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Posted to user@hbase.apache.org by Bryan Beaudreault <bb...@hubspot.com> on 2016/05/23 16:55:17 UTC
File descriptor leak, possibly new in CDH5.7.0
Hey everyone,
We are noticing a file descriptor leak that is only affecting nodes in our
cluster running 5.7.0, not those still running 5.3.8. I ran an lsof against
an affected regionserver, and noticed that there were 10k+ unix sockets
that are just called "socket", as well as another 10k+ of the form
"/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>". The
2 seem related based on how closely the counts match.
We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
handled the namenode upgrade separately). The 5.3.8 nodes *do not*
experience this issue. The 5.7.0 nodes *do. *We are holding off upgrading
more regionservers until we can figure this out. I'm not sure if any
intermediate versions between the 2 have the issue.
We traced the root cause to a hadoop job running against a basic table:
'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
{'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
This is very similar to all of our other tables (we have many). However,
it's regions are getting up there in size, 40+gb per region, compressed.
This has not been an issue for us previously.
The hadoop job is a simple TableMapper job with no special parameters,
though we haven't updated our client yet to the latest (will do that once
we finish the server side). The hadoop job runs on a separate hadoop
cluster, remotely accessing the HBase cluster. It does not do any other
reads or writes, outside of the TableMapper scans.
Moving the regions off of an affected server, or killing the hadoop job,
causes the file descriptors to gradually go back down to normal.
Any ideas?
Thanks,
Bryan
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Stack <st...@duboce.net>.
On Mon, May 23, 2016 at 11:19 AM, Bryan Beaudreault <
bbeaudreault@hubspot.com> wrote:
> We run MR against many tables in all of our clusters, they mostly have
> similar schema definitions though vary in terms of key length, # columns,
> etc. This is the only cluster and only table we've seen leak so far. It's
> probably the table with the biggest regions which we MR against, though
> it's hard to verify that (anyone in engineering can run such a job).
>
> dfs.client.read.shortcircuit.streams.cache.size = 256
>
> Our typical FD amount is around 3000. When this hadoop job runs, that can
> climb up to our limit of over 30k if we don't act -- it is a gradual build
> up over the course of a couple hours. When we move the regions off or kill
> the job, the FDs will gradually go back down at roughly the same pace. It
> forms a graph in the shape of a pyramid.
>
> We don't use CM, we use mostly the default *-site.xml. We haven't
> overridden anything related to this. The configs between CDH5.3.8 and 5.7.0
> are identical for us.
>
> Chatting w/ our Colin, Mr ShortCircuit, he notes that it doesn't sound
like a leak if it comes down when you kill the job. Anything about the job
itself that is holding open references or throwing away files w/o closing
them? It could also just be the size that you note.
Seems like the expiry is set to 5minutes by default for the fd cache:
2099 <property>
2100 <name>dfs.client.read.shortcircuit.streams.cache.expiry.ms</name>
2101 <value>300000</value>
2102 <description>
2103 This controls the minimum amount of time
2104 file descriptors need to sit in the client cache context
2105 before they can be closed for being inactive for too long.
2106 </description>
2107 </property>
Even waiting a while, the fd count doesn't fall?
St.Ack
> On Mon, May 23, 2016 at 2:03 PM Stack <st...@duboce.net> wrote:
>
> > On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
> > bbeaudreault@hubspot.com
> > > wrote:
> >
> > > Hey everyone,
> > >
> > > We are noticing a file descriptor leak that is only affecting nodes in
> > our
> > > cluster running 5.7.0, not those still running 5.3.8.
> >
> >
> > Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs
> hbase-0.98.6+hadoop-2.5.0.
> >
> >
> > > I ran an lsof against
> > > an affected regionserver, and noticed that there were 10k+ unix sockets
> > > that are just called "socket", as well as another 10k+ of the form
> > > "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>".
> > The
> > > 2 seem related based on how closely the counts match.
> > >
> > > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
> > > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> > > experience this issue. The 5.7.0 nodes *do. *We are holding off
> upgrading
> > > more regionservers until we can figure this out. I'm not sure if any
> > > intermediate versions between the 2 have the issue.
> > >
> > > We traced the root cause to a hadoop job running against a basic table:
> > >
> > > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> > > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> > > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> > > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
> > >
> > > This is very similar to all of our other tables (we have many).
> >
> >
> > You are doing MR against some of these also? They have different schemas?
> > No leaks here?
> >
> >
> >
> > > However,
> > > it's regions are getting up there in size, 40+gb per region,
> compressed.
> > > This has not been an issue for us previously.
