Error: Call to undefined function posix_kill() in jobs.php

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Error: Call to undefined function posix_kill() in jobs.php

Collett, James R-2
Hello,
 
I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.
 
Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):
 
]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin
 
I get this error:
 
Tripal Job Launcher
-------------------
PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313
 
Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.
 
Thanks,
 
Jim
 
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
 
Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN P8-60
Richland, WA  99352 USA
Tel:  509-372-6345
Fax: 509-372-4732
 
 
 

------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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Re: Error: Call to undefined function posix_kill() in jobs.php

Collett, James R-2

After reading jobs.php, I went  into the tripal_jobs table in psql  and set the end_time of the hung job to start_time+1.  I then ran tripal_launch_jobs, and the gene ontology OBO file started loading again.  I’m getting some errors in stdout, though, about unhandled tags as the OBO file loads.  Is this a problem?

 

Thanks,

 

Jim

 

From: Collett, James R
Sent: Tuesday, October 04, 2011 12:22 AM
To: [hidden email]
Subject: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hello,

 

I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.

 

Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):

 

]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

I get this error:

 

Tripal Job Launcher

-------------------

PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313

 

Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  509-372-6345

Fax: 509-372-4732

 

 

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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Re: Error: Call to undefined function posix_kill() in jobs.php

stacy xu
Hi, James,

I am not sure whether this would solve your problem, I was having similar problem when uploading GO ontology through internet with hanging jobs. As suggested by other experts from Tripal, I rerun "cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator" from server side. And the hanging job disappeared from my terminal. I installed php-poxit package as well. Maybe you want to rerun your php command?

Thanks,
Stacy

On Tue, Oct 4, 2011 at 4:05 PM, Collett, James R <[hidden email]> wrote:

After reading jobs.php, I went  into the tripal_jobs table in psql  and set the end_time of the hung job to start_time+1.  I then ran tripal_launch_jobs, and the gene ontology OBO file started loading again.  I’m getting some errors in stdout, though, about unhandled tags as the OBO file loads.  Is this a problem?

 

Thanks,

 

Jim

 

From: Collett, James R
Sent: Tuesday, October 04, 2011 12:22 AM
To: [hidden email]
Subject: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hello,

 

I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.

 

Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):

 

]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

I get this error:

 

Tripal Job Launcher

-------------------

PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313

 

Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  <a href="tel:509-372-6345" value="+15093726345" target="_blank">509-372-6345

Fax: <a href="tel:509-372-4732" value="+15093724732" target="_blank">509-372-4732

 

 

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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Re: Error: Call to undefined function posix_kill() in jobs.php

Stephen Ficklin-2
Hi James & Stacy,

Stacy, was the package named 'php-posix'?

James, what version of Linux/Unix are you using?  Just curious because if installing the php-posix module for your distribution works then I'd like to update the Tutorial to add in the extra step for other non-Ubuntu versions of Linux.

Thanks,
Stephen

On 10/4/2011 9:52 AM, stacy xu wrote:
Hi, James,

I am not sure whether this would solve your problem, I was having similar problem when uploading GO ontology through internet with hanging jobs. As suggested by other experts from Tripal, I rerun "cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator" from server side. And the hanging job disappeared from my terminal. I installed php-poxit package as well. Maybe you want to rerun your php command?

Thanks,
Stacy

On Tue, Oct 4, 2011 at 4:05 PM, Collett, James R <[hidden email]> wrote:

After reading jobs.php, I went  into the tripal_jobs table in psql  and set the end_time of the hung job to start_time+1.  I then ran tripal_launch_jobs, and the gene ontology OBO file started loading again.  I’m getting some errors in stdout, though, about unhandled tags as the OBO file loads.  Is this a problem?

 

Thanks,

 

Jim

 

From: Collett, James R
Sent: Tuesday, October 04, 2011 12:22 AM
To: [hidden email]
Subject: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hello,

 

I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.

 

Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):

 

]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

I get this error:

 

Tripal Job Launcher

-------------------

PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313

 

Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  <a moz-do-not-send="true" href="tel:509-372-6345" value="+15093726345" target="_blank">509-372-6345

Fax: <a moz-do-not-send="true" href="tel:509-372-4732" value="+15093724732" target="_blank">509-372-4732

 

 

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
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Re: Error: Call to undefined function posix_kill() in jobs.php

Stephen Ficklin-2
In reply to this post by Collett, James R-2
Hi James,

You can safely ignore the messages about unhandled tags.  There are a few tags in the OBO files that are currently not handled by the loaders.  For example the 'subset' tag of the gene ontology is used to identify terms that belong to specific GO "slims", such as the Plant GO Slim (http://www.geneontology.org/GO.slims.shtml).  Currently, the OBO loader doesn't use that tag to organize the terms into subsets.  There are a few other tags that are not handled.   In the future we would like to find a way to support tags like the subset tags but for now the loader does not.   Perhaps we should remove the warning message from the output.  It is simply there to remind us to support those tags later.

Also, you should be able to relaunch your job without having to make changes in the database.  After you get past the 'posix_kill' problem (hopefully by simply installing the php-posix module for your version of Linux), then all you need to do is run the 'tripal_launch_jobs' to clear the state of the job.  Afterwards a 'Re-run' job link should appear next to the job on the Jobs administrative page in Tripal.

Stephen

On 10/4/2011 4:05 AM, Collett, James R wrote:

After reading jobs.php, I went  into the tripal_jobs table in psql  and set the end_time of the hung job to start_time+1.  I then ran tripal_launch_jobs, and the gene ontology OBO file started loading again.  I’m getting some errors in stdout, though, about unhandled tags as the OBO file loads.  Is this a problem?

 

Thanks,

 

Jim

 

From: Collett, James R
Sent: Tuesday, October 04, 2011 12:22 AM
To: [hidden email]
Subject: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hello,

 

I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.

 

Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):

 

]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

I get this error:

 

Tripal Job Launcher

-------------------

PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313

 

Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  509-372-6345

Fax: 509-372-4732

 

 

 



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal
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Re: Error: Call to undefined function posix_kill() in jobs.php

Collett, James R-2

Thanks Stephen.

 

My Gene Ontology OBO file loading job ran successfully overnight.  

 

I have also installed php-posix following your suggestion and by Stacy Xu in another post.  I’m running Red Hat EL 6 (on a VirtualBox VM), so this was done with “yum install php-process” as described previously by Evan.

 

Jim

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: Tuesday, October 04, 2011 12:40 PM
To: [hidden email]
Subject: Re: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hi James,

You can safely ignore the messages about unhandled tags.  There are a few tags in the OBO files that are currently not handled by the loaders.  For example the 'subset' tag of the gene ontology is used to identify terms that belong to specific GO "slims", such as the Plant GO Slim (http://www.geneontology.org/GO.slims.shtml).  Currently, the OBO loader doesn't use that tag to organize the terms into subsets.  There are a few other tags that are not handled.   In the future we would like to find a way to support tags like the subset tags but for now the loader does not.   Perhaps we should remove the warning message from the output.  It is simply there to remind us to support those tags later.

Also, you should be able to relaunch your job without having to make changes in the database.  After you get past the 'posix_kill' problem (hopefully by simply installing the php-posix module for your version of Linux), then all you need to do is run the 'tripal_launch_jobs' to clear the state of the job.  Afterwards a 'Re-run' job link should appear next to the job on the Jobs administrative page in Tripal.

Stephen

On 10/4/2011 4:05 AM, Collett, James R wrote:

After reading jobs.php, I went  into the tripal_jobs table in psql  and set the end_time of the hung job to start_time+1.  I then ran tripal_launch_jobs, and the gene ontology OBO file started loading again.  I’m getting some errors in stdout, though, about unhandled tags as the OBO file loads.  Is this a problem?

 

Thanks,

 

Jim

 

From: Collett, James R
Sent: Tuesday, October 04, 2011 12:22 AM
To: [hidden email]
Subject: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hello,

 

I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.

 

Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):

 

]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

I get this error:

 

Tripal Job Launcher

-------------------

PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313

 

Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  509-372-6345

Fax: 509-372-4732

 

 

 




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1




_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
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Re: Error: Call to undefined function posix_kill() in jobs.php

stacy xu
In reply to this post by Stephen Ficklin-2
Hi, Stephen,

I am using SUSE and php5-posix is one php package that enables POSIX-like functions in PHP. I installed this package and the complain to "undefined function posix_kill()" disappeared after thsi installation. I guess it is SUSE-specific problem. 

Thanks,
Stacy

On Wed, Oct 5, 2011 at 3:32 AM, Stephen Ficklin <[hidden email]> wrote:
Hi James & Stacy,

Stacy, was the package named 'php-posix'?

James, what version of Linux/Unix are you using?  Just curious because if installing the php-posix module for your distribution works then I'd like to update the Tutorial to add in the extra step for other non-Ubuntu versions of Linux.

Thanks,
Stephen


On 10/4/2011 9:52 AM, stacy xu wrote:
Hi, James,

I am not sure whether this would solve your problem, I was having similar problem when uploading GO ontology through internet with hanging jobs. As suggested by other experts from Tripal, I rerun "cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator" from server side. And the hanging job disappeared from my terminal. I installed php-poxit package as well. Maybe you want to rerun your php command?

Thanks,
Stacy

On Tue, Oct 4, 2011 at 4:05 PM, Collett, James R <[hidden email]> wrote:

After reading jobs.php, I went  into the tripal_jobs table in psql  and set the end_time of the hung job to start_time+1.  I then ran tripal_launch_jobs, and the gene ontology OBO file started loading again.  I’m getting some errors in stdout, though, about unhandled tags as the OBO file loads.  Is this a problem?

 

Thanks,

 

Jim

 

From: Collett, James R
Sent: Tuesday, October 04, 2011 12:22 AM
To: [hidden email]
Subject: [Gmod-tripal] Error: Call to undefined function posix_kill() in jobs.php

 

Hello,

 

I lost my terminal connection while loading the gene ontology OBO file into Chado into a new installation of Tripal.  When I reconnected, the OBO file loading job was hung.  I wasn’t able to rerun the job, because the tripal jobs manager said that I couldn’t rerun or cancel a job in progress.

 

Now when I directly start the job launcher using this command as directed in the tutorial (v0.31b):

 

]$ php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php drupal_admin

 

I get this error:

 

Tripal Job Launcher

-------------------

PHP Fatal error:  Call to undefined function posix_kill() in /var/www/html/sites/all/modules/tripal-6.x-0.3.1b/tripal_core/jobs.php on line 313

 

Can you help me get back on track?  I’m running Red Hat Enterprise Linux 6, and Drupal seems to be running fine except for the Tripal job launcher problem.

 

Thanks,

 

Jim

 

__________________________________________________

James R. Collett, Ph.D.

Senior Scientist

Chemical and Biological Process Development Group

Energy and Environment Directorate

 

Pacific Northwest National Laboratory

902 Battelle Boulevard

P.O. Box 999, MSIN P8-60

Richland, WA  99352 USA

Tel:  <a href="tel:509-372-6345" value="+15093726345" target="_blank">509-372-6345

Fax: <a href="tel:509-372-4732" value="+15093724732" target="_blank">509-372-4732

 

 

 


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1


_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal


------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal



------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal