[Gmod-tripal-devel] Problem with dropping chado schema during New chado installation

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[Gmod-tripal-devel] Problem with dropping chado schema during New chado installation

Michael Dondrup
Hi Stephen,

I have now narrowed down my second issue which has possibly nothing to do with the update.

I am trying to install a new chado schema into a database which already contains chado via:
"New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)"

which yields a job named Install Chado v1.2. This job completes, but the log shows a lot of errors and the cause
right in the beginning:

Calling: tripal_core_install_chado(Install Chado v1.2, 123)
Dropping existing 'chado' schema
pg_query(): Query failed: ERROR:  out of shared memory               ESC[1;33;40mESC[1m[warning]ESC[0m
HINT:  You might need to increase max_locks_per_transaction.
database.pgsql.inc:138
ERROR:  out of shared memory                                         ESC[1;33;40mESC[1m[warning]ESC[0m
HINT:  You might need to increase max_locks_per_transaction.
query: drop schema chado cascade database.pgsql.inc:159
Dropping existing 'genetic_code' schema
Dropping existing 'so' schema
Dropping existing 'frange' schema
Creating 'chado' schema
pg_query(): Query failed: ERROR:  schema "chado" already exists      ESC[1;33;40mESC[1m[warning]ESC[0m
database.pgsql.inc:138
[more errors because drop failed….]

Thus, dropping the chado schema failed, while other schemata can be dropped.
If I understand [1] correctly, this is because max_locks_per_transaction is set to the default (64)
and chado has more than 64 tables that need to be locked before dropping. I hope there is
a way around without having to reconfigure the db server, because I don't have access to that myself.

PostgreSQL server version is 8.4.13

Cheers
Michael




[1] http://www.databasesoup.com/2012/06/postgresqlconf-maxlockspertransaction.html
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Re: [Gmod-tripal-devel] Problem with dropping chado schema during New chado installation

Michael Dondrup
Hi again,

just to confirm, I cannot drop chado in psql either:

licebase=> drop schema chado;
WARNING:  out of shared memory
ERROR:  out of shared memory
HINT:  You might need to increase max_locks_per_transaction.

I have asked our admin to increase the value to 640 for further testing. It seems that
the default setting is not sufficient for chado.


Michael Dondrup
Postdoctoral fellow
Sea Lice Research Centre/Department of Informatics
University of Bergen
Thormøhlensgate 55, N-5008 Bergen,
Norway

On Jan 23, 2013, at 10:39 AM, Michael Dondrup wrote:

> Hi Stephen,
>
> I have now narrowed down my second issue which has possibly nothing to do with the update.
>
> I am trying to install a new chado schema into a database which already contains chado via:
> "New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)"
>
> which yields a job named Install Chado v1.2. This job completes, but the log shows a lot of errors and the cause
> right in the beginning:
>
> Calling: tripal_core_install_chado(Install Chado v1.2, 123)
> Dropping existing 'chado' schema
> pg_query(): Query failed: ERROR:  out of shared memory               ESC[1;33;40mESC[1m[warning]ESC[0m
> HINT:  You might need to increase max_locks_per_transaction.
> database.pgsql.inc:138
> ERROR:  out of shared memory                                         ESC[1;33;40mESC[1m[warning]ESC[0m
> HINT:  You might need to increase max_locks_per_transaction.
> query: drop schema chado cascade database.pgsql.inc:159
> Dropping existing 'genetic_code' schema
> Dropping existing 'so' schema
> Dropping existing 'frange' schema
> Creating 'chado' schema
> pg_query(): Query failed: ERROR:  schema "chado" already exists      ESC[1;33;40mESC[1m[warning]ESC[0m
> database.pgsql.inc:138
> [more errors because drop failed….]
>
> Thus, dropping the chado schema failed, while other schemata can be dropped.
> If I understand [1] correctly, this is because max_locks_per_transaction is set to the default (64)
> and chado has more than 64 tables that need to be locked before dropping. I hope there is
> a way around without having to reconfigure the db server, because I don't have access to that myself.
>
> PostgreSQL server version is 8.4.13
>
> Cheers
> Michael
>
>
>
>
> [1] http://www.databasesoup.com/2012/06/postgresqlconf-maxlockspertransaction.html
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Re: [Gmod-tripal-devel] Problem with dropping chado schema during New chado installation

Stephen Ficklin-2
Hi Michael,

Oh good to know it was a shared memory issue.  What is the OS
distribution you are using?  I've not encountered this error before but
I usually use an Ubuntu distribution.   If this is an issue custom for
the distribution you are using we can make a note of it in the tutorial.

