Re: [vcap-dev] Java OOM debugging


Daniel Mikusa
 

On Thu, May 14, 2015 at 10:23 AM, Daniel Jones <
daniel.jones(a)engineerbetter.com> wrote:

Hi Lari,

Thanks again for your input. Have you seen this problem with versions of
Tomcat before 8.0.20?

David and I think we've narrowed down the issue to a change from using
Tomcat 8.0.18 to 8.0.21. We're running more tests and collaborating with
Pivotal support. We also noticed that non-prod versions of our apps were
taking longer to crash, so it would seem to be activity-related at least.
Since it seems activity related, have you tried monitoring the number of
threads in the JVM?

While you can cap the number of threads Tomcat uses for processing
requests, I don't believe that you can cap the number of threads it's
possible to create in the JVM. The reason I mention this is because each
thread causes the amount of memory required to go up by the thread stack
size (Xss * <threads> = total thread memory). Perhaps as activity
increases, so does the thread count and that's pushing you over the limit.

Are you setting a custom -Xss value or using the default? From memory, the
default is pretty large. If you're not using a custom one, you might try a
smaller one, like 256k and see if that has any impact on the problem.

Alternatively, you could adjust the memory weightings in the build pack so
that heap consumes a smaller amount of the total memory and there's more
memory available for native / stack and other memory.



Do you know how Tomcat's APR/NIO memory gets allocated?
I'm not sure I follow your question, but in terms of NIO I suspect the JVM
is going to handle memory allocation not Tomcat. Given that, I it should
happen just like any other Java code that uses the NIO. APR is unlikely to
be an issue, see my next comment.


Is there a way of telling from pmap whether pages are being used for NIO
buffers or by the APR?
Unless you compile the APR native library and include it with your version
of the build pack, Tomcat's not going to use it. It'll use NIO by default,
with Tomcat version 8. You can confirm by looking at the logs when you
start your app. One of the first things it logs will be the protocol
handler. This is from a test app, where it's using NIO.

Ex:

```
[CONTAINER] org.apache.coyote.http11.Http11NioProtocol INFO
Initializing ProtocolHandler ["http-nio-63227"]
```

Dan




I wonder if the other folks that have reported CF out of memory errors
with later versions of Tomcat are seeing slow creeps in native memory
consumption?

On Mon, May 11, 2015 at 2:19 PM, Lari Hotari <Lari(a)hotari.net> wrote:


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 <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/
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> 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:

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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