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From Kai Wang <dep...@gmail.com>
Subject Re: Timeout error in fetching million rows as results using clustering keys
Date Thu, 19 Mar 2015 12:57:25 GMT
With your reading path and data model, it doesn't matter how many nodes you
have. All data with the same image_caseid is physically located on one node
(Well, on RF nodes but only one of those will try to server your query).
You are not taking advantage of Cassandra by creating hot spots on both
reading and writing. The first step I would take is to use
image_caseid-Area as the partition key. This breaks the query to small
parallel ones on partitions on different nodes.

On Wed, Mar 18, 2015 at 6:12 AM, Mehak Mehta <memehta@cs.stonybrook.edu>
wrote:

> ya I have cluster total 10 nodes but I am just testing with one node
> currently.
> Total data for all nodes will exceed 5 billion rows. But I may have memory
> on other nodes.
>
> On Wed, Mar 18, 2015 at 6:06 AM, Ali Akhtar <ali.rac200@gmail.com> wrote:
>
>> 4g also seems small for the kind of load you are trying to handle
>> (billions of rows) etc.
>>
>> I would also try adding more nodes to the cluster.
>>
>> On Wed, Mar 18, 2015 at 2:53 PM, Ali Akhtar <ali.rac200@gmail.com> wrote:
>>
>>> Yeah, it may be that the process is being limited by swap. This page:
>>>
>>>
>>> https://gist.github.com/aliakhtar/3649e412787034156cbb#file-cassandra-install-sh-L42
>>>
>>> Lines 42 - 48 list a few settings that you could try out for increasing
>>> / reducing the memory limits (assuming you're on linux).
>>>
>>> Also, are you using an SSD? If so make sure the IO scheduler is noop or
>>> deadline .
>>>
>>> On Wed, Mar 18, 2015 at 2:48 PM, Mehak Mehta <memehta@cs.stonybrook.edu>
>>> wrote:
>>>
>>>> Currently Cassandra java process is taking 1% of cpu (total 8% is being
>>>> used) and 14.3% memory (out of total 4G memory).
>>>> As you can see there is not much load from other processes.
>>>>
>>>> Should I try changing default parameters of memory in Cassandra
>>>> settings.
>>>>
>>>> On Wed, Mar 18, 2015 at 5:33 AM, Ali Akhtar <ali.rac200@gmail.com>
>>>> wrote:
>>>>
>>>>> What's your memory / CPU usage at? And how much ram + cpu do you have
>>>>> on this server?
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Mar 18, 2015 at 2:31 PM, Mehak Mehta <
>>>>> memehta@cs.stonybrook.edu> wrote:
>>>>>
>>>>>> Currently there is only single node which I am calling directly with
>>>>>> around 150000 rows. Full data will be in around billions per node.
>>>>>> The code is working only for size 100/200. Also the consecutive
>>>>>> fetching is taking around 5-10 secs.
>>>>>>
>>>>>> I have a parallel script which is inserting the data while I am
>>>>>> reading it. When I stopped the script it worked for 500/1000 but
not more
>>>>>> than that.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Mar 18, 2015 at 5:08 AM, Ali Akhtar <ali.rac200@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>>  If even 500-1000 isn't working, then your cassandra node might
not
>>>>>>> be up.
>>>>>>>
>>>>>>> 1) Try running nodetool status from shell on your cassandra server,
>>>>>>> make sure the nodes are up.
>>>>>>>
>>>>>>> 2) Are you calling this on the same server where cassandra is
>>>>>>> running? Its trying to connect to localhost . If you're running
it on a
>>>>>>> different server, try passing in the direct ip of your cassandra
server.
>>>>>>>
>>>>>>> On Wed, Mar 18, 2015 at 2:05 PM, Mehak Mehta <
>>>>>>> memehta@cs.stonybrook.edu> wrote:
>>>>>>>
>>>>>>>> Data won't change much but queries will be different.
>>>>>>>> I am not working on the rendering tool myself so I don't
know much
>>>>>>>> details about it.
>>>>>>>>
>>>>>>>> Also as suggested by you I tried to fetch data in size of
500 or
>>>>>>>> 1000 with java driver auto pagination.
>>>>>>>> It fails when the number of records are high (around 100000)
with
>>>>>>>> following error:
>>>>>>>>
>>>>>>>> Exception in thread "main"
>>>>>>>> com.datastax.driver.core.exceptions.NoHostAvailableException:
All host(s)
>>>>>>>> tried for query failed (tried: localhost/127.0.0.1:9042
>>>>>>>> (com.datastax.driver.core.exceptions.DriverException: Timed
out waiting for
>>>>>>>> server response))
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, Mar 18, 2015 at 4:47 AM, Ali Akhtar <ali.rac200@gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> How often does the data change?
>>>>>>>>>
>>>>>>>>> I would still recommend a caching of some kind, but without
>>>>>>>>> knowing more details (how often the data is changing,
what you're doing
>>>>>>>>> with the 1m rows after getting them, etc) I can't recommend
a solution.
>>>>>>>>>
>>>>>>>>> I did see your other thread. I would also vote for elasticsearch
/
>>>>>>>>> solr , they are more suited for the kind of analytics
you seem to be doing.
>>>>>>>>> Cassandra is more for storing data, it isn't all that
great for complex
>>>>>>>>> queries / analytics.
>>>>>>>>>
>>>>>>>>> If you want to stick to cassandra, you might have better
luck if
>>>>>>>>> you made your range columns part of the primary key,
so something like
>>>>>>>>> PRIMARY KEY(caseId, x, y)
>>>>>>>>>
>>>>>>>>> On Wed, Mar 18, 2015 at 1:41 PM, Mehak Mehta <
>>>>>>>>> memehta@cs.stonybrook.edu> wrote:
>>>>>>>>>
>>>>>>>>>> The rendering tool renders a portion a very large
image. It may
>>>>>>>>>> fetch different data each time from billions of rows.
>>>>>>>>>> So I don't think I can cache such large results.
Since same
>>>>>>>>>> results will rarely fetched again.
>>>>>>>>>>
>>>>>>>>>> Also do you know how I can do 2d range queries using
Cassandra.
>>>>>>>>>> Some other users suggested me using Solr.
>>>>>>>>>> But is there any way I can achieve that without using
any other
>>>>>>>>>> technology.
>>>>>>>>>>
>>>>>>>>>> On Wed, Mar 18, 2015 at 4:33 AM, Ali Akhtar <ali.rac200@gmail.com
>>>>>>>>>> > wrote:
>>>>>>>>>>
>>>>>>>>>>> Sorry, meant to say "that way when you have to
render, you can
>>>>>>>>>>> just display the latest cache."
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Mar 18, 2015 at 1:30 PM, Ali Akhtar <
>>>>>>>>>>> ali.rac200@gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> I would probably do this in a background
thread and cache the
>>>>>>>>>>>> results, that way when you have to render,
you can just cache the latest
>>>>>>>>>>>> results.
>>>>>>>>>>>>
>>>>>>>>>>>> I don't know why Cassandra can't seem to
be able to fetch large
>>>>>>>>>>>> batch sizes, I've also run into these timeouts
but reducing the batch size
>>>>>>>>>>>> to 2k seemed to work for me.
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Mar 18, 2015 at 1:24 PM, Mehak Mehta
<
>>>>>>>>>>>> memehta@cs.stonybrook.edu> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> We have UI interface which needs this
data for rendering.
>>>>>>>>>>>>> So efficiency of pulling this data matters
a lot. It should be
>>>>>>>>>>>>> fetched within a minute.
>>>>>>>>>>>>> Is there a way to achieve such efficiency
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Mar 18, 2015 at 4:06 AM, Ali
Akhtar <
>>>>>>>>>>>>> ali.rac200@gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Perhaps just fetch them in batches
of 1000 or 2000? For 1m
>>>>>>>>>>>>>> rows, it seems like the difference
would only be a few minutes. Do you have
>>>>>>>>>>>>>> to do this all the time, or only
once in a while?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Wed, Mar 18, 2015 at 12:34 PM,
Mehak Mehta <
>>>>>>>>>>>>>> memehta@cs.stonybrook.edu> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> yes it works for 1000 but not
more than that.
>>>>>>>>>>>>>>> How can I fetch all rows using
this efficiently?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Wed, Mar 18, 2015 at 3:29
AM, Ali Akhtar <
>>>>>>>>>>>>>>> ali.rac200@gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Have you tried a smaller
fetch size, such as 5k - 2k ?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Wed, Mar 18, 2015 at 12:22
PM, Mehak Mehta <
>>>>>>>>>>>>>>>> memehta@cs.stonybrook.edu>
wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Jens,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I have tried with fetch
size of 10000 still its not giving
>>>>>>>>>>>>>>>>> any results.
>>>>>>>>>>>>>>>>> My expectations were
that Cassandra can handle a million
>>>>>>>>>>>>>>>>> rows easily.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Is there any mistake
in the way I am defining the keys or
>>>>>>>>>>>>>>>>> querying them.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>> Mehak
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Wed, Mar 18, 2015
at 3:02 AM, Jens Rantil <
>>>>>>>>>>>>>>>>> jens.rantil@tink.se>
wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Try setting fetchsize
before querying. Assuming you don't
>>>>>>>>>>>>>>>>>> set it too high,
and you don't have too many tombstones, that should do it.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>> Jens
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> –
>>>>>>>>>>>>>>>>>> Skickat från Mailbox
<https://www.dropbox.com/mailbox>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Wed, Mar 18, 2015
at 2:58 AM, Mehak Mehta <
>>>>>>>>>>>>>>>>>> memehta@cs.stonybrook.edu>
wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> I have requirement
to fetch million row as result of my
>>>>>>>>>>>>>>>>>>> query which is
giving timeout errors.
>>>>>>>>>>>>>>>>>>> I am fetching
results by selecting clustering columns,
>>>>>>>>>>>>>>>>>>> then why the
queries are taking so long. I can change the timeout settings
>>>>>>>>>>>>>>>>>>> but I need the
data to fetched faster as per my requirement.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> My table definition
is:
>>>>>>>>>>>>>>>>>>> *CREATE TABLE
images.results (uuid uuid,
>>>>>>>>>>>>>>>>>>> analysis_execution_id
varchar, analysis_execution_uuid uuid, x  double, y
>>>>>>>>>>>>>>>>>>> double, loc varchar,
w double, h double, normalized varchar, type varchar,
>>>>>>>>>>>>>>>>>>> filehost varchar,
filename varchar, image_uuid uuid, image_uri varchar,
>>>>>>>>>>>>>>>>>>> image_caseid
varchar, image_mpp_x double, image_mpp_y double, image_width
>>>>>>>>>>>>>>>>>>> double, image_height
double, objective double, cancer_type varchar,  Area
>>>>>>>>>>>>>>>>>>> float, submit_date
timestamp, points list<double>,  PRIMARY KEY
>>>>>>>>>>>>>>>>>>> ((image_caseid),Area,uuid));*
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Here each row
is uniquely identified on the basis of
>>>>>>>>>>>>>>>>>>> unique uuid.
But since my data is generally queried based upon *image_caseid
>>>>>>>>>>>>>>>>>>> *I have made
it partition key.
>>>>>>>>>>>>>>>>>>> I am currently
using Java Datastax api to fetch the
>>>>>>>>>>>>>>>>>>> results. But
the query is taking a lot of time resulting in timeout errors:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>  Exception in
thread "main"
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.exceptions.NoHostAvailableException:
All host(s)
>>>>>>>>>>>>>>>>>>> tried for query
failed (tried: localhost/127.0.0.1:9042
>>>>>>>>>>>>>>>>>>> (com.datastax.driver.core.exceptions.DriverException:
Timed out waiting for
>>>>>>>>>>>>>>>>>>> server response))
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.exceptions.NoHostAvailableException.copy(NoHostAvailableException.java:84)
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.DefaultResultSetFuture.extractCauseFromExecutionException(DefaultResultSetFuture.java:289)
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.DefaultResultSetFuture.getUninterruptibly(DefaultResultSetFuture.java:205)
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.AbstractSession.execute(AbstractSession.java:52)
>>>>>>>>>>>>>>>>>>>  at QueryDB.queryArea(TestQuery.java:59)
>>>>>>>>>>>>>>>>>>>  at TestQuery.main(TestQuery.java:35)
>>>>>>>>>>>>>>>>>>> Caused by:
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.exceptions.NoHostAvailableException:
All host(s)
>>>>>>>>>>>>>>>>>>> tried for query
failed (tried: localhost/127.0.0.1:9042
>>>>>>>>>>>>>>>>>>> (com.datastax.driver.core.exceptions.DriverException:
Timed out waiting for
>>>>>>>>>>>>>>>>>>> server response))
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.RequestHandler.sendRequest(RequestHandler.java:108)
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> com.datastax.driver.core.RequestHandler$1.run(RequestHandler.java:179)
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>>>>>>>>>>>>>>>>>>  at
>>>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>>>>>>>>>>>>>>>>>>  at java.lang.Thread.run(Thread.java:744)
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Also when I try
the same query on console even while
>>>>>>>>>>>>>>>>>>> using limit of
2000 rows:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> cqlsh:images>
select count(*) from results where
>>>>>>>>>>>>>>>>>>> image_caseid='TCGA-HN-A2NL-01Z-00-DX1'
and Area<100 and Area>20 limit 2000;
>>>>>>>>>>>>>>>>>>> errors={}, last_host=127.0.0.1
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks and Regards,
>>>>>>>>>>>>>>>>>>> Mehak
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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