> > >
> > > The hadoop job is a simple TableMapper job with no special parameters,
> > > though we haven't updated our client yet to the latest (will do that
> once
> > > we finish the server side). The hadoop job runs on a separate hadoop
> > > cluster, remotely accessing the HBase cluster. It does not do any other
> > > reads or writes, outside of the TableMapper scans.
> > >
> > > Moving the regions off of an affected server, or killing the hadoop
> job,
> > > causes the file descriptors to gradually go back down to normal.
> > >
> > >
> > Any ideas?
> > >
> > >
> > Is it just the FD cache running 'normally'? 10k seems like a lot though.
> > 256 seems to be the default in hdfs but maybe it is different in CM or in
> > hbase?
> >
> > What is your dfs.client.read.shortcircuit.streams.cache.size set to?
> > St.Ack
> >
> >
> >
> > > Thanks,
> > >
> > > Bryan
> > >
> >
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Bryan Beaudreault <bb...@hubspot.com>.
I'll try to run with a higher caching to see how that changes things, thanks
On Mon, May 23, 2016 at 4:07 PM Stack <st...@duboce.net> wrote:
> How hard to change the below if only temporarily (Trying to get a datapoint
> or two to act on; the short circuit code hasn't changed that we know of...
> perhaps the scan chunking facility in 1.1 has some side effect we've not
> noticed up to this).
>
> If you up the caching to be bigger does it lower the rate of FD leak
> creation?
>
> If you cache the blocks, assuming it does not blow the cache for others,
> does that make a difference.
>
> Hang on... will be back in a sec... just sending this in meantime...
>
> St.Ack
>
> On Mon, May 23, 2016 at 12:20 PM, Bryan Beaudreault <
> bbeaudreault@hubspot.com> wrote:
>
> > For reference, the Scan backing the job is pretty basic:
> >
> > Scan scan = new Scan();
> > scan.setCaching(500); // probably too small for the datasize we're
> dealing
> > with
> > scan.setCacheBlocks(false);
> > scan.setScanMetricsEnabled(true);
> > scan.setMaxVersions(1);
> > scan.setTimeRange(startTime, stopTime);
> >
> > Otherwise it is using the out-of-the-box TableInputFormat.
> >
> >
> >
> > On Mon, May 23, 2016 at 3:13 PM Bryan Beaudreault <
> > bbeaudreault@hubspot.com>
> > wrote:
> >
> > > I've forced the issue to happen again. netstat takes a while to run on
> > > this host while it's happening, but I do not see an abnormal amount of
> > > CLOSE_WAIT (compared to other hosts).
> > >
> > > I forced more than usual number of regions for the affected table onto
> > the
> > > host to speed up the process. File Descriptors are now growing quite
> > > rapidly, about 8-10 per second.
> > >
> > > This is what lsof looks like, multiplied by a couple thousand:
> > >
> > > COMMAND PID USER FD TYPE DEVICE SIZE/OFF
> > > NODE NAME
> > > java 23180 hbase DEL REG 0,16
> 3848784656
> > >
> >
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1702253823
> > > java 23180 hbase DEL REG 0,16
> 3847643924
> > >
> >
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1614925966
> > > java 23180 hbase DEL REG 0,16
> 3847614191
> > >
> >
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_888427288
> > >
> > > The only thing that varies is the last int on the end.
> > >
> > > > Anything about the job itself that is holding open references or
> > > throwing away files w/o closing them?
> > >
> > > The MR job does a TableMapper directly against HBase, which as far as I
> > > know uses the HBase RPC and does not hit HDFS directly at all. Is it
> > > possible that a long running scan (one with many, many next() calls)
> > could
> > > keep some references to HDFS open for the duration of the overall scan?
> > >
> > >
> > > On Mon, May 23, 2016 at 2:19 PM Bryan Beaudreault <
> > > bbeaudreault@hubspot.com> wrote:
> > >
> > >> We run MR against many tables in all of our clusters, they mostly have
> > >> similar schema definitions though vary in terms of key length, #
> > columns,
> > >> etc. This is the only cluster and only table we've seen leak so far.
> > It's
> > >> probably the table with the biggest regions which we MR against,
> though
> > >> it's hard to verify that (anyone in engineering can run such a job).
> > >>
> > >> dfs.client.read.shortcircuit.streams.cache.size = 256
> > >>
> > >> Our typical FD amount is around 3000. When this hadoop job runs, that
> > >> can climb up to our limit of over 30k if we don't act -- it is a
> gradual
> > >> build up over the course of a couple hours. When we move the regions
> > off or
> > >> kill the job, the FDs will gradually go back down at roughly the same
> > pace.
> > >> It forms a graph in the shape of a pyramid.
> > >>
> > >> We don't use CM, we use mostly the default *-site.xml. We haven't
> > >> overridden anything related to this. The configs between CDH5.3.8 and
> > 5.7.0
> > >> are identical for us.
> > >>
> > >> On Mon, May 23, 2016 at 2:03 PM Stack <st...@duboce.net> wrote:
> > >>
> > >>> On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
> > >>> bbeaudreault@hubspot.com
> > >>> > wrote:
> > >>>
> > >>> > Hey everyone,
> > >>> >
> > >>> > We are noticing a file descriptor leak that is only affecting nodes
> > in
> > >>> our
> > >>> > cluster running 5.7.0, not those still running 5.3.8.
> > >>>
> > >>>
> > >>> Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs
> > >>> hbase-0.98.6+hadoop-2.5.0.
> > >>>
> > >>>
> > >>> > I ran an lsof against
> > >>> > an affected regionserver, and noticed that there were 10k+ unix
> > sockets
> > >>> > that are just called "socket", as well as another 10k+ of the form
> > >>> >
> > >>>
> > "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>".
> The
> > >>> > 2 seem related based on how closely the counts match.
> > >>> >
> > >>> > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0
> > (we
> > >>> > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> > >>> > experience this issue. The 5.7.0 nodes *do. *We are holding off
> > >>> upgrading
> > >>> > more regionservers until we can figure this out. I'm not sure if
> any
> > >>> > intermediate versions between the 2 have the issue.
> > >>> >
> > >>> > We traced the root cause to a hadoop job running against a basic
> > table:
> > >>> >
> > >>> > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> > >>> > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> > >>> > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> > >>> > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
> > >>> >
> > >>> > This is very similar to all of our other tables (we have many).
> > >>>
> > >>>
> > >>> You are doing MR against some of these also? They have different
> > schemas?
> > >>> No leaks here?
> > >>>
> > >>>
> > >>>
> > >>> > However,
> > >>> > it's regions are getting up there in size, 40+gb per region,
> > >>> compressed.
> > >>> > This has not been an issue for us previously.
> > >>> >
> > >>> > The hadoop job is a simple TableMapper job with no special
> > parameters,
> > >>> > though we haven't updated our client yet to the latest (will do
> that
> > >>> once
> > >>> > we finish the server side). The hadoop job runs on a separate
> hadoop
> > >>> > cluster, remotely accessing the HBase cluster. It does not do any
> > other
> > >>> > reads or writes, outside of the TableMapper scans.
> > >>> >
> > >>> > Moving the regions off of an affected server, or killing the hadoop
> > >>> job,
> > >>> > causes the file descriptors to gradually go back down to normal.
> > >>> >
> > >>> >
> > >>> Any ideas?
> > >>> >
> > >>> >
> > >>> Is it just the FD cache running 'normally'? 10k seems like a lot
> > though.
> > >>> 256 seems to be the default in hdfs but maybe it is different in CM
> or
> > in
> > >>> hbase?
> > >>>
> > >>> What is your dfs.client.read.shortcircuit.streams.cache.size set to?
> > >>> St.Ack
> > >>>
> > >>>
> > >>>
> > >>> > Thanks,
> > >>> >
> > >>> > Bryan
> > >>> >
> > >>>
> > >>
> >
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Stack <st...@duboce.net>.
How hard to change the below if only temporarily (Trying to get a datapoint
or two to act on; the short circuit code hasn't changed that we know of...
perhaps the scan chunking facility in 1.1 has some side effect we've not
noticed up to this).
If you up the caching to be bigger does it lower the rate of FD leak
creation?
If you cache the blocks, assuming it does not blow the cache for others,
does that make a difference.
Hang on... will be back in a sec... just sending this in meantime...
St.Ack
On Mon, May 23, 2016 at 12:20 PM, Bryan Beaudreault <
bbeaudreault@hubspot.com> wrote:
> For reference, the Scan backing the job is pretty basic:
>
> Scan scan = new Scan();
> scan.setCaching(500); // probably too small for the datasize we're dealing
> with
> scan.setCacheBlocks(false);
> scan.setScanMetricsEnabled(true);
> scan.setMaxVersions(1);
> scan.setTimeRange(startTime, stopTime);
>
> Otherwise it is using the out-of-the-box TableInputFormat.
>
>
>
> On Mon, May 23, 2016 at 3:13 PM Bryan Beaudreault <
> bbeaudreault@hubspot.com>
> wrote:
>
> > I've forced the issue to happen again. netstat takes a while to run on
> > this host while it's happening, but I do not see an abnormal amount of
> > CLOSE_WAIT (compared to other hosts).
> >
> > I forced more than usual number of regions for the affected table onto
> the
> > host to speed up the process. File Descriptors are now growing quite
> > rapidly, about 8-10 per second.
