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Posted to user@madlib.apache.org by Anthony Thomas <ah...@eng.ucsd.edu> on 2017/12/04 23:07:22 UTC
kmeanspp error on GPDB
Hi MADLib Users,
I'm running MADLib on Greenplum 5.1.0 under Ubuntu 16.04. If I try to run
the example for KMeanspp given here
<http://madlib.apache.org/docs/latest/group__grp__kmeans.html>, I get the
following error message:
NOTICE: Releasing segworker groups to finish aborting the transaction.
ERROR: could not connect to segment: initialization of segworker group
failed (cdbgang.c:236)
CONTEXT: PL/Python function "internal_compute_kmeanspp_seeding"
SQL statement "SELECT ( SELECT madlib.internal_compute_kmeanspp_seeding(
'_madlib_kmeanspp_args', '_madlib_kmeanspp_state', textin(regclassout( $1
)), $2 ) )"
PL/pgSQL function "kmeanspp_seeding" line 79 at assignment
SQL statement "SELECT madlib.kmeans( $1 , $2 , madlib.kmeanspp_seeding(
$1 , $2 , $3 , $4 , NULL, $5 ), $4 , $6 , $7 , $8 )"
PL/pgSQL function "kmeanspp" line 4 at assignment
I've tried running a few other built-in ML algorithms and they all seem to
work fine. The error message seems to suggest its a problem with Greenplum,
but some preliminary Googling has not yielded useful results. Has anyone
seen this error before or have any ideas about how to diagnose it?
Thanks,
Anthony
Re: kmeanspp error on GPDB
Posted by Rahul Iyer <ri...@apache.org>.
Thanks for getting back, Anthony. Hopefully the problem is resolved with
GCC 4.x.
The gist of the GCC issue is that there is a memory allocation/deallocation
issue in MADlib for specific C++ in-built types. These types are used in
elastic_net and others but not in the primitive modules. We'll get to
investigating and fixing it soon after the 1.13 release.
Best,
Rahul
On Tue, Dec 5, 2017 at 12:38 PM, Anthony Thomas <ah...@eng.ucsd.edu>
wrote:
> Hi Nikhil and Luis,
>
> Thanks for the follow up. Nikhil: to your questions about my environment:
>
> 1. yes - I downloaded the source tarball for 1.12 from
> http://apache.org/dyn/closer.cgi?filename=madlib/1.12/
> apache-madlib-1.12-src.tar.gz&action=download
> <http://apache.org/dyn/closer.cgi?filename=madlib/1.12/apache-madlib-1.12-src.tar.gz&action=download>
> 2. I compiled using GCC 5.4.0 so perhaps that's the source of the
> issue. I'll try recompiling with GCC < 5 and see if that fixes the problem.
> 3. When running madlib install-check I see the same error in the
> elastic_net test.
> 4. Thanks for the tip about CentOS - I'm using GPDB alongside several
> other tools that recommend/need Ubuntu and so if at all possible I'd like
> to try and get it to work on Ubuntu.
>
> Thanks for the tips - hopefully this is just the result of compiling using
> GCC 5+. It seems a little strange though that the primitive matrix/array
> ops seem to work fine as do some of the other built-in algorithms, but
> KMeans and Elastic Net seem to have trouble.
>
> Anthony
>
> On Tue, Dec 5, 2017 at 10:44 AM, Nikhil Kak <nk...@pivotal.io> wrote:
>
>> Hi Anthony,
>>
>> Thank you for reporting the issue. It does look like that the exception
>> is coming from greenplum.
>>
>> A few follow up questions:-
>> 1. Did you compile madlib from source? If yes, which branch?
>> 2. What version of gcc did you use to compile madlib? Please note that
>> madlib does not work with gcc5 and up.
>> 3. Did you run madlib install-check?
>> 4. As Luis mentioned, you may want to try using CentOS 6/7.
>>
>> Thanks,
>> Nikhil Kak
>>
>> On Mon, Dec 4, 2017 at 3:32 PM Luis Macedo <lm...@pivotal.io> wrote:
>>
>>> Yep... Greenplum had an issue with that job. Maybe you could also post
>>> on GPDB user list.
>>>
>>> Check greenplum.org for the instructions.
>>>
>>> Not sure about running on Ubuntu... Ubuntu support is new so you might
>>> want to try on CentOS if you can.
