/blob/22e0f6a/config/open_jdk_jre.yml#L25
that was how I got the app I'm running on CF to stay within the
memory bounds. I'm sure there is now also a way to get the keys
without forking the buildpack. I could have also adjusted the
percentage portions, but I wanted to set a hard minimum for this case.

It was also required to do some other tuning.

I added this to JAVA_OPTS:
-XX:CompressedClassSpaceSize=256M -XX:InitialCodeCacheSize=64M
-XX:CodeCacheExpansionSize=1M -XX:CodeCacheMinimumFreeSpace=1M
-XX:ReservedCodeCacheSize=200M -XX:MinMetaspaceExpansion=1M
-XX:MaxMetaspaceExpansion=8M -XX:MaxDirectMemorySize=96M
while trying to keep the Java process from growing in RSS memory size.

The memory overhead of a 64 bit Java process on Linux can be
reduced by specifying these environment variables:

stack: cflinuxfs2
.
.
.
env:
MALLOC_ARENA_MAX: 2
MALLOC_MMAP_THRESHOLD_: 131072
MALLOC_TRIM_THRESHOLD_: 131072
MALLOC_TOP_PAD_: 131072
MALLOC_MMAP_MAX_: 65536

MALLOC_ARENA_MAX works only on cflinuxfs2 stack (the lucid64 stack
has a buggy version of glibc).

explanation about MALLOC_ARENA_MAX from Heroku:
https://devcenter.heroku.com/articles/tuning-glibc-memory-behavior
some measurement data how it reduces memory consumption:
https://devcenter.heroku.com/articles/testing-cedar-14-memory-use

I have created a PR to add this to CF java-buildpack:
https://github.com/cloudfoundry/java-buildpack/pull/160

I also created an issues
https://github.com/cloudfoundry/java-buildpack/issues/163 and
https://github.com/cloudfoundry/java-buildpack/pull/159 .

I hope this information helps others struggling with OOM problems
in CF.
I'm not saying that this is a ready made solution just for you.
YMMV. It worked for me.

-Lari




On 15-04-29 10:53 AM, Head-Rapson, David wrote:

Hi,

I’m after some guidance on how to get profile Java apps in CF,
in order to get to the bottom of memory issues.

We have an app that’s crashing every few hours with OOM error,
most likely it’s a memory leak.

I’d like to profile the JVM and work out what’s eating memory,
however tools like yourkit require connectivity INTO the JVM
server (i.e. the warden container), either via host / port or
via SSH.

Since warden containers cannot be connected to on ports other
than for HTTP and cannot be SSHd to, neither of these works
for me.



I tried installed a standalone JDK onto the warden container,
however as soon as I ran ‘jmap’ to invoke the dump, warden
cleaned up the container – most likely for memory
over-consumption.



I had previously found a hack in the Weblogic buildpack
(https://github.com/pivotal-cf/weblogic-buildpack/blob/master/docs/container-wls-monitoring.md)
for modifying the start script which, when used with
–XX:HeapDumpOnOutOfMemoryError, should copy any heapdump files
to a file share somewhere. I have my own custom buildpack so
I could use something similar.

Has anyone got a better solution than this?



We would love to use newrelic / app dynamics for this however
we’re not allowed. And I’m not 100% certain they could help
with this either.



Dave



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