> >
> > This is what lsof looks like, multiplied by a couple thousand:
> >
> > COMMAND PID USER FD TYPE DEVICE SIZE/OFF
> > NODE NAME
> > java 23180 hbase DEL REG 0,16 3848784656
> >
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1702253823
> > java 23180 hbase DEL REG 0,16 3847643924
> >
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1614925966
> > java 23180 hbase DEL REG 0,16 3847614191
> >
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_888427288
> >
> > The only thing that varies is the last int on the end.
> >
> > > Anything about the job itself that is holding open references or
> > throwing away files w/o closing them?
> >
> > The MR job does a TableMapper directly against HBase, which as far as I
> > know uses the HBase RPC and does not hit HDFS directly at all. Is it
> > possible that a long running scan (one with many, many next() calls)
> could
> > keep some references to HDFS open for the duration of the overall scan?
> >
> >
> > On Mon, May 23, 2016 at 2:19 PM Bryan Beaudreault <
> > bbeaudreault@hubspot.com> wrote:
> >
> >> We run MR against many tables in all of our clusters, they mostly have
> >> similar schema definitions though vary in terms of key length, #
> columns,
> >> etc. This is the only cluster and only table we've seen leak so far.
> It's
> >> probably the table with the biggest regions which we MR against, though
> >> it's hard to verify that (anyone in engineering can run such a job).
> >>
> >> dfs.client.read.shortcircuit.streams.cache.size = 256
> >>
> >> Our typical FD amount is around 3000. When this hadoop job runs, that
> >> can climb up to our limit of over 30k if we don't act -- it is a gradual
> >> build up over the course of a couple hours. When we move the regions
> off or
> >> kill the job, the FDs will gradually go back down at roughly the same
> pace.
> >> It forms a graph in the shape of a pyramid.
> >>
> >> We don't use CM, we use mostly the default *-site.xml. We haven't
> >> overridden anything related to this. The configs between CDH5.3.8 and
> 5.7.0
> >> are identical for us.
> >>
> >> On Mon, May 23, 2016 at 2:03 PM Stack <st...@duboce.net> wrote:
> >>
> >>> On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
> >>> bbeaudreault@hubspot.com
> >>> > wrote:
> >>>
> >>> > Hey everyone,
> >>> >
> >>> > We are noticing a file descriptor leak that is only affecting nodes
> in
> >>> our
> >>> > cluster running 5.7.0, not those still running 5.3.8.
> >>>
> >>>
> >>> Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs
> >>> hbase-0.98.6+hadoop-2.5.0.
> >>>
> >>>
> >>> > I ran an lsof against
> >>> > an affected regionserver, and noticed that there were 10k+ unix
> sockets
> >>> > that are just called "socket", as well as another 10k+ of the form
> >>> >
> >>>
> "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>". The
> >>> > 2 seem related based on how closely the counts match.
> >>> >
> >>> > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0
> (we
> >>> > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> >>> > experience this issue. The 5.7.0 nodes *do. *We are holding off
> >>> upgrading
> >>> > more regionservers until we can figure this out. I'm not sure if any
> >>> > intermediate versions between the 2 have the issue.
> >>> >
> >>> > We traced the root cause to a hadoop job running against a basic
> table:
> >>> >
> >>> > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> >>> > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> >>> > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> >>> > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
> >>> >
> >>> > This is very similar to all of our other tables (we have many).
> >>>
> >>>
> >>> You are doing MR against some of these also? They have different
> schemas?
> >>> No leaks here?
> >>>
> >>>
> >>>
> >>> > However,
> >>> > it's regions are getting up there in size, 40+gb per region,
> >>> compressed.
> >>> > This has not been an issue for us previously.
> >>> >
> >>> > The hadoop job is a simple TableMapper job with no special
> parameters,
> >>> > though we haven't updated our client yet to the latest (will do that
> >>> once
> >>> > we finish the server side). The hadoop job runs on a separate hadoop
> >>> > cluster, remotely accessing the HBase cluster. It does not do any
> other
> >>> > reads or writes, outside of the TableMapper scans.
> >>> >
> >>> > Moving the regions off of an affected server, or killing the hadoop
> >>> job,
> >>> > causes the file descriptors to gradually go back down to normal.
> >>> >
> >>> >
> >>> Any ideas?
> >>> >
> >>> >
> >>> Is it just the FD cache running 'normally'? 10k seems like a lot
> though.
> >>> 256 seems to be the default in hdfs but maybe it is different in CM or
> in
> >>> hbase?
> >>>
> >>> What is your dfs.client.read.shortcircuit.streams.cache.size set to?
> >>> St.Ack
> >>>
> >>>
> >>>
> >>> > Thanks,
> >>> >
> >>> > Bryan
> >>> >
> >>>
> >>
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Bryan Beaudreault <bb...@hubspot.com>.