>>>
>>> Tks
>>>
>>> *Luis Macedo | Sr Platform Architect | **Pivotal Inc *
>>>
>>> *Call Me @ **+55 11 97616-6438 <+55%2011%2097616-6438>*
>>> *Take care of the customers and the rest takes care of itself*
>>> *---*
>>> *Pivotal POV Blog* <https://content.pivotal.io/blog>
>>>
>>> *Pivotal Mission: Help Developers Do What They Love
>>> <https://www.youtube.com/watch?v=xdw_9dADM-4&list=PLAdzTan_eSPQ1fuLSBhyB4eEZF7JQM0Mx>*
>>> *Big Data Problems? Go here!* <https://pivotal.io/pivotal-greenplum>
>>> *Latency Issues? No more! <https://pivotal.io/pivotal-gemfire>*
>>> <https://pivotal.io/pivotal-gemfire>
>>> ---
>>>
>>>
>>> 2017-12-04 15:07 GMT-08:00 Anthony Thomas <ah...@eng.ucsd.edu>:
>>>
>>>> Hi MADLib Users,
>>>>
>>>> I'm running MADLib on Greenplum 5.1.0 under Ubuntu 16.04. If I try to
>>>> run the example for KMeanspp given here
>>>> <http://madlib.apache.org/docs/latest/group__grp__kmeans.html>, I get
>>>> the following error message:
>>>>
>>>> NOTICE: Releasing segworker groups to finish aborting the transaction.
>>>> ERROR: could not connect to segment: initialization of segworker group
>>>> failed (cdbgang.c:236)
>>>> CONTEXT: PL/Python function "internal_compute_kmeanspp_seeding"
>>>> SQL statement "SELECT ( SELECT madlib.internal_compute_kmeanspp_seeding(
>>>> '_madlib_kmeanspp_args', '_madlib_kmeanspp_state', textin(regclassout( $1
>>>> )), $2 ) )"
>>>> PL/pgSQL function "kmeanspp_seeding" line 79 at assignment
>>>> SQL statement "SELECT madlib.kmeans( $1 , $2 ,
>>>> madlib.kmeanspp_seeding( $1 , $2 , $3 , $4 , NULL, $5 ), $4 , $6 ,
>>>> $7 , $8 )"
>>>> PL/pgSQL function "kmeanspp" line 4 at assignment
>>>>
>>>> I've tried running a few other built-in ML algorithms and they all seem
>>>> to work fine. The error message seems to suggest its a problem with
>>>> Greenplum, but some preliminary Googling has not yielded useful results. Has
>>>> anyone seen this error before or have any ideas about how to diagnose it?
>>>>
>>>> Thanks,
>>>>
>>>> Anthony
>>>>
>>>
>>>
>
Re: kmeanspp error on GPDB
Posted by Anthony Thomas <ah...@eng.ucsd.edu>.
Hi Nikhil and Luis,
Thanks for the follow up. Nikhil: to your questions about my environment:
1. yes - I downloaded the source tarball for 1.12 from
http://apache.org/dyn/closer.cgi?filename=madlib/1.12/apache-madlib-1.12-src.tar.gz&action=download
2. I compiled using GCC 5.4.0 so perhaps that's the source of the issue.
I'll try recompiling with GCC < 5 and see if that fixes the problem.
3. When running madlib install-check I see the same error in the
elastic_net test.
4. Thanks for the tip about CentOS - I'm using GPDB alongside several
other tools that recommend/need Ubuntu and so if at all possible I'd like
to try and get it to work on Ubuntu.
Thanks for the tips - hopefully this is just the result of compiling using
GCC 5+. It seems a little strange though that the primitive matrix/array
ops seem to work fine as do some of the other built-in algorithms, but
KMeans and Elastic Net seem to have trouble.
Anthony
On Tue, Dec 5, 2017 at 10:44 AM, Nikhil Kak <nk...@pivotal.io> wrote:
> Hi Anthony,
>
> Thank you for reporting the issue. It does look like that the exception is
> coming from greenplum.
>
> A few follow up questions:-
> 1. Did you compile madlib from source? If yes, which branch?
> 2. What version of gcc did you use to compile madlib? Please note that
> madlib does not work with gcc5 and up.
> 3. Did you run madlib install-check?
> 4. As Luis mentioned, you may want to try using CentOS 6/7.
>
> Thanks,
> Nikhil Kak
>
> On Mon, Dec 4, 2017 at 3:32 PM Luis Macedo <lm...@pivotal.io> wrote:
>
>> Yep... Greenplum had an issue with that job. Maybe you could also post on
>> GPDB user list.
