Tripal installation: Ontology loading problem

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Tripal installation: Ontology loading problem

Sudhansu Dash-2
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: Tripal installation: Ontology loading problem

Stephen Ficklin-2
Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.  
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:

> Hi,
> Somebody at ISU is having problem installing Tripal and we received the
> following query from them.
> Please give some pointers to them or if more info is needed I will ask
> them to be in touch with this list.
>
> "We've been trying to install Tripal and are struggling to get the Ontology
> job to run.  It continues to fail with an error like this:
>
> WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
> too complex: 7 ERROR:  stack depth limit exceeded"
>
> Thanks in advance.
>
> Sudhansu Dash
>
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Tripal installation: Ontology loading problem

Baber, Levi C [LAS]
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:

> Hi,
> Somebody at ISU is having problem installing Tripal and we received the
> following query from them.
> Please give some pointers to them or if more info is needed I will ask
> them to be in touch with this list.
>
> "We've been trying to install Tripal and are struggling to get the Ontology
> job to run.  It continues to fail with an error like this:
>
> WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
> too complex: 7 ERROR:  stack depth limit exceeded"
>
> Thanks in advance.
>
> Sudhansu Dash
>
>
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Tripal installation: Ontology loading problem

Stephen Ficklin-2
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen


On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:

> Thanks for the replies.
>
> We'll try the install on Ubuntu 14.04 and see how it goes.
>
> ________________________________________
> From: Stephen Ficklin <[hidden email]>
> Sent: Tuesday, May 10, 2016 4:16:04 PM
> To: Sudhansu Dash; [hidden email]
> Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
> Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem
>
> Hi Sudhansu,
>
> It seems there may be an issue with PostgreSQL on some UNIX flavors.
> The problem occurs when Tripal tries to use the PL/PgSQL function that
> comes with Chado for updating the cvtermpath table.  Tripal simply calls
> it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
> and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
> the default settings for Postgres.  I did this just last week.
>
> Perhaps we're talking with the same group at ISU.  I spoke with Nick
> Booher (CC'ing now) there who has been struggling with this problem on
> both an OS X and RedHat installation and he has the same problem.  Last
> we spoke he's going to try it on an Ubuntu system to see if this is an
> OS dependent problem.
>
> So, once I hear we'll report back.
>
> Stephen
>
>
> On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
>> Hi,
>> Somebody at ISU is having problem installing Tripal and we received the
>> following query from them.
>> Please give some pointers to them or if more info is needed I will ask
>> them to be in touch with this list.
>>
>> "We've been trying to install Tripal and are struggling to get the Ontology
>> job to run.  It continues to fail with an error like this:
>>
>> WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
>> too complex: 7 ERROR:  stack depth limit exceeded"
>>
>> Thanks in advance.
>>
>> Sudhansu Dash
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Tripal installation: Ontology loading problem

Nick Booher
Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Tripal installation: Ontology loading problem

Stephen Ficklin-2

Hi Nick,

Thanks for the breadth of your testing!    I'm anxious to hear the results.

The relationship ontology is a problem at the moment.  It has been completely overhauled and now uses terms from other vocabularies which is the cause of the loading problem.   We're working on a fix for that but in the meantime, we've removed it from the next version Tripal v2.1 which will be released soon.   For folks who wish to use an older version of that ontology, a copy of it is available on this issue:  https://www.drupal.org/node/2629382

Stephen


On 6/12/2016 9:08 PM, Nick Booher wrote:
Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Tripal installation: Ontology loading problem

Kucheran, Lacey Sanderson
In reply to this post by Nick Booher
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Tripal installation: Ontology loading problem

Nick Booher
Hi,

It's on the tripal-vm branch within the fork. Alternatively, here's a zip file. Or GitHub's nice compare view.

scripts/run_test.sh is just a wrapper around vagrant up that loops over the different machine versions.

-Nick

On Mon, Jun 13, 2016 at 2:39 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
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consuming the most bandwidth. Provides multi-vendor support for NetFlow,
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Re: Tripal installation: Ontology loading problem

Nick Booher
Hi,

Loading Gene Ontology on 2.0 seems to work on all platforms and only takes a couple hours. Meanwhile, rather than the 'stack depth limit exceeded' errors I used to get loading the Gene Ontology on 2.x, now it just seems to run forever. I launched VMs for a 2.x GO load for each platform Monday and when I came back Tuesday morning they were still running. The last log message says 'Updating cvtermpath for biological_process...' and postgresql is using 100% CPU. I killed 3 of the VMs to free up resources, but left the Ubuntu 14.04 VM running. Today it's still going and on the same step.

-Nick

On Mon, Jun 13, 2016 at 2:50 PM, Nick Booher <[hidden email]> wrote:
Hi,

It's on the tripal-vm branch within the fork. Alternatively, here's a zip file. Or GitHub's nice compare view.

scripts/run_test.sh is just a wrapper around vagrant up that loops over the different machine versions.