Thanks,
Stephen


On 1/23/2013 5:28 AM, Michael Dondrup wrote:

> Hi again,
>
> just to confirm, I cannot drop chado in psql either:
>
> licebase=> drop schema chado;
> WARNING:  out of shared memory
> ERROR:  out of shared memory
> HINT:  You might need to increase max_locks_per_transaction.
>
> I have asked our admin to increase the value to 640 for further testing. It seems that
> the default setting is not sufficient for chado.
>
>
> Michael Dondrup
> Postdoctoral fellow
> Sea Lice Research Centre/Department of Informatics
> University of Bergen
> Thormøhlensgate 55, N-5008 Bergen,
> Norway
>
> On Jan 23, 2013, at 10:39 AM, Michael Dondrup wrote:
>
>> Hi Stephen,
>>
>> I have now narrowed down my second issue which has possibly nothing to do with the update.
>>
>> I am trying to install a new chado schema into a database which already contains chado via:
>> "New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)"
>>
>> which yields a job named Install Chado v1.2. This job completes, but the log shows a lot of errors and the cause
>> right in the beginning:
>>
>> Calling: tripal_core_install_chado(Install Chado v1.2, 123)
>> Dropping existing 'chado' schema
>> pg_query(): Query failed: ERROR:  out of shared memory               ESC[1;33;40mESC[1m[warning]ESC[0m
>> HINT:  You might need to increase max_locks_per_transaction.
>> database.pgsql.inc:138
>> ERROR:  out of shared memory                                         ESC[1;33;40mESC[1m[warning]ESC[0m
>> HINT:  You might need to increase max_locks_per_transaction.
>> query: drop schema chado cascade database.pgsql.inc:159
>> Dropping existing 'genetic_code' schema
>> Dropping existing 'so' schema
>> Dropping existing 'frange' schema
>> Creating 'chado' schema
>> pg_query(): Query failed: ERROR:  schema "chado" already exists      ESC[1;33;40mESC[1m[warning]ESC[0m
>> database.pgsql.inc:138
>> [more errors because drop failed….]
>>
>> Thus, dropping the chado schema failed, while other schemata can be dropped.
>> If I understand [1] correctly, this is because max_locks_per_transaction is set to the default (64)
>> and chado has more than 64 tables that need to be locked before dropping. I hope there is
>> a way around without having to reconfigure the db server, because I don't have access to that myself.
>>
>> PostgreSQL server version is 8.4.13
>>
>> Cheers
>> Michael
>>
>>
>>
>>
>> [1] http://www.databasesoup.com/2012/06/postgresqlconf-maxlockspertransaction.html
>> ------------------------------------------------------------------------------
>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>> MVPs and experts. ON SALE this month only -- learn more at:
>> http://p.sf.net/sfu/learnnow-d2d
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>> Gmod-tripal-devel mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>
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Re: [Gmod-tripal-devel] Problem with dropping chado schema during New chado installation

Michael Dondrup
Hi Stephen,
yes this seems to be totally unrelated to Tripal. The distribution of the database server is RedHat or CentOS 6 (a fact I dislike but cannot do anything about). I cannot login on that machine
so I cannot say much more. version() says however:
PostgreSQL 8.4.13 on x86_64-redhat-linux-gnu, compiled by GCC gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4), 64-bit

So it is seemingly RedHat. I have to wait for IT stuff to increase  max_locks_per_transaction, possibly this might solve the problem.
I will let you know, what we find out.