For reference, the Scan backing the job is pretty basic:
Scan scan = new Scan();
scan.setCaching(500); // probably too small for the datasize we're dealing
with
scan.setCacheBlocks(false);
scan.setScanMetricsEnabled(true);
scan.setMaxVersions(1);
scan.setTimeRange(startTime, stopTime);
Otherwise it is using the out-of-the-box TableInputFormat.
On Mon, May 23, 2016 at 3:13 PM Bryan Beaudreault <bb...@hubspot.com>
wrote:
> I've forced the issue to happen again. netstat takes a while to run on
> this host while it's happening, but I do not see an abnormal amount of
> CLOSE_WAIT (compared to other hosts).
>
> I forced more than usual number of regions for the affected table onto the
> host to speed up the process. File Descriptors are now growing quite
> rapidly, about 8-10 per second.
>
> This is what lsof looks like, multiplied by a couple thousand:
>
> COMMAND PID USER FD TYPE DEVICE SIZE/OFF
> NODE NAME
> java 23180 hbase DEL REG 0,16 3848784656
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1702253823
> java 23180 hbase DEL REG 0,16 3847643924
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1614925966
> java 23180 hbase DEL REG 0,16 3847614191
> /dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_888427288
>
> The only thing that varies is the last int on the end.
>
> > Anything about the job itself that is holding open references or
> throwing away files w/o closing them?
>
> The MR job does a TableMapper directly against HBase, which as far as I
> know uses the HBase RPC and does not hit HDFS directly at all. Is it
> possible that a long running scan (one with many, many next() calls) could
> keep some references to HDFS open for the duration of the overall scan?
>
>
> On Mon, May 23, 2016 at 2:19 PM Bryan Beaudreault <
> bbeaudreault@hubspot.com> wrote:
>
>> We run MR against many tables in all of our clusters, they mostly have
>> similar schema definitions though vary in terms of key length, # columns,
>> etc. This is the only cluster and only table we've seen leak so far. It's
>> probably the table with the biggest regions which we MR against, though
>> it's hard to verify that (anyone in engineering can run such a job).
>>
>> dfs.client.read.shortcircuit.streams.cache.size = 256
>>
>> Our typical FD amount is around 3000. When this hadoop job runs, that
>> can climb up to our limit of over 30k if we don't act -- it is a gradual
>> build up over the course of a couple hours. When we move the regions off or
>> kill the job, the FDs will gradually go back down at roughly the same pace.
>> It forms a graph in the shape of a pyramid.
>>
>> We don't use CM, we use mostly the default *-site.xml. We haven't
>> overridden anything related to this. The configs between CDH5.3.8 and 5.7.0
>> are identical for us.
>>
>> On Mon, May 23, 2016 at 2:03 PM Stack <st...@duboce.net> wrote:
>>
>>> On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
>>> bbeaudreault@hubspot.com
>>> > wrote:
>>>
>>> > Hey everyone,
>>> >
>>> > We are noticing a file descriptor leak that is only affecting nodes in
>>> our
>>> > cluster running 5.7.0, not those still running 5.3.8.
>>>
>>>
>>> Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs
>>> hbase-0.98.6+hadoop-2.5.0.
>>>
>>>
>>> > I ran an lsof against
>>> > an affected regionserver, and noticed that there were 10k+ unix sockets
>>> > that are just called "socket", as well as another 10k+ of the form
>>> >
>>> "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>". The
>>> > 2 seem related based on how closely the counts match.
>>> >
>>> > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
>>> > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
>>> > experience this issue. The 5.7.0 nodes *do. *We are holding off
>>> upgrading
>>> > more regionservers until we can figure this out. I'm not sure if any
>>> > intermediate versions between the 2 have the issue.
>>> >
>>> > We traced the root cause to a hadoop job running against a basic table:
>>> >
>>> > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
>>> > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
>>> > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
>>> > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
>>> >
>>> > This is very similar to all of our other tables (we have many).
>>>
>>>
>>> You are doing MR against some of these also? They have different schemas?
>>> No leaks here?
>>>
>>>
>>>
>>> > However,
>>> > it's regions are getting up there in size, 40+gb per region,
>>> compressed.
>>> > This has not been an issue for us previously.
>>> >
>>> > The hadoop job is a simple TableMapper job with no special parameters,
>>> > though we haven't updated our client yet to the latest (will do that
>>> once
>>> > we finish the server side). The hadoop job runs on a separate hadoop
>>> > cluster, remotely accessing the HBase cluster. It does not do any other
>>> > reads or writes, outside of the TableMapper scans.
>>> >
>>> > Moving the regions off of an affected server, or killing the hadoop
>>> job,
>>> > causes the file descriptors to gradually go back down to normal.
