Re: [Postgres-xc-general] tracing cause of datanode crash

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Forgot to mention  that the error is still the same "invalid string in
message".

-Sandeep

On Fri, Nov 15, 2013 at 8:27 PM, Sandeep Gupta <gup...@gm...>wrote:

> Hi Koichi,
>
>  We tried the  copy with the patch but it did not fix the problem for us.
> If you need any additional details then let me know.
>
> Best,
> -Sandeep
>
>
> On Fri, Nov 15, 2013 at 6:13 AM, Sandeep Gupta <gup...@gm...>wrote:
>
>> Hi Koichi,
>>
>>  Many thanks for sharing the patch. We would test this in our environment
>> and would report back on the result.
>>
>> Regarding the very high memory consumption, it is not the coordinator
>>  that sees the high memory usage.
>> The setup is following: We have one coordinator and 4 datanodes. All the
>> datanodes run on separate machine
>> then the coordinator.  It is the machine where the datanodes are running
>> that have 48GB memory usage.
>> The other caveat is that that "top" doesn't show that it is the datanodes
>> processes using the memory.
>>
>> In any case, the last run of copy even with the high usage went through
>> fine.
>>
>>
>> Best,
>> Sandeep
>>
>>
>>
>> On Fri, Nov 15, 2013 at 2:29 AM, Koichi Suzuki <koi...@gm...>wrote:
>>
>>> Yes, I've already found this kind of failure.   When disk write is
>>> quite slower than read, coordinator overshoots.  However, in this
>>> case, I thought we will see that palloc() overflows.   If each piece
>>> of COPY TO text data is less than 1GB, then each COPY TO succeeds.
>>> If the write is much slower than read,  each coordinator will allocate
>>> memory for each COPY TO cache going to datanodes, ending up with
>>> enormous amount of memory consumption and have a good chance to run
>>> OOM killer.    Your memory usage looks enormous.    Maybe you have
>>> many COPY TO instances each of which allocates too much memory.
>>>
>>> Attached patch fixes COPY TO.   Because we have a chance to have
>>> similar overshoots in COPY FROM, I'd like to write a patch to fix this
>>> too before committing.   This is for the current master but will work
>>> with 1.1.x (even with 1.0.x hopefully).
>>>
>>> The patch looks to be fine.   I asked to test it in such an
>>> environment and they reported the patch fixed their issue.
>>>
>>> I'm not sure but hope this works in your case.   May reduce memory
>>> consumption drastically.   Please let me know the result.
>>>
>>> I have to allocate some of my resource to fix the same issue in COPY
>>> FROM.    I have another request to fix this so if the patch works for
>>> you, I may be able to commit only COPY TO fix first.
>>>
>>> Regards;
>>> ---
>>> Koichi Suzuki
>>>
>>>
>>> 2013/11/15 Sandeep Gupta <gup...@gm...>:
>>> > Hi Koichi,
>>> >
>>> >  I am using the copy command over the text file to populate a table.
>>> >
>>> > Sorry for the confusion. I meant 628 -- 638 lines in the pqformat.c.
>>> > Let me explain this a bit more. I get  error in some of the datanode
>>> > logfiles
>>> > as "invalid string in message". The message is mentioned only in
>>> pqformat.c
>>> > at line 628. Although I am not able to trace back as to where  error
>>> may
>>> > have first ordered in the datanode that triggered this error.
>>> >
>>> > In order to debug this I started printing out the rows the coordinator
>>> is
>>> > sending to the datanode (in function DataNodeCopyIn). For some reason
>>> the
>>> > error invalid string in messge error has  not happened so far.  It
>>> seems
>>> > there is some issue with the flow control of message between
>>> coordinator and
>>> > datanode.
>>> > Hope this helps in narrowing down what is causing the problem in the
>>> first
>>> > place.
>>> >
>>> >
>>> > However, the new problem I see is that the memory usage goes very
>>> high. Of
>>> > the 48 GB almost all of the memory is getting used. Is this normal?
>>> > If not can you give suggestion as to how to keep the memory
>>>  consumption
>>> > low.
>>> >
>>> > -Sandeep
>>> >
>>> >
>>> >
>>> > On Thu, Nov 14, 2013 at 8:57 PM, Koichi Suzuki <koi...@gm...>
>>> > wrote:
>>> >>
>>> >> Could you let me know what "line 682 -- 637" means?
>>> >>
>>> >> Because any communication between coordinator and datanode is done
>>> >> using libpq, I don't think XC populates information using raw
>>> >> stringinfo.   In fact, from datanodes, coordinator is just a client
>>> >> except for supplying XID and snapshot.   However,  COPY TO uses
>>> >> send()/receive(), not through libpq, to send data to datanode.  In
>>> >> this case, if incoming data file contains NULL in the data, such data
>>> >> may be sent via send() to datanodes.   COPY TO assumes incoming data
>>> >> in a text format.   Do you think you have such situations?
>>> >>
>>> >> Analysis may take a bit but let me try.
>>> >>
>>> >> Regards;
>>> >> ---
>>> >> Koichi Suzuki
>>> >>
>>> >>
>>> >> 2013/11/15 Sandeep Gupta <gup...@gm...>:
>>> >> > Hi Koichi, Masataka,
>>> >> >
>>> >> >  Thanks for taking a look. I double checked both memory usage and
>>> the
>>> >> > dmesg
>>> >> > log. The kill is not happening due to the out of memory. The kernel
>>> >> > doesn't
>>> >> > show any processes being killed.
>>> >> >
>>> >> > My current suspicion is that something amiss is happening over the
>>> >> > network.
>>> >> > This happens consistently when performing copy over large datasets.
>>> Few
>>> >> > of
>>> >> > datanodes end up with "invalid string in message".
>>> >> > Going over the code in pqformat.c this happens because the invariant
>>> >> > "StringInfo is guaranteed to have a trailing null byte" is not valid
>>> >> > (line
>>> >> > 682 -- 637). I am not sure why this happens.
>>> >> >
>>> >> >
>>> >> > After this the datanodes do something illegal (probably buffer
>>> overflow
>>> >> > on
>>> >> > the port..just a guess) that the OS decides to issue a sigkill.  I
>>> am
>>> >> > also
>>> >> > not sure why the OS is not logging this killed operation.
>>> >> >
>>> >> >
>>> >> > Please let me know of  suggestions you may have regarding the
>>> "invalid
>>> >> > string in message". In particular, where in the code is StringInfo
>>> msg
>>> >> > is
>>> >> > getting populated i.e. which code reads the message over the
>>> network and
>>> >> > keeps it ready for the copy operation on the datanode. Any other
>>> >> > suggestion
>>> >> > would also be helpful to trace this bug.
>>> >> >
>>> >> > Best,
>>> >> > Sandeep
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> >
>>> >> > On Thu, Nov 14, 2013 at 10:25 AM, Masataka Saito <pg...@gm...>
>>> >> > wrote:
>>> >> >>
>>> >> >> Hi,
>>> >> >>
>>> >> >> I think I may be onto something.
>>> >> >>
>>> >> >> When the memory is exhausted, the Linux kernel kills process
>>> randomly
>>> >> >> by SIGKILL.
>>> >> >> The mechanism is called OOM(Out Of Memory) killer.
>>> >> >> OOM killer logs its activity to kernel mesage buffer.
>>> >> >>
>>> >> >> Could you check display message (dmesg) and memory resource?
>>> >> >>
>>> >> >> Regards.
>>> >> >>
>>> >> >> On Tue, Nov 12, 2013 at 3:55 AM, Sandeep Gupta
>>> >> >> <gup...@gm...>
>>> >> >> wrote:
>>> >> >> > Hi Koichi,
>>> >> >> >
>>> >> >> >    It is a bit of mystery  because it does not happen
>>> consistently.
>>> >> >> > Thanks
>>> >> >> > for the clarification though. It is indeed helpful.
>>> >> >> >
>>> >> >> > -Sandeep
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > On Mon, Nov 11, 2013 at 1:58 AM, 鈴木 幸市 <ko...@in...
>>> >
>>> >> >> > wrote:
>>> >> >> >>
>>> >> >> >> Someone is sending SIGKILL to coordinator/datanode backend
>>> >> >> >> processes.
>>> >> >> >> Although XC (originally PG) code has a handler for SIGKILL, I
>>> didn’t
>>> >> >> >> found
>>> >> >> >> any code in XC sending SIGKILL to other processes.   I’m afraid
>>> >> >> >> there
>>> >> >> >> could
>>> >> >> >> be another process sending SIGKILL to them.
>>> >> >> >>
>>> >> >> >> Best Regards;
>>> >> >> >> ---
>>> >> >> >> Koichi Suzuki
>>> >> >> >>
>>> >> >> >> 2013/11/09 2:54、Sandeep Gupta <gup...@gm...> のメール：
>>> >> >> >>
>>> >> >> >> > I am running single instance of postgres-xc with  several
>>> datanode
>>> >> >> >> > Each data node runs on its own machine.
>>> >> >> >> > After instantiating the cluster the database sits idle. I do
>>> not
>>> >> >> >> > perform
>>> >> >> >> > any create table or insert operations. However, after some
>>> time
>>> >> >> >> > all
>>> >> >> >> > the
>>> >> >> >> > datanode  automatically shuts down (log messages attached).
>>> >> >> >> >
>>> >> >> >> > Any pointers as to why this maybe happening would be very
>>> useful.
>>> >> >> >> >
>>> >> >> >> > -Sandeep
>>> >> >> >> >
>>> >> >> >> > The log files across all datanode contain various error
>>> messages.
>>> >> >> >> > These
>>> >> >> >> > include:
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > LOG:  statistics collector process (PID 23073) was terminated
>>> by
>>> >> >> >> > signal
>>> >> >> >> > 9: Killed
>>> >> >> >> > LOG:  WAL writer process (PID 23071) was terminated by signal
>>> 9:
>>> >> >> >> > Killed
>>> >> >> >> > LOG:  terminating any other active server processes
>>> >> >> >> > WARNING:  terminating connection because of crash of another
>>> >> >> >> > server
>>> >> >> >> > process
>>> >> >> >> > DETAIL:  The postmaster has commanded this server process to
>>> roll
>>> >> >> >> > back
>>> >> >> >> > the current transaction and exit, because another server
>>> process
>>> >> >> >> > exited
>>> >> >> >> > abnormally and possibly corrupted shared memory.
>>> >> >> >> > HINT:  In a moment you should be able to reconnect to the
>>> database
>>> >> >> >> > and
>>> >> >> >> > repeat your command.
>>> >> >> >> > LOG:  all server processes terminated; reinitializing
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > LOG:  checkpointer process (PID 21406) was terminated by
>>> signal 9:
>>> >> >> >> > Killed
>>> >> >> >> > LOG:  terminating any other active server processes
>>> >> >> >> > WARNING:  terminating connection because of crash of another
>>> >> >> >> > server
>>> >> >> >> > process
>>> >> >> >> > DETAIL:  The postmaster has commanded this server process to
>>> roll
>>> >> >> >> > back
>>> >> >> >> > the current transaction and exit, because another server
>>> process
>>> >> >> >> > exited
>>> >> >> >> > abnormally and possibly corrupted shared memory.
>>> >> >> >> > LOG:  statistics collector process (PID 28881) was terminated
>>> by
>>> >> >> >> > signal
>>> >> >> >> > 9: Killed
>>> >> >> >> > LOG:  autovacuum launcher process (PID 28880) was terminated
>>> by
>>> >> >> >> > signal
>>> >> >> >> > 9: Killed
>>> >> >> >> > LOG:  terminating any other active server processes
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
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