Best
Michael


On Jan 23, 2013, at 4:28 PM, Stephen Ficklin wrote:

> Hi Michael,
>
> Oh good to know it was a shared memory issue.  What is the OS distribution you are using?  I've not encountered this error before but I usually use an Ubuntu distribution.   If this is an issue custom for the distribution you are using we can make a note of it in the tutorial.
>
> Thanks,
> Stephen
>
>
> On 1/23/2013 5:28 AM, Michael Dondrup wrote:
>> Hi again,
>>
>> just to confirm, I cannot drop chado in psql either:
>>
>> licebase=> drop schema chado;
>> WARNING:  out of shared memory
>> ERROR:  out of shared memory
>> HINT:  You might need to increase max_locks_per_transaction.
>>
>> I have asked our admin to increase the value to 640 for further testing. It seems that
>> the default setting is not sufficient for chado.
>>
>>
>> Michael Dondrup
>> Postdoctoral fellow
>> Sea Lice Research Centre/Department of Informatics
>> University of Bergen
>> Thormøhlensgate 55, N-5008 Bergen,
>> Norway
>>
>> On Jan 23, 2013, at 10:39 AM, Michael Dondrup wrote:
>>
>>> Hi Stephen,
>>>
>>> I have now narrowed down my second issue which has possibly nothing to do with the update.
>>>
>>> I am trying to install a new chado schema into a database which already contains chado via:
>>> "New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)"
>>>
>>> which yields a job named Install Chado v1.2. This job completes, but the log shows a lot of errors and the cause
>>> right in the beginning:
>>>
>>> Calling: tripal_core_install_chado(Install Chado v1.2, 123)
>>> Dropping existing 'chado' schema
>>> pg_query(): Query failed: ERROR:  out of shared memory               ESC[1;33;40mESC[1m[warning]ESC[0m
>>> HINT:  You might need to increase max_locks_per_transaction.
>>> database.pgsql.inc:138
>>> ERROR:  out of shared memory                                         ESC[1;33;40mESC[1m[warning]ESC[0m
>>> HINT:  You might need to increase max_locks_per_transaction.
>>> query: drop schema chado cascade database.pgsql.inc:159
>>> Dropping existing 'genetic_code' schema
>>> Dropping existing 'so' schema
>>> Dropping existing 'frange' schema
>>> Creating 'chado' schema
>>> pg_query(): Query failed: ERROR:  schema "chado" already exists      ESC[1;33;40mESC[1m[warning]ESC[0m
>>> database.pgsql.inc:138
>>> [more errors because drop failed….]
>>>
>>> Thus, dropping the chado schema failed, while other schemata can be dropped.
>>> If I understand [1] correctly, this is because max_locks_per_transaction is set to the default (64)
>>> and chado has more than 64 tables that need to be locked before dropping. I hope there is
>>> a way around without having to reconfigure the db server, because I don't have access to that myself.
>>>
>>> PostgreSQL server version is 8.4.13
>>>
>>> Cheers
>>> Michael
>>>
>>>
>>>
>>>
>>> [1] http://www.databasesoup.com/2012/06/postgresqlconf-maxlockspertransaction.html
>>> ------------------------------------------------------------------------------
>>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>>> MVPs and experts. ON SALE this month only -- learn more at:
>>> http://p.sf.net/sfu/learnnow-d2d
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>>> Gmod-tripal-devel mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>
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>


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Re: [Gmod-tripal-devel] Problem with dropping chado schema during New chado installation

Michael Dondrup
Hi,

our admin has set max_locks_per_transaction = 640 in postgresql.conf and restarted the postgres server.
This has solved the problem of not beeing able to drop the chado schema in psql:

licebase=> drop schema chado cascade;
NOTICE:  drop cascades to 4049 other objects
DETAIL:  drop cascades to table chado.tableinfo
drop cascades to table chado.db
drop cascades to table chado.dbxref
[…]
drop cascades to view chado.intron
and 3949 other objects (see server log for list)
DROP SCHEMA

Given the number of objects contained, it seems plausible that the default setting is too low.
I cc this mail to the gmod-schema list, in case someone experiences similar problems.

Best
Michael

On Jan 24, 2013, at 10:16 AM, Michael Dondrup wrote:

> Hi Stephen,
> yes this seems to be totally unrelated to Tripal. The distribution of the database server is RedHat or CentOS 6 (a fact I dislike but cannot do anything about). I cannot login on that machine
> so I cannot say much more. version() says however:
> PostgreSQL 8.4.13 on x86_64-redhat-linux-gnu, compiled by GCC gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4), 64-bit
>
> So it is seemingly RedHat. I have to wait for IT stuff to increase  max_locks_per_transaction, possibly this might solve the problem.
> I will let you know, what we find out.
>
> Best
> Michael
>
>
> On Jan 23, 2013, at 4:28 PM, Stephen Ficklin wrote:
>
>> Hi Michael,
>>
>> Oh good to know it was a shared memory issue.  What is the OS distribution you are using?  I've not encountered this error before but I usually use an Ubuntu distribution.   If this is an issue custom for the distribution you are using we can make a note of it in the tutorial.
>>
>> Thanks,
>> Stephen
>>
>>
>> On 1/23/2013 5:28 AM, Michael Dondrup wrote:
>>> Hi again,
>>>
>>> just to confirm, I cannot drop chado in psql either:
>>>
>>> licebase=> drop schema chado;
>>> WARNING:  out of shared memory
>>> ERROR:  out of shared memory
>>> HINT:  You might need to increase max_locks_per_transaction.
>>>
>>> I have asked our admin to increase the value to 640 for further testing. It seems that
>>> the default setting is not sufficient for chado.
>>>
>>>
>>> Michael Dondrup
>>> Postdoctoral fellow
>>> Sea Lice Research Centre/Department of Informatics
>>> University of Bergen
>>> Thormøhlensgate 55, N-5008 Bergen,
>>> Norway
>>>
>>> On Jan 23, 2013, at 10:39 AM, Michael Dondrup wrote:
>>>
>>>> Hi Stephen,
>>>>
>>>> I have now narrowed down my second issue which has possibly nothing to do with the update.
>>>>
>>>> I am trying to install a new chado schema into a database which already contains chado via:
>>>> "New Install of Chado v1.2 (erases all existing Chado data if Chado already exists)"
>>>>
>>>> which yields a job named Install Chado v1.2. This job completes, but the log shows a lot of errors and the cause
>>>> right in the beginning:
>>>>
>>>> Calling: tripal_core_install_chado(Install Chado v1.2, 123)
>>>> Dropping existing 'chado' schema
>>>> pg_query(): Query failed: ERROR:  out of shared memory               ESC[1;33;40mESC[1m[warning]ESC[0m
>>>> HINT:  You might need to increase max_locks_per_transaction.
>>>> database.pgsql.inc:138
>>>> ERROR:  out of shared memory                                         ESC[1;33;40mESC[1m[warning]ESC[0m
>>>> HINT:  You might need to increase max_locks_per_transaction.
>>>> query: drop schema chado cascade database.pgsql.inc:159
>>>> Dropping existing 'genetic_code' schema
>>>> Dropping existing 'so' schema
>>>> Dropping existing 'frange' schema
>>>> Creating 'chado' schema
>>>> pg_query(): Query failed: ERROR:  schema "chado" already exists      ESC[1;33;40mESC[1m[warning]ESC[0m
>>>> database.pgsql.inc:138
>>>> [more errors because drop failed….]
>>>>
>>>> Thus, dropping the chado schema failed, while other schemata can be dropped.
>>>> If I understand [1] correctly, this is because max_locks_per_transaction is set to the default (64)
>>>> and chado has more than 64 tables that need to be locked before dropping. I hope there is
>>>> a way around without having to reconfigure the db server, because I don't have access to that myself.
>>>>
>>>> PostgreSQL server version is 8.4.13
>>>>
>>>> Cheers
>>>> Michael
>>>>
>>>>
>>>>
>>>>
>>>> [1] http://www.databasesoup.com/2012/06/postgresqlconf-maxlockspertransaction.html
>>>> ------------------------------------------------------------------------------
>>>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS,
>>>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
>>>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
>>>> MVPs and experts. ON SALE this month only -- learn more at:
>>>> http://p.sf.net/sfu/learnnow-d2d
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>>>> Gmod-tripal-devel mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
>>>
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>>
>
>
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