>>> >
>>> >
>>> Any ideas?
>>> >
>>> >
>>> Is it just the FD cache running 'normally'? 10k seems like a lot though.
>>> 256 seems to be the default in hdfs but maybe it is different in CM or in
>>> hbase?
>>>
>>> What is your dfs.client.read.shortcircuit.streams.cache.size set to?
>>> St.Ack
>>>
>>>
>>>
>>> > Thanks,
>>> >
>>> > Bryan
>>> >
>>>
>>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Bryan Beaudreault <bb...@hubspot.com>.
I've forced the issue to happen again. netstat takes a while to run on this
host while it's happening, but I do not see an abnormal amount of
CLOSE_WAIT (compared to other hosts).
I forced more than usual number of regions for the affected table onto the
host to speed up the process. File Descriptors are now growing quite
rapidly, about 8-10 per second.
This is what lsof looks like, multiplied by a couple thousand:
COMMAND PID USER FD TYPE DEVICE SIZE/OFF
NODE NAME
java 23180 hbase DEL REG 0,16 3848784656
/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1702253823
java 23180 hbase DEL REG 0,16 3847643924
/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_1614925966
java 23180 hbase DEL REG 0,16 3847614191
/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_377023711_1_888427288
The only thing that varies is the last int on the end.
> Anything about the job itself that is holding open references or throwing
away files w/o closing them?
The MR job does a TableMapper directly against HBase, which as far as I
know uses the HBase RPC and does not hit HDFS directly at all. Is it
possible that a long running scan (one with many, many next() calls) could
keep some references to HDFS open for the duration of the overall scan?
On Mon, May 23, 2016 at 2:19 PM Bryan Beaudreault <bb...@hubspot.com>
wrote:
> We run MR against many tables in all of our clusters, they mostly have
> similar schema definitions though vary in terms of key length, # columns,
> etc. This is the only cluster and only table we've seen leak so far. It's
> probably the table with the biggest regions which we MR against, though
> it's hard to verify that (anyone in engineering can run such a job).
>
> dfs.client.read.shortcircuit.streams.cache.size = 256
>
> Our typical FD amount is around 3000. When this hadoop job runs, that can
> climb up to our limit of over 30k if we don't act -- it is a gradual build
> up over the course of a couple hours. When we move the regions off or kill
> the job, the FDs will gradually go back down at roughly the same pace. It
> forms a graph in the shape of a pyramid.
>
> We don't use CM, we use mostly the default *-site.xml. We haven't
> overridden anything related to this. The configs between CDH5.3.8 and 5.7.0
> are identical for us.
>
> On Mon, May 23, 2016 at 2:03 PM Stack <st...@duboce.net> wrote:
>
>> On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
>> bbeaudreault@hubspot.com
>> > wrote:
>>
>> > Hey everyone,
>> >
>> > We are noticing a file descriptor leak that is only affecting nodes in
>> our
>> > cluster running 5.7.0, not those still running 5.3.8.
>>
>>
>> Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs
>> hbase-0.98.6+hadoop-2.5.0.
>>
>>
>> > I ran an lsof against
>> > an affected regionserver, and noticed that there were 10k+ unix sockets
>> > that are just called "socket", as well as another 10k+ of the form
>> > "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>".
>> The
>> > 2 seem related based on how closely the counts match.
>> >
>> > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
>> > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
>> > experience this issue. The 5.7.0 nodes *do. *We are holding off
>> upgrading
>> > more regionservers until we can figure this out. I'm not sure if any
>> > intermediate versions between the 2 have the issue.
>> >
>> > We traced the root cause to a hadoop job running against a basic table:
>> >
>> > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
>> > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
>> > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
>> > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
>> >
>> > This is very similar to all of our other tables (we have many).
>>
>>
>> You are doing MR against some of these also? They have different schemas?
>> No leaks here?
>>
>>
>>
>> > However,
>> > it's regions are getting up there in size, 40+gb per region, compressed.
>> > This has not been an issue for us previously.
>> >
>> > The hadoop job is a simple TableMapper job with no special parameters,
>> > though we haven't updated our client yet to the latest (will do that
>> once
>> > we finish the server side). The hadoop job runs on a separate hadoop
>> > cluster, remotely accessing the HBase cluster. It does not do any other
>> > reads or writes, outside of the TableMapper scans.
>> >
>> > Moving the regions off of an affected server, or killing the hadoop job,
>> > causes the file descriptors to gradually go back down to normal.
>> >
>> >
>> Any ideas?
>> >
>> >
>> Is it just the FD cache running 'normally'? 10k seems like a lot though.
>> 256 seems to be the default in hdfs but maybe it is different in CM or in
>> hbase?
>>
>> What is your dfs.client.read.shortcircuit.streams.cache.size set to?
>> St.Ack
>>
>>
>>
>> > Thanks,
>> >
>> > Bryan
>> >
>>
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Bryan Beaudreault <bb...@hubspot.com>.
We run MR against many tables in all of our clusters, they mostly have
similar schema definitions though vary in terms of key length, # columns,
etc. This is the only cluster and only table we've seen leak so far. It's
probably the table with the biggest regions which we MR against, though
it's hard to verify that (anyone in engineering can run such a job).
dfs.client.read.shortcircuit.streams.cache.size = 256
Our typical FD amount is around 3000. When this hadoop job runs, that can
climb up to our limit of over 30k if we don't act -- it is a gradual build
up over the course of a couple hours. When we move the regions off or kill
the job, the FDs will gradually go back down at roughly the same pace. It
forms a graph in the shape of a pyramid.
We don't use CM, we use mostly the default *-site.xml. We haven't
overridden anything related to this. The configs between CDH5.3.8 and 5.7.0
are identical for us.
On Mon, May 23, 2016 at 2:03 PM Stack <st...@duboce.net> wrote:
> On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
> bbeaudreault@hubspot.com
> > wrote:
>
> > Hey everyone,
> >
> > We are noticing a file descriptor leak that is only affecting nodes in
> our
> > cluster running 5.7.0, not those still running 5.3.8.
>
>
> Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs hbase-0.98.6+hadoop-2.5.0.
>
>
> > I ran an lsof against
> > an affected regionserver, and noticed that there were 10k+ unix sockets
> > that are just called "socket", as well as another 10k+ of the form
> > "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>".
> The
> > 2 seem related based on how closely the counts match.
> >
> > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
> > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> > experience this issue. The 5.7.0 nodes *do. *We are holding off upgrading
> > more regionservers until we can figure this out. I'm not sure if any
> > intermediate versions between the 2 have the issue.
> >
> > We traced the root cause to a hadoop job running against a basic table:
> >
> > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
> >
> > This is very similar to all of our other tables (we have many).
>
>
> You are doing MR against some of these also? They have different schemas?
> No leaks here?
>
>
>
> > However,
> > it's regions are getting up there in size, 40+gb per region, compressed.
> > This has not been an issue for us previously.
> >
> > The hadoop job is a simple TableMapper job with no special parameters,
> > though we haven't updated our client yet to the latest (will do that once
> > we finish the server side). The hadoop job runs on a separate hadoop
> > cluster, remotely accessing the HBase cluster. It does not do any other
> > reads or writes, outside of the TableMapper scans.
> >
> > Moving the regions off of an affected server, or killing the hadoop job,
> > causes the file descriptors to gradually go back down to normal.
> >
> >
> Any ideas?
> >
> >
> Is it just the FD cache running 'normally'? 10k seems like a lot though.
> 256 seems to be the default in hdfs but maybe it is different in CM or in
> hbase?
>
> What is your dfs.client.read.shortcircuit.streams.cache.size set to?
> St.Ack
>
>
>
> > Thanks,
> >
> > Bryan
> >
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Stack <st...@duboce.net>.
On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <bbeaudreault@hubspot.com
> wrote:
> Hey everyone,
>
> We are noticing a file descriptor leak that is only affecting nodes in our
> cluster running 5.7.0, not those still running 5.3.8.
Translation: roughly hbase-1.2.0+hadoop-2.6.0 vs hbase-0.98.6+hadoop-2.5.0.
> I ran an lsof against
> an affected regionserver, and noticed that there were 10k+ unix sockets
> that are just called "socket", as well as another 10k+ of the form
> "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>". The
> 2 seem related based on how closely the counts match.
>
> We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
> handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> experience this issue. The 5.7.0 nodes *do. *We are holding off upgrading
> more regionservers until we can figure this out. I'm not sure if any
> intermediate versions between the 2 have the issue.
>
> We traced the root cause to a hadoop job running against a basic table:
>
> 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
>
> This is very similar to all of our other tables (we have many).
You are doing MR against some of these also? They have different schemas?
No leaks here?
> However,
> it's regions are getting up there in size, 40+gb per region, compressed.
> This has not been an issue for us previously.
>
> The hadoop job is a simple TableMapper job with no special parameters,
> though we haven't updated our client yet to the latest (will do that once
> we finish the server side). The hadoop job runs on a separate hadoop
> cluster, remotely accessing the HBase cluster. It does not do any other
> reads or writes, outside of the TableMapper scans.
>
> Moving the regions off of an affected server, or killing the hadoop job,
> causes the file descriptors to gradually go back down to normal.
>
>
Any ideas?
>
>
Is it just the FD cache running 'normally'? 10k seems like a lot though.
