problems about loading Load OBO Relationship Ontology into Chado using Tripal

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problems about loading Load OBO Relationship Ontology into Chado using Tripal

stacy xu
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy

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definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
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Re: problems about loading Load OBO Relationship Ontology into Chado using Tripal

Stephen Ficklin-2
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen

On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


------------------------------------------------------------------------------
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threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
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threats, fraudulent activity and more. Splunk takes this data and makes
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Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

stacy xu
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


------------------------------------------------------------------------------
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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[hidden email]
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------------------------------------------------------------------------------
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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------------------------------------------------------------------------------
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: problems about loading Load OBO Relationship Ontology into Chado using Tripal

Evan Ernst
In reply to this post by Stephen Ficklin-2
In Centos, Fedora, and probably RHEL, I believe you need to install the php-process package (yum install php-process) to get the posix functionality. 

Evan

On Thu, Sep 29, 2011 at 10:10 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "

  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


------------------------------------------------------------------------------
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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------------------------------------------------------------------------------
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: Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

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

The job is most likely not running.   Tripal does not poll the system to see when a process completes or not.  And if a job fails unexpectedly and stops execution Tripal won't know about it until it tries to run the next round of jobs.  This will happen the next time the cron fires (if you have the cron setup) or when you try to run a job manually from the command-line (like you did).  But, in your case the 'posix_kill' which is part of the process that checks for running jobs, is not running so Tripal is not able to update the status of the job.

I also forgot to respond to another of your questions about changing the priority of a users job. This hasn't been worked into the jobs scheduler just yet.  The place-holder is there for it.  And in the API there is an argument for it.   But we haven't programmed in the ability to set or change the priority of a job.   This wouldn't be too hard a thing to do, it just hasn't been a high priority yet.  If you need this functionality let me know and we can see about bumping this up on our TODO list.

Stephen



On 9/29/2011 10:37 AM, stacy xu wrote:
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


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


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


------------------------------------------------------------------------------
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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: problems about loading Load OBO Relationship Ontology into Chado using Tripal

stacy xu
In reply to this post by Evan Ernst
Hi, Evan,

Thanks for the hints! I looked at my php packages and found out that I did not install php-posix (I do not have php-process in SUSE yast management system.) I have it installed. I now rerun the "cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator" and I could see the job7 terminating now due to an error. 

Thanks,
Stacy

On Thu, Sep 29, 2011 at 10:42 PM, Evan Ernst <[hidden email]> wrote:
In Centos, Fedora, and probably RHEL, I believe you need to install the php-process package (yum install php-process) to get the posix functionality. 

Evan


On Thu, Sep 29, 2011 at 10:10 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


------------------------------------------------------------------------------
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.
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------------------------------------------------------------------------------
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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------------------------------------------------------------------------------
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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------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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Re: problems about loading Load OBO Relationship Ontology into Chado using Tripal

Stephen Ficklin-2
Hi Stacy,

Did installing the php-posix module also allow you to install the reslationship OBO?

Stephen

On 9/29/2011 9:20 PM, stacy xu wrote:
Hi, Evan,

Thanks for the hints! I looked at my php packages and found out that I did not install php-posix (I do not have php-process in SUSE yast management system.) I have it installed. I now rerun the "cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator" and I could see the job7 terminating now due to an error. 

Thanks,
Stacy

On Thu, Sep 29, 2011 at 10:42 PM, Evan Ernst <[hidden email]> wrote:
In Centos, Fedora, and probably RHEL, I believe you need to install the php-process package (yum install php-process) to get the posix functionality. 

Evan


On Thu, Sep 29, 2011 at 10:10 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


------------------------------------------------------------------------------
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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------------------------------------------------------------------------------
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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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------------------------------------------------------------------------------
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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------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2


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------------------------------------------------------------------------------
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threats, fraudulent activity, and more. Splunk takes this data and makes
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Re: Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

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

I have "php-posix" installed now after seeing Evan's message and can see the updated status now. And I rerun the "relationship" ontology jobs to find that it takes a long long long time for "Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT" while when installing "features", it seems that tripal is looking for local file and it works successfully. I am using proxy in my server network for both ftp and http. Is there any way to configure proxy set up to connect to the internet using Tripal?

By the way, please see the error message when installing "relationship" ontology manually
"
Calling: tripal_cv_load_obo_v1_2_id(2, 14)
Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT

PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 467 bytes) in /var/www/drupal6/includes/database.pgsql.inc on line 364
"

And I did go into php.ini to enlarge my php memory:
"
;;;;;;;;;;;;;;;;;;;
; Resource Limits ;
;;;;;;;;;;;;;;;;;;;

max_execution_time = 60     ; Maximum execution time of each script, in seconds
max_input_time = 120    ; Maximum amount of time each script may spend parsing request data
;max_input_nesting_level = 64 ; Maximum input variable nesting level
memory_limit = 128M      ; Maximum amount of memory a script may consume (128MB)
"

Thanks,
Stacy

On Thu, Sep 29, 2011 at 10:54 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

The job is most likely not running.   Tripal does not poll the system to see when a process completes or not.  And if a job fails unexpectedly and stops execution Tripal won't know about it until it tries to run the next round of jobs.  This will happen the next time the cron fires (if you have the cron setup) or when you try to run a job manually from the command-line (like you did).  But, in your case the 'posix_kill' which is part of the process that checks for running jobs, is not running so Tripal is not able to update the status of the job.

I also forgot to respond to another of your questions about changing the priority of a users job. This hasn't been worked into the jobs scheduler just yet.  The place-holder is there for it.  And in the API there is an argument for it.   But we haven't programmed in the ability to set or change the priority of a job.   This wouldn't be too hard a thing to do, it just hasn't been a high priority yet.  If you need this functionality let me know and we can see about bumping this up on our TODO list.

Stephen




On 9/29/2011 10:37 AM, stacy xu wrote:
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


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



------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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Re: Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

stacy xu
I am using drupal 6.22 by the way. I am not sure but it may also be drupal's problem?

On Fri, Sep 30, 2011 at 9:40 AM, stacy xu <[hidden email]> wrote:
Hi, Stephen, 

I have "php-posix" installed now after seeing Evan's message and can see the updated status now. And I rerun the "relationship" ontology jobs to find that it takes a long long long time for "Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT" while when installing "features", it seems that tripal is looking for local file and it works successfully. I am using proxy in my server network for both ftp and http. Is there any way to configure proxy set up to connect to the internet using Tripal?

By the way, please see the error message when installing "relationship" ontology manually
"
Calling: tripal_cv_load_obo_v1_2_id(2, 14)
Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT

PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 467 bytes) in /var/www/drupal6/includes/database.pgsql.inc on line 364
"

And I did go into php.ini to enlarge my php memory:
"
;;;;;;;;;;;;;;;;;;;
; Resource Limits ;
;;;;;;;;;;;;;;;;;;;

max_execution_time = 60     ; Maximum execution time of each script, in seconds
max_input_time = 120    ; Maximum amount of time each script may spend parsing request data
;max_input_nesting_level = 64 ; Maximum input variable nesting level
memory_limit = 128M      ; Maximum amount of memory a script may consume (128MB)
"

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:54 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

The job is most likely not running.   Tripal does not poll the system to see when a process completes or not.  And if a job fails unexpectedly and stops execution Tripal won't know about it until it tries to run the next round of jobs.  This will happen the next time the cron fires (if you have the cron setup) or when you try to run a job manually from the command-line (like you did).  But, in your case the 'posix_kill' which is part of the process that checks for running jobs, is not running so Tripal is not able to update the status of the job.

I also forgot to respond to another of your questions about changing the priority of a users job. This hasn't been worked into the jobs scheduler just yet.  The place-holder is there for it.  And in the API there is an argument for it.   But we haven't programmed in the ability to set or change the priority of a job.   This wouldn't be too hard a thing to do, it just hasn't been a high priority yet.  If you need this functionality let me know and we can see about bumping this up on our TODO list.

Stephen




On 9/29/2011 10:37 AM, stacy xu wrote:
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


------------------------------------------------------------------------------
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
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-tripal




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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Re: Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

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

You're definitely hitting a PHP configuration error with "allowed memory size" error.   I'm not familiar with SUSE but with Ubuntu there are two php.ini files. One for the Apache webserver and one for the command-line.  You have to set the memory limit in both of the php.ini files.  Perhaps SUSE has a similar setup?