>>
>> Check greenplum.org for the instructions.
>>
>> Not sure about running on Ubuntu... Ubuntu support is new so you might
>> want to try on CentOS if you can.
>>
>> Tks
>>
>> *Luis Macedo | Sr Platform Architect | **Pivotal Inc *
>>
>> *Call Me @ **+55 11 97616-6438 <+55%2011%2097616-6438>*
>> *Take care of the customers and the rest takes care of itself*
>> *---*
>> *Pivotal POV Blog* <https://content.pivotal.io/blog>
>>
>> *Pivotal Mission: Help Developers Do What They Love
>> <https://www.youtube.com/watch?v=xdw_9dADM-4&list=PLAdzTan_eSPQ1fuLSBhyB4eEZF7JQM0Mx>*
>> *Big Data Problems? Go here!* <https://pivotal.io/pivotal-greenplum>
>> *Latency Issues? No more! <https://pivotal.io/pivotal-gemfire>*
>> <https://pivotal.io/pivotal-gemfire>
>> ---
>>
>>
>> 2017-12-04 15:07 GMT-08:00 Anthony Thomas <ah...@eng.ucsd.edu>:
>>
>>> Hi MADLib Users,
>>>
>>> I'm running MADLib on Greenplum 5.1.0 under Ubuntu 16.04. If I try to
>>> run the example for KMeanspp given here
>>> <http://madlib.apache.org/docs/latest/group__grp__kmeans.html>, I get
>>> the following error message:
>>>
>>> NOTICE: Releasing segworker groups to finish aborting the transaction.
>>> ERROR: could not connect to segment: initialization of segworker group
>>> failed (cdbgang.c:236)
>>> CONTEXT: PL/Python function "internal_compute_kmeanspp_seeding"
>>> SQL statement "SELECT ( SELECT madlib.internal_compute_kmeanspp_seeding(
>>> '_madlib_kmeanspp_args', '_madlib_kmeanspp_state', textin(regclassout( $1
>>> )), $2 ) )"
>>> PL/pgSQL function "kmeanspp_seeding" line 79 at assignment
>>> SQL statement "SELECT madlib.kmeans( $1 , $2 ,
>>> madlib.kmeanspp_seeding( $1 , $2 , $3 , $4 , NULL, $5 ), $4 , $6 ,
>>> $7 , $8 )"
>>> PL/pgSQL function "kmeanspp" line 4 at assignment
>>>
>>> I've tried running a few other built-in ML algorithms and they all seem
>>> to work fine. The error message seems to suggest its a problem with
>>> Greenplum, but some preliminary Googling has not yielded useful results. Has
>>> anyone seen this error before or have any ideas about how to diagnose it?
>>>
>>> Thanks,
>>>
>>> Anthony
>>>
>>
>>
Re: kmeanspp error on GPDB
Posted by Nikhil Kak <nk...@pivotal.io>.
Hi Anthony,
Thank you for reporting the issue. It does look like that the exception is
coming from greenplum.
A few follow up questions:-
1. Did you compile madlib from source? If yes, which branch?
2. What version of gcc did you use to compile madlib? Please note that
madlib does not work with gcc5 and up.
3. Did you run madlib install-check?
4. As Luis mentioned, you may want to try using CentOS 6/7.
Thanks,
Nikhil Kak
On Mon, Dec 4, 2017 at 3:32 PM Luis Macedo <lm...@pivotal.io> wrote:
> Yep... Greenplum had an issue with that job. Maybe you could also post on
> GPDB user list.
>
> Check greenplum.org for the instructions.
>
> Not sure about running on Ubuntu... Ubuntu support is new so you might
> want to try on CentOS if you can.
>
> Tks
>
> *Luis Macedo | Sr Platform Architect | **Pivotal Inc *
>
> *Call Me @ **+55 11 97616-6438 <+55%2011%2097616-6438>*
> *Take care of the customers and the rest takes care of itself*
> *---*
> *Pivotal POV Blog* <https://content.pivotal.io/blog>
>
> *Pivotal Mission: Help Developers Do What They Love
> <https://www.youtube.com/watch?v=xdw_9dADM-4&list=PLAdzTan_eSPQ1fuLSBhyB4eEZF7JQM0Mx>*
> *Big Data Problems? Go here!* <https://pivotal.io/pivotal-greenplum>
> *Latency Issues? No more! <https://pivotal.io/pivotal-gemfire>*
> <https://pivotal.io/pivotal-gemfire>
> ---
>
>
> 2017-12-04 15:07 GMT-08:00 Anthony Thomas <ah...@eng.ucsd.edu>:
>
>> Hi MADLib Users,
>>
>> I'm running MADLib on Greenplum 5.1.0 under Ubuntu 16.04. If I try to run
>> the example for KMeanspp given here
>> <http://madlib.apache.org/docs/latest/group__grp__kmeans.html>, I get
>> the following error message:
>>
>> NOTICE: Releasing segworker groups to finish aborting the transaction.
>> ERROR: could not connect to segment: initialization of segworker group
>> failed (cdbgang.c:236)
>> CONTEXT: PL/Python function "internal_compute_kmeanspp_seeding"
>> SQL statement "SELECT ( SELECT madlib.internal_compute_kmeanspp_seeding(
>> '_madlib_kmeanspp_args', '_madlib_kmeanspp_state', textin(regclassout( $1
>> )), $2 ) )"
>> PL/pgSQL function "kmeanspp_seeding" line 79 at assignment
>> SQL statement "SELECT madlib.kmeans( $1 , $2 ,
>> madlib.kmeanspp_seeding( $1 , $2 , $3 , $4 , NULL, $5 ), $4 , $6 ,
>> $7 , $8 )"
>> PL/pgSQL function "kmeanspp" line 4 at assignment
>>
>> I've tried running a few other built-in ML algorithms and they all seem
>> to work fine. The error message seems to suggest its a problem with
>> Greenplum, but some preliminary Googling has not yielded useful results. Has
>> anyone seen this error before or have any ideas about how to diagnose it?
>>
>> Thanks,
>>
>> Anthony
>>
>
>
Re: kmeanspp error on GPDB
Posted by Luis Macedo <lm...@pivotal.io>.
Yep... Greenplum had an issue with that job. Maybe you could also post on
GPDB user list.
Check greenplum.org for the instructions.
Not sure about running on Ubuntu... Ubuntu support is new so you might want
to try on CentOS if you can.
Tks
*Luis Macedo | Sr Platform Architect | **Pivotal Inc *
*Call Me @ **+55 11 97616-6438*
*Take care of the customers and the rest takes care of itself*
*---*
*Pivotal POV Blog* <https://content.pivotal.io/blog>
*Pivotal Mission: Help Developers Do What They Love
<https://www.youtube.com/watch?v=xdw_9dADM-4&list=PLAdzTan_eSPQ1fuLSBhyB4eEZF7JQM0Mx>*
*Big Data Problems? Go here!* <https://pivotal.io/pivotal-greenplum>
*Latency Issues? No more! <https://pivotal.io/pivotal-gemfire>*
<https://pivotal.io/pivotal-gemfire>
---
2017-12-04 15:07 GMT-08:00 Anthony Thomas <ah...@eng.ucsd.edu>:
> Hi MADLib Users,
>
> I'm running MADLib on Greenplum 5.1.0 under Ubuntu 16.04. If I try to run
> the example for KMeanspp given here
> <http://madlib.apache.org/docs/latest/group__grp__kmeans.html>, I get the
> following error message:
>
> NOTICE: Releasing segworker groups to finish aborting the transaction.
> ERROR: could not connect to segment: initialization of segworker group
> failed (cdbgang.c:236)
> CONTEXT: PL/Python function "internal_compute_kmeanspp_seeding"
> SQL statement "SELECT ( SELECT madlib.internal_compute_kmeanspp_seeding(
> '_madlib_kmeanspp_args', '_madlib_kmeanspp_state', textin(regclassout( $1
> )), $2 ) )"
> PL/pgSQL function "kmeanspp_seeding" line 79 at assignment
> SQL statement "SELECT madlib.kmeans( $1 , $2 , madlib.kmeanspp_seeding(
> $1 , $2 , $3 , $4 , NULL, $5 ), $4 , $6 , $7 , $8 )"
> PL/pgSQL function "kmeanspp" line 4 at assignment
>
> I've tried running a few other built-in ML algorithms and they all seem to
> work fine. The error message seems to suggest its a problem with Greenplum,
> but some preliminary Googling has not yielded useful results. Has anyone
> seen this error before or have any ideas about how to diagnose it?
>
> Thanks,
>
> Anthony
>