256 seems to be the default in hdfs but maybe it is different in CM or in
hbase?
What is your dfs.client.read.shortcircuit.streams.cache.size set to?
St.Ack
> Thanks,
>
> Bryan
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Bryan Beaudreault <bb...@hubspot.com>.
Thanks Ted,
I was not familiar with that JIRA, though I have read it now. The next time
it happens I will run the test at the top: netstat -nap |grep CLOSE_WAIT
|grep 21592 |wc -l
However, from what I can tell in the JIRA this should affect almost all
versions of HBase above 0.94. The issue we are hitting does not appear to
affect 0.98/CDH5.3.8. We also never saw it when we were on 0.94. This seems
new in either 1.0+ or 1.2+.
On Mon, May 23, 2016 at 12:59 PM Ted Yu <yu...@gmail.com> wrote:
> Have you taken a look at HBASE-9393 ?
>
> On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <
> bbeaudreault@hubspot.com
> > wrote:
>
> > Hey everyone,
> >
> > We are noticing a file descriptor leak that is only affecting nodes in
> our
> > cluster running 5.7.0, not those still running 5.3.8. I ran an lsof
> against
> > an affected regionserver, and noticed that there were 10k+ unix sockets
> > that are just called "socket", as well as another 10k+ of the form
> > "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>".
> The
> > 2 seem related based on how closely the counts match.
> >
> > We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
> > handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> > experience this issue. The 5.7.0 nodes *do. *We are holding off upgrading
> > more regionservers until we can figure this out. I'm not sure if any
> > intermediate versions between the 2 have the issue.
> >
> > We traced the root cause to a hadoop job running against a basic table:
> >
> > 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> > MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> > BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> > {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
> >
> > This is very similar to all of our other tables (we have many). However,
> > it's regions are getting up there in size, 40+gb per region, compressed.
> > This has not been an issue for us previously.
> >
> > The hadoop job is a simple TableMapper job with no special parameters,
> > though we haven't updated our client yet to the latest (will do that once
> > we finish the server side). The hadoop job runs on a separate hadoop
> > cluster, remotely accessing the HBase cluster. It does not do any other
> > reads or writes, outside of the TableMapper scans.
> >
> > Moving the regions off of an affected server, or killing the hadoop job,
> > causes the file descriptors to gradually go back down to normal.
> >
> > Any ideas?
> >
> > Thanks,
> >
> > Bryan
> >
>
Re: File descriptor leak, possibly new in CDH5.7.0
Posted by Ted Yu <yu...@gmail.com>.
Have you taken a look at HBASE-9393 ?
On Mon, May 23, 2016 at 9:55 AM, Bryan Beaudreault <bbeaudreault@hubspot.com
> wrote:
> Hey everyone,
>
> We are noticing a file descriptor leak that is only affecting nodes in our
> cluster running 5.7.0, not those still running 5.3.8. I ran an lsof against
> an affected regionserver, and noticed that there were 10k+ unix sockets
> that are just called "socket", as well as another 10k+ of the form
> "/dev/shm/HadoopShortCircuitShm_DFSClient_NONMAPREDUCE_-<int>_1_<int>". The
> 2 seem related based on how closely the counts match.
>
> We are in the middle of a rolling upgrade from CDH5.3.8 to CDH5.7.0 (we
> handled the namenode upgrade separately). The 5.3.8 nodes *do not*
> experience this issue. The 5.7.0 nodes *do. *We are holding off upgrading
> more regionservers until we can figure this out. I'm not sure if any
> intermediate versions between the 2 have the issue.
>
> We traced the root cause to a hadoop job running against a basic table:
>
> 'my-table-1', {TABLE_ATTRIBUTES => {MAX_FILESIZE => '107374182400',
> MEMSTORE_FLUSHSIZE => '67108864'}, {NAME => '0', VERSIONS => '50',
> BLOOMFILTER => 'NONE', COMPRESSION => 'LZO', METADATA =>
> {'COMPRESSION_COMPACT' => 'LZO', 'ENCODE_ON_DISK' => 'true'}}
>
> This is very similar to all of our other tables (we have many). However,
> it's regions are getting up there in size, 40+gb per region, compressed.
> This has not been an issue for us previously.
>
> The hadoop job is a simple TableMapper job with no special parameters,
> though we haven't updated our client yet to the latest (will do that once
> we finish the server side). The hadoop job runs on a separate hadoop
> cluster, remotely accessing the HBase cluster. It does not do any other
> reads or writes, outside of the TableMapper scans.
>
> Moving the regions off of an affected server, or killing the hadoop job,
> causes the file descriptors to gradually go back down to normal.
>
> Any ideas?
>
> Thanks,
>
> Bryan
>