There is currently no way to configure Tripal to use a proxy when trying to connect to the internet.  We've never hit that particular issue before.   If you cannot get around the connectivity problems, then you can download the OBO files manually on another machine and transfer them to your server.   Then when you go to import the ontologies you can specify the file path and file name rather than use the drop down menu.  

Stephen

On 9/29/2011 9:40 PM, stacy xu wrote:
Hi, Stephen, 

I have "php-posix" installed now after seeing Evan's message and can see the updated status now. And I rerun the "relationship" ontology jobs to find that it takes a long long long time for "Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT" while when installing "features", it seems that tripal is looking for local file and it works successfully. I am using proxy in my server network for both ftp and http. Is there any way to configure proxy set up to connect to the internet using Tripal?

By the way, please see the error message when installing "relationship" ontology manually
"
Calling: tripal_cv_load_obo_v1_2_id(2, 14)
Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT

PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 467 bytes) in /var/www/drupal6/includes/database.pgsql.inc on line 364
"

And I did go into php.ini to enlarge my php memory:
"
;;;;;;;;;;;;;;;;;;;
; Resource Limits ;
;;;;;;;;;;;;;;;;;;;

max_execution_time = 60     ; Maximum execution time of each script, in seconds
max_input_time = 120    ; Maximum amount of time each script may spend parsing request data
;max_input_nesting_level = 64 ; Maximum input variable nesting level
memory_limit = 128M      ; Maximum amount of memory a script may consume (128MB)
"

Thanks,
Stacy

On Thu, Sep 29, 2011 at 10:54 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

The job is most likely not running.   Tripal does not poll the system to see when a process completes or not.  And if a job fails unexpectedly and stops execution Tripal won't know about it until it tries to run the next round of jobs.  This will happen the next time the cron fires (if you have the cron setup) or when you try to run a job manually from the command-line (like you did).  But, in your case the 'posix_kill' which is part of the process that checks for running jobs, is not running so Tripal is not able to update the status of the job.

I also forgot to respond to another of your questions about changing the priority of a users job. This hasn't been worked into the jobs scheduler just yet.  The place-holder is there for it.  And in the API there is an argument for it.   But we haven't programmed in the ability to set or change the priority of a job.   This wouldn't be too hard a thing to do, it just hasn't been a high priority yet.  If you need this functionality let me know and we can see about bumping this up on our TODO list.

Stephen




On 9/29/2011 10:37 AM, stacy xu wrote:
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


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




------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
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Re: Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

stacy xu
Aha, it works for installing from local file! I guess my internet connection has been a problem. (I can download from internet browser, but somehow when I have "download" script it does not always work.) But it is great that local installation is enabled in Tripal!

Thanks a lot,
Stacy

On Fri, Sep 30, 2011 at 10:27 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

You're definitely hitting a PHP configuration error with "allowed memory size" error.   I'm not familiar with SUSE but with Ubuntu there are two php.ini files. One for the Apache webserver and one for the command-line.  You have to set the memory limit in both of the php.ini files.  Perhaps SUSE has a similar setup?

There is currently no way to configure Tripal to use a proxy when trying to connect to the internet.  We've never hit that particular issue before.   If you cannot get around the connectivity problems, then you can download the OBO files manually on another machine and transfer them to your server.   Then when you go to import the ontologies you can specify the file path and file name rather than use the drop down menu.  

Stephen


On 9/29/2011 9:40 PM, stacy xu wrote:
Hi, Stephen, 

I have "php-posix" installed now after seeing Evan's message and can see the updated status now. And I rerun the "relationship" ontology jobs to find that it takes a long long long time for "Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT" while when installing "features", it seems that tripal is looking for local file and it works successfully. I am using proxy in my server network for both ftp and http. Is there any way to configure proxy set up to connect to the internet using Tripal?

By the way, please see the error message when installing "relationship" ontology manually
"
Calling: tripal_cv_load_obo_v1_2_id(2, 14)
Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT

PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 467 bytes) in /var/www/drupal6/includes/database.pgsql.inc on line 364
"

And I did go into php.ini to enlarge my php memory:
"
;;;;;;;;;;;;;;;;;;;
; Resource Limits ;
;;;;;;;;;;;;;;;;;;;

max_execution_time = 60     ; Maximum execution time of each script, in seconds
max_input_time = 120    ; Maximum amount of time each script may spend parsing request data
;max_input_nesting_level = 64 ; Maximum input variable nesting level
memory_limit = 128M      ; Maximum amount of memory a script may consume (128MB)
"

Thanks,
Stacy

On Thu, Sep 29, 2011 at 10:54 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

The job is most likely not running.   Tripal does not poll the system to see when a process completes or not.  And if a job fails unexpectedly and stops execution Tripal won't know about it until it tries to run the next round of jobs.  This will happen the next time the cron fires (if you have the cron setup) or when you try to run a job manually from the command-line (like you did).  But, in your case the 'posix_kill' which is part of the process that checks for running jobs, is not running so Tripal is not able to update the status of the job.

I also forgot to respond to another of your questions about changing the priority of a users job. This hasn't been worked into the jobs scheduler just yet.  The place-holder is there for it.  And in the API there is an argument for it.   But we haven't programmed in the ability to set or change the priority of a job.   This wouldn't be too hard a thing to do, it just hasn't been a high priority yet.  If you need this functionality let me know and we can see about bumping this up on our TODO list.

Stephen




On 9/29/2011 10:37 AM, stacy xu wrote:
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


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





------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
Gmod-tripal mailing list
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|

Re: Fwd: problems about loading Load OBO Relationship Ontology into Chado using Tripal

stacy xu
Hi, Stephen,

And to reply to your previous email. There are also 2 php.ini in SUSE and it turns out both needs to be modified for "Resource_limit" variable. Appreciate your help!

Thanks,
Stacy

On Fri, Sep 30, 2011 at 10:36 AM, stacy xu <[hidden email]> wrote:
Aha, it works for installing from local file! I guess my internet connection has been a problem. (I can download from internet browser, but somehow when I have "download" script it does not always work.) But it is great that local installation is enabled in Tripal!

Thanks a lot,
Stacy


On Fri, Sep 30, 2011 at 10:27 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

You're definitely hitting a PHP configuration error with "allowed memory size" error.   I'm not familiar with SUSE but with Ubuntu there are two php.ini files. One for the Apache webserver and one for the command-line.  You have to set the memory limit in both of the php.ini files.  Perhaps SUSE has a similar setup?

There is currently no way to configure Tripal to use a proxy when trying to connect to the internet.  We've never hit that particular issue before.   If you cannot get around the connectivity problems, then you can download the OBO files manually on another machine and transfer them to your server.   Then when you go to import the ontologies you can specify the file path and file name rather than use the drop down menu.  

Stephen


On 9/29/2011 9:40 PM, stacy xu wrote:
Hi, Stephen, 

I have "php-posix" installed now after seeing Evan's message and can see the updated status now. And I rerun the "relationship" ontology jobs to find that it takes a long long long time for "Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT" while when installing "features", it seems that tripal is looking for local file and it works successfully. I am using proxy in my server network for both ftp and http. Is there any way to configure proxy set up to connect to the internet using Tripal?

By the way, please see the error message when installing "relationship" ontology manually
"
Calling: tripal_cv_load_obo_v1_2_id(2, 14)
Downloading URL http://www.obofoundry.org/ro/ro.obo, saving to /tmp/obo_1kDiJT

PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 467 bytes) in /var/www/drupal6/includes/database.pgsql.inc on line 364
"

And I did go into php.ini to enlarge my php memory:
"
;;;;;;;;;;;;;;;;;;;
; Resource Limits ;
;;;;;;;;;;;;;;;;;;;

max_execution_time = 60     ; Maximum execution time of each script, in seconds
max_input_time = 120    ; Maximum amount of time each script may spend parsing request data
;max_input_nesting_level = 64 ; Maximum input variable nesting level
memory_limit = 128M      ; Maximum amount of memory a script may consume (128MB)
"

Thanks,
Stacy

On Thu, Sep 29, 2011 at 10:54 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

The job is most likely not running.   Tripal does not poll the system to see when a process completes or not.  And if a job fails unexpectedly and stops execution Tripal won't know about it until it tries to run the next round of jobs.  This will happen the next time the cron fires (if you have the cron setup) or when you try to run a job manually from the command-line (like you did).  But, in your case the 'posix_kill' which is part of the process that checks for running jobs, is not running so Tripal is not able to update the status of the job.

I also forgot to respond to another of your questions about changing the priority of a users job. This hasn't been worked into the jobs scheduler just yet.  The place-holder is there for it.  And in the API there is an argument for it.   But we haven't programmed in the ability to set or change the priority of a job.   This wouldn't be too hard a thing to do, it just hasn't been a high priority yet.  If you need this functionality let me know and we can see about bumping this up on our TODO list.

Stephen




On 9/29/2011 10:37 AM, stacy xu wrote:
Opps. I forgot to CC the group.

---------- Forwarded message ----------
From: stacy xu <[hidden email]>
Date: Thu, Sep 29, 2011 at 10:36 PM
Subject: Re: [Gmod-tripal] problems about loading Load OBO Relationship Ontology into Chado using Tripal
To: Stephen Ficklin <[hidden email]>


Hi, Stephen,

Thanks for quick reply and pointing out the problem! I am using Suse 10.0 and PHP 5.2.5 (installed from Yast) with only limited number of php packages. I am not around my server now, but I will check the write permission of my /tmp directory earliest tomorrow morning. 

In that case is there any way for me to kill that process? In the last tab of "job 7" from my previous email, I only see "Rerun" and "view" link, but not "cancel"..

Thanks,
Stacy


On Thu, Sep 29, 2011 at 10:10 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Stacy,

Thanks for your detailed explanation of the problem! I've never seen this error before.  What version of Unix/Linux and PHP are you using? 

The error message "supplied argument is not a valid stream" is ocurring when the the source code tries to download the OBO relationship file from the web and store it in the system-wide temporary directory (i.e. /tmp on Linux).  After the file gets downloaded the parser then opens the OBO file and parses it for loading.   The problem you are encountering that it can't open a file in the temp directory.   All users typically have read/write access to /tmp.  So, it's odd you would be having that problem.  So, I just want to check on your OS type and version.

But I'm wondering if the problem is with PHP because of the second error you encountered when you tried to rerun the job from the command-line.    'posix_kill' is a PHP function in version 4 and 5 so it is odd you would get a message that you are making a call to an "undefined function". 

Stephen


On 9/29/2011 6:05 AM, stacy xu wrote:
Hi, everyone,

I was installing Tripal to my 64 bit linux today and everything went smoothly thanks to the detailed tutorial and documentations. However, I got trapped in the last stage of loading Chado schema into Chado. I am "adding/updating ontology with OBO file" in the sequence of "Chado Feature, Relationship, Sequence, Gene Ontology". Chado Feature was loaded within one minute, however, it took forever to load "relationship" into Chado. I went to the reports page to find out the errors: 

php09/29/2011 - 15:03fread(): supplied argument is not a valid stream ...stacy
php09/29/2011 - 15:03feof(): supplied argument is not a valid stream ...stacy

Or

fread(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 69.
feof(): supplied argument is not a valid stream resource in/srv/www/htdocs/drupal6/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 68.

I went to the "jobs" panel under Tripal and the table below:
7 stacy Load OBO Relationship Ontology Submit Date: Thu, 09/29/2011 - 14:40 
Start Time: Thu, 09/29/2011 - 14:45 
End Time:
10 0% Running Re-run
View
Here by copying and pasting, I can see the table with "Rerun" and "View" options as the last tab. However, on my Chrome browser, the last column of this table was truncated and I can only view up to part of "Running" tab.. I went into my Linux console to run "
  cd /var/www; php ./sites/all/modules/tripal-6.x-0.3.1b/tripal_core/tripal_launch_jobs.php administrator
" according to tutorial's webpage, and I got the error as below:

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

I am using postgres 9.0.4 and drupal 6. Could anyone suggest what is happening and how I can resolve it? Thanks!

By the way, does anyone know how to increase a user's running priority?

Thanks,
Stacy


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






------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2dcopy2
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal