postgres-xc-general Mailing List for Postgres-XC

Thanks.   I'll be looking forward to your test result.   I talked with
Masataka and he was interested that no relevant messages were found in
dmsg.

Regards;
---
Koichi Suzuki


2013/11/19 Sandeep Gupta <gup...@gm...>:
> Hi Koichi,
>
>  Thanks for taking a look. I did some further debugging and I won't rule
> out the possibility of the the OS killing some postgres processes which
> leads to copy execution reaching in a inconsistent state.
> Will do some further tests to confirm this as well.
>
> -Sandeep
>
>
>
>
> On Mon, Nov 18, 2013 at 1:06 AM, Koichi Suzuki <koi...@gm...>
> wrote:
>>
>> This happens when the message is not null-terminated properly.   Most
>> case is a bug.   In this case, different from vanilla PostgreSQL, copy
>> data is involved in.    Please let me find a time to look into it.
>>
>> Regards;
>> ---
>> Koichi Suzuki
>>
>>
>> 2013/11/16 Sandeep Gupta <gup...@gm...>:
>> > 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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