-Nick

On Mon, Jun 13, 2016 at 2:39 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
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restrictions. Mobile Device Manager Plus allows you to control only the
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https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
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consuming the most bandwidth. Provides multi-vendor support for NetFlow,
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Re: Tripal installation: Ontology loading problem

Nick Booher
Hi,

Loading Gene Ontology using Tripal 2.x on Ubuntu 14.04 has now been running for 6 days with no signs of finishing.


top output:

top - 13:41:32 up 6 days, 13:50,  2 users,  load average: 0.94, 0.98, 1.03
Tasks: 123 total,   2 running, 121 sleeping,   0 stopped,   0 zombie
%Cpu(s): 47.6 us,  2.7 sy,  0.0 ni, 49.8 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem:   2049928 total,   999412 used,  1050516 free,   179364 buffers
KiB Swap:   524284 total,    16204 used,   508080 free.   530972 cached Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                                                                                                                                                              
26008 postgres  20   0  172772  64420  20116 R 100.0  3.1   9275:49 postgres

pg_top output:

Current query for procpid 26008:

SELECT * FROM fill_cvtermpath('biological_process')


We did get 2.0 working, so this is no longer a blocker for us. Let me know if there's any information from the VM that would be useful for debugging; otherwise, I'm going to shutdown the VM later today.

-Nick

On Wed, Jun 15, 2016 at 10:33 AM, Nick Booher <[hidden email]> wrote:
Hi,

Loading Gene Ontology on 2.0 seems to work on all platforms and only takes a couple hours. Meanwhile, rather than the 'stack depth limit exceeded' errors I used to get loading the Gene Ontology on 2.x, now it just seems to run forever. I launched VMs for a 2.x GO load for each platform Monday and when I came back Tuesday morning they were still running. The last log message says 'Updating cvtermpath for biological_process...' and postgresql is using 100% CPU. I killed 3 of the VMs to free up resources, but left the Ubuntu 14.04 VM running. Today it's still going and on the same step.

-Nick

On Mon, Jun 13, 2016 at 2:50 PM, Nick Booher <[hidden email]> wrote:
Hi,

It's on the tripal-vm branch within the fork. Alternatively, here's a zip file. Or GitHub's nice compare view.

scripts/run_test.sh is just a wrapper around vagrant up that loops over the different machine versions.

-Nick

On Mon, Jun 13, 2016 at 2:39 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity planning
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Re: Tripal installation: Ontology loading problem

Stephen Ficklin-2

Hi Nick,

Loading the GO should not take 6 days.  It takes several hours on my Ubuntu installation.  The only reason I can think that it would take so long is if your VM is doing a lot of swapping.  But, from your top output it doesn't appear to be the case.  Since that's just a snapshot, do you know if swapping is occurring? 

Stephen


On 6/20/2016 6:59 AM, Nick Booher wrote:
Hi,

Loading Gene Ontology using Tripal 2.x on Ubuntu 14.04 has now been running for 6 days with no signs of finishing.


top output:

top - 13:41:32 up 6 days, 13:50,  2 users,  load average: 0.94, 0.98, 1.03
Tasks: 123 total,   2 running, 121 sleeping,   0 stopped,   0 zombie
%Cpu(s): 47.6 us,  2.7 sy,  0.0 ni, 49.8 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem:   2049928 total,   999412 used,  1050516 free,   179364 buffers
KiB Swap:   524284 total,    16204 used,   508080 free.   530972 cached Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                                                                                                                                                              
26008 postgres  20   0  172772  64420  20116 R 100.0  3.1   9275:49 postgres

pg_top output:

Current query for procpid 26008:

SELECT * FROM fill_cvtermpath('biological_process')


We did get 2.0 working, so this is no longer a blocker for us. Let me know if there's any information from the VM that would be useful for debugging; otherwise, I'm going to shutdown the VM later today.

-Nick

On Wed, Jun 15, 2016 at 10:33 AM, Nick Booher <[hidden email]> wrote:
Hi,

Loading Gene Ontology on 2.0 seems to work on all platforms and only takes a couple hours. Meanwhile, rather than the 'stack depth limit exceeded' errors I used to get loading the Gene Ontology on 2.x, now it just seems to run forever. I launched VMs for a 2.x GO load for each platform Monday and when I came back Tuesday morning they were still running. The last log message says 'Updating cvtermpath for biological_process...' and postgresql is using 100% CPU. I killed 3 of the VMs to free up resources, but left the Ubuntu 14.04 VM running. Today it's still going and on the same step.

-Nick

On Mon, Jun 13, 2016 at 2:50 PM, Nick Booher <[hidden email]> wrote:
Hi,

It's on the tripal-vm branch within the fork. Alternatively, here's a zip file. Or GitHub's nice compare view.

scripts/run_test.sh is just a wrapper around vagrant up that loops over the different machine versions.

-Nick

On Mon, Jun 13, 2016 at 2:39 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a moz-do-not-send="true" href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal





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Re: Tripal installation: Ontology loading problem

Nick Booher
Doesn't seem to be.

-Nick

On Mon, Jun 20, 2016 at 11:15 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Nick,

Loading the GO should not take 6 days.  It takes several hours on my Ubuntu installation.  The only reason I can think that it would take so long is if your VM is doing a lot of swapping.  But, from your top output it doesn't appear to be the case.  Since that's just a snapshot, do you know if swapping is occurring? 

Stephen


On 6/20/2016 6:59 AM, Nick Booher wrote:
Hi,

Loading Gene Ontology using Tripal 2.x on Ubuntu 14.04 has now been running for 6 days with no signs of finishing.


top output:

top - 13:41:32 up 6 days, 13:50,  2 users,  load average: 0.94, 0.98, 1.03
Tasks: 123 total,   2 running, 121 sleeping,   0 stopped,   0 zombie
%Cpu(s): 47.6 us,  2.7 sy,  0.0 ni, 49.8 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem:   2049928 total,   999412 used,  1050516 free,   179364 buffers
KiB Swap:   524284 total,    16204 used,   508080 free.   530972 cached Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                                                                                                                                                              
26008 postgres  20   0  172772  64420  20116 R 100.0  3.1   9275:49 postgres

pg_top output:

Current query for procpid 26008:

SELECT * FROM fill_cvtermpath('biological_process')


We did get 2.0 working, so this is no longer a blocker for us. Let me know if there's any information from the VM that would be useful for debugging; otherwise, I'm going to shutdown the VM later today.

-Nick

On Wed, Jun 15, 2016 at 10:33 AM, Nick Booher <[hidden email]> wrote:
Hi,

Loading Gene Ontology on 2.0 seems to work on all platforms and only takes a couple hours. Meanwhile, rather than the 'stack depth limit exceeded' errors I used to get loading the Gene Ontology on 2.x, now it just seems to run forever. I launched VMs for a 2.x GO load for each platform Monday and when I came back Tuesday morning they were still running. The last log message says 'Updating cvtermpath for biological_process...' and postgresql is using 100% CPU. I killed 3 of the VMs to free up resources, but left the Ubuntu 14.04 VM running. Today it's still going and on the same step.

-Nick

On Mon, Jun 13, 2016 at 2:50 PM, Nick Booher <[hidden email][hidden email]> wrote:
Hi,

It's on the tripal-vm branch within the fork. Alternatively, here's a zip file. Or GitHub's nice compare view.

scripts/run_test.sh is just a wrapper around vagrant up that loops over the different machine versions.

-Nick

On Mon, Jun 13, 2016 at 2:39 PM, Kucheran, Lacey Sanderson <[hidden email][hidden email]> wrote:
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email][hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email][hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email][hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email][hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



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Re: Tripal installation: Ontology loading problem

Stephen Ficklin-2

Okay, well I'm happy to help debug this further with you if you'd like. It sounds like you have a working 2.0 version.   Just let me know.

Also, you may want to upgrade to the most recent 2.x development version. We have made lots of bug fixes and we're nearing release of 2.1.   We're using it on quite a few production sites so it should be okay to use.

Stephen


On 6/21/2016 3:05 PM, Nick Booher wrote:
Doesn't seem to be.

-Nick

On Mon, Jun 20, 2016 at 11:15 PM, Stephen Ficklin <[hidden email]> wrote:

Hi Nick,

Loading the GO should not take 6 days.  It takes several hours on my Ubuntu installation.  The only reason I can think that it would take so long is if your VM is doing a lot of swapping.  But, from your top output it doesn't appear to be the case.  Since that's just a snapshot, do you know if swapping is occurring? 

Stephen


On 6/20/2016 6:59 AM, Nick Booher wrote:
Hi,

Loading Gene Ontology using Tripal 2.x on Ubuntu 14.04 has now been running for 6 days with no signs of finishing.


top output:

top - 13:41:32 up 6 days, 13:50,  2 users,  load average: 0.94, 0.98, 1.03
Tasks: 123 total,   2 running, 121 sleeping,   0 stopped,   0 zombie
%Cpu(s): 47.6 us,  2.7 sy,  0.0 ni, 49.8 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem:   2049928 total,   999412 used,  1050516 free,   179364 buffers
KiB Swap:   524284 total,    16204 used,   508080 free.   530972 cached Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND                                                                                                                                                                                                                              
26008 postgres  20   0  172772  64420  20116 R 100.0  3.1   9275:49 postgres

pg_top output:

Current query for procpid 26008:

SELECT * FROM fill_cvtermpath('biological_process')


We did get 2.0 working, so this is no longer a blocker for us. Let me know if there's any information from the VM that would be useful for debugging; otherwise, I'm going to shutdown the VM later today.

-Nick

On Wed, Jun 15, 2016 at 10:33 AM, Nick Booher <[hidden email]> wrote:
Hi,

Loading Gene Ontology on 2.0 seems to work on all platforms and only takes a couple hours. Meanwhile, rather than the 'stack depth limit exceeded' errors I used to get loading the Gene Ontology on 2.x, now it just seems to run forever. I launched VMs for a 2.x GO load for each platform Monday and when I came back Tuesday morning they were still running. The last log message says 'Updating cvtermpath for biological_process...' and postgresql is using 100% CPU. I killed 3 of the VMs to free up resources, but left the Ubuntu 14.04 VM running. Today it's still going and on the same step.

-Nick

On Mon, Jun 13, 2016 at 2:50 PM, Nick Booher <[hidden email]> wrote:
Hi,

It's on the tripal-vm branch within the fork. Alternatively, here's a zip file. Or GitHub's nice compare view.

scripts/run_test.sh is just a wrapper around vagrant up that loops over the different machine versions.

-Nick

On Mon, Jun 13, 2016 at 2:39 PM, Kucheran, Lacey Sanderson <[hidden email]> wrote:
Hi Nick,

Great minds think alike -I was working on a Tripal version of the Drupal VM over the weekend too. I cloned your repository to see how you approached the problem and compare/contrast but when I build it using vagrant up I end up with a Drupal 8 MySQL stock site (no Tripal). You mention editing scripts/env.sh and running scripts/run_tests.sh but I don’t see these in your repo… Can you point me in the right direction? Also, do you still run vagrant up after scripts/run_tests.sh?

Thanks!
~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a moz-do-not-send="true" href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On June 12, 2016 at 10:09:01 PM, Nick Booher ([hidden email]) wrote:

Over the weekend I made a TripalVM out of DrupalVM. Clone the tripal-vm branch, edit scripts/env.sh to set the working directory, and then run scripts/run_tests.sh. It will install Tripal 2.0 and the latest commit of Tripal 2.x on each of CentOS 6, CentOS 7, Ubuntu 12.04, and Ubuntu 14.04, and try to load the Relationship Ontology and Gene Ontology on each.

The Relationship Ontology loading errors out with either branch on all platforms. With 2.0 there's a foreign key constraint violation. With 2.x it's the 'WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR: stack depth limit exceeded"' problem. 

Gene Ontology loads are still running. I'll let you know how they turn out.

-Nick

On Thu, May 26, 2016 at 2:00 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Baber,

Just curious were you able to get Tripal working on an Ubuntu 14.04 setup?

Stephen



On 5/11/2016 5:58 AM, Baber, Levi C [LAS] wrote:
Thanks for the replies.

We'll try the install on Ubuntu 14.04 and see how it goes.

________________________________________
From: Stephen Ficklin <[hidden email]>
Sent: Tuesday, May 10, 2016 4:16:04 PM
To: Sudhansu Dash; [hidden email][hidden email]
Cc: Baber, Levi C [LAS]; Booher, Nicholas J [ENT]
Subject: Re: [Gmod-tripal] Tripal installation: Ontology loading problem

Hi Sudhansu,

It seems there may be an issue with PostgreSQL on some UNIX flavors.
The problem occurs when Tripal tries to use the PL/PgSQL function that
comes with Chado for updating the cvtermpath table.  Tripal simply calls
it so this seems to be a PostgreSQL issue...  I'm able to install Tripal
and load the Gene Ontology just fine on an Ubuntu 14.04 machine using
the default settings for Postgres.  I did this just last week.

Perhaps we're talking with the same group at ISU.  I spoke with Nick
Booher (CC'ing now) there who has been struggling with this problem on
both an OS X and RedHat installation and he has the same problem.  Last
we spoke he's going to try it on an Ubuntu system to see if this is an
OS dependent problem.

So, once I hear we'll report back.

Stephen


On 5/10/2016 1:52 PM, Sudhansu Dash wrote:
Hi,
Somebody at ISU is having problem installing Tripal and we received the
following query from them.
Please give some pointers to them or if more info is needed I will ask
them to be in touch with this list.

"We've been trying to install Tripal and are struggling to get the Ontology
job to run.  It continues to fail with an error like this:

WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement
too complex: 7 ERROR:  stack depth limit exceeded"

Thanks in advance.

Sudhansu Dash



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
Gmod-tripal mailing list
[hidden email]
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------------------------------------------------------------------------------
Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
_______________________________________________
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