Re: [Gmod-tripal] setting up Tripal and memory issue

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Re: [Gmod-tripal] setting up Tripal and memory issue

Block,Andrew
Hi Stephen, Naama, Sook, and GMOD,

I was able to update the OBO file and load OBO Gene Ontology.  I followed your instructions on how to remove the unwanted species.  When I synced the species, my species of interests were skipped.  I believe this has to deal with error in the next paragraph.  

I went to the organism tab at the top of the page to look at the results, but the tab and several other were missing.  I know I had the tabs before the update.  Every page contained a long list of error messages following the same format but with different file names and paths.  I have gone looking for these and they are not present.  Here is the first complete message and a list of the different files that were missing:

warning: include(./sites/all/modules/tripal-6.x-0.3.1b/tripal/tripal_feature/tripal_organism_feature_counts.tpl.php) [function.include]: failed to open stream: No such file or directory in /Users/andrew/Sites/drupal/includes/theme.inc on line 1079.

warning: include() [function.include]: Failed opening './sites/all/modules/tripal-6.x-0.3.1b/tripal/tripal_feature/tripal_organism_feature_counts.tpl.php' for inclusion (include_path='.:') in /Users/andrew/Sites/drupal/includes/theme.inc on line 1079.


/tripal_feature/tripal_organism_feature_browser.tpl.php, tripal_library/tripal_organism_libraries.tpl.php, /tripal_stock/tripal_organism_stocks.tpl.php, /tripal_feature/tripal_organism_feature_counts.tpl.php, /tripal_feature/tripal_organism_feature_browser.tpl.php, /Tripal_library/tripal_organism_libraries.tpl.php, and /tripal_stock/tripal_organism_stocks.tpl.php  


The Natural Diversity module is what I am looking for.  We do not need all of the nd_epriment_protocol section, but all of the other tables I will implement.  I am confused on the method of  implementation.  The GitHub code has not be update over two years, so I do not know if the code still works.  Should I use the custom tables module to create the tables?  How do you integrate the new tables into Tripal?

I would like to receive some in-depth training for GMOD, but I am not able to go to the conference in the UK.  The spring training and summers school looks great, but no information about this year yet.  What would be the best way to receive some training or is there any information about the schools?

Thank you,

Andrew Block

Research Associate
-------------------------------------------------------
Colorado State University
Dept. of Biochemistry & Molecular Biology
Molecular and Radiological Biosciences 139
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
-------------------------------------------------------
(970) 491-0271    Lab
-------------------------------------------------------


From: Stephen Ficklin [[hidden email]]
Sent: Wednesday, February 13, 2013 2:41 PM
To: Block,Andrew
Cc: [hidden email]
Subject: Re: [Gmod-tripal] setting up Tripal and memory issue

HI Andrew,

It just so happens that I just pushed up a fix to the OBO loader last night to address memory issues.  Loading the GO should now maintain a constant memory usage, which I believe is within the restrictions you have in your php.ini file for the allowed memory size.  Can you pull the most recent code and see if that fixes your problem?  If you change directories to where you have the Tripal module installed and run 'git pull' it should update the code for you.

Can you tell me on what page(s) you are seeing the error message about the form? 

I'm going to answer your question about mutants in a separate email and CC the gmod-schema mailing list.

Thanks,
Stephen

On 2/13/2013 4:00 PM, Block,Andrew wrote:
Hello Trupal,

I have installed Tripal and am starting to set up our database.  I am creating a website for RNA dependent RNA polymerases (RdRp) with many different mutants for different viruses species.  The goal of the database is to analysis structure, sequences, & molecular data and keep track of storage through a webpage.

When I run the "Load OBO Gene Ontology" using cron I get an error.  I was able to instal other OBOs after this one, but for some reason I can not install this OBO.  I went into the obo_loader.php file to change line 564, but could not see how to change the file.  How would I fix this problem?

The error code is: Calling: tripal_cv_load_obo_v1_2_id(4, 15)
Downloading URL http://www.geneontology.org/ontology/gene_ontology.obo, saving to /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx
Opening File /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx

Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 71 bytes) in /Users/andrew/Sites/drupal/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php on line 564

I also keep getting: Invalid argument supplied for foreach() in /Users/andrew/Sites/drupal/includes/form.inc on line 1217.  Does anybody know about this error?

As I stated before, we will have many mutants for individual species.  Looking at several websites that use GMOD, there does not seem to be a way to have different mutants just version of the same species.  Ho would I set up Tripal/Chado to allow for mutants?  How would I remove the other species that are found in Tripal?

Thank you,

Andrew Block

Research Associate
-------------------------------------------------------
Colorado State University
Dept. of Biochemistry & Molecular Biology
Molecular and Radiological Biosciences 139
1870 Campus Delivery
Colorado State University
Ft. Collins, CO  80523-1870
-------------------------------------------------------
(970) 491-0271    Lab
-------------------------------------------------------



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Re: [Gmod-tripal] setting up Tripal and memory issue

Scott Cain
Hi Andrew,

You're concerned about the Chado github repository?  It isn't used;
that repository is leftover from a failed attempt to move from svn at
sourceforge, which is where current development still takes place.
There was a Chado release in December (1.23) but the schema hasn't
changed since the 1.2 release a few years ago.

About the summer school--info should be coming soon, but there are
still logistics to work out.

Scott


On Fri, Feb 15, 2013 at 1:37 PM, Block,Andrew
<[hidden email]> wrote:

> Hi Stephen, Naama, Sook, and GMOD,
>
> I was able to update the OBO file and load OBO Gene Ontology.  I followed
> your instructions on how to remove the unwanted species.  When I synced the
> species, my species of interests were skipped.  I believe this has to deal
> with error in the next paragraph.
>
> I went to the organism tab at the top of the page to look at the results,
> but the tab and several other were missing.  I know I had the tabs before
> the update.  Every page contained a long list of error messages following
> the same format but with different file names and paths.  I have gone
> looking for these and they are not present.  Here is the first complete
> message and a list of the different files that were missing:
>
> warning:
> include(./sites/all/modules/tripal-6.x-0.3.1b/tripal/tripal_feature/tripal_organism_feature_counts.tpl.php)
> [function.include]: failed to open stream: No such file or directory in
> /Users/andrew/Sites/drupal/includes/theme.inc on line 1079.
>
> warning: include() [function.include]: Failed opening
> './sites/all/modules/tripal-6.x-0.3.1b/tripal/tripal_feature/tripal_organism_feature_counts.tpl.php'
> for inclusion (include_path='.:') in
> /Users/andrew/Sites/drupal/includes/theme.inc on line 1079.
>
>
> /tripal_feature/tripal_organism_feature_browser.tpl.php,
> tripal_library/tripal_organism_libraries.tpl.php,
> /tripal_stock/tripal_organism_stocks.tpl.php,
> /tripal_feature/tripal_organism_feature_counts.tpl.php,
> /tripal_feature/tripal_organism_feature_browser.tpl.php,
> /Tripal_library/tripal_organism_libraries.tpl.php, and
> /tripal_stock/tripal_organism_stocks.tpl.php
>
>
> The Natural Diversity module is what I am looking for.  We do not need all
> of the nd_epriment_protocol section, but all of the other tables I will
> implement.  I am confused on the method of  implementation.  The GitHub code
> has not be update over two years, so I do not know if the code still works.
> Should I use the custom tables module to create the tables?  How do you
> integrate the new tables into Tripal?
>
> I would like to receive some in-depth training for GMOD, but I am not able
> to go to the conference in the UK.  The spring training and summers school
> looks great, but no information about this year yet.  What would be the best
> way to receive some training or is there any information about the schools?
>
> Thank you,
>
> Andrew Block
>
> Research Associate
> -------------------------------------------------------
> Colorado State University
> Dept. of Biochemistry & Molecular Biology
> Molecular and Radiological Biosciences 139
> 1870 Campus Delivery
> Colorado State University
> Ft. Collins, CO  80523-1870
> -------------------------------------------------------
> (970) 491-0271    Lab
> [hidden email]
> -------------------------------------------------------
>
> ________________________________
> From: Stephen Ficklin [[hidden email]]
> Sent: Wednesday, February 13, 2013 2:41 PM
> To: Block,Andrew
> Cc: [hidden email]
> Subject: Re: [Gmod-tripal] setting up Tripal and memory issue
>
> HI Andrew,
>
> It just so happens that I just pushed up a fix to the OBO loader last night
> to address memory issues.  Loading the GO should now maintain a constant
> memory usage, which I believe is within the restrictions you have in your
> php.ini file for the allowed memory size.  Can you pull the most recent code
> and see if that fixes your problem?  If you change directories to where you
> have the Tripal module installed and run 'git pull' it should update the
> code for you.
>
> Can you tell me on what page(s) you are seeing the error message about the
> form?
>
> I'm going to answer your question about mutants in a separate email and CC
> the gmod-schema mailing list.
>
> Thanks,
> Stephen
>
> On 2/13/2013 4:00 PM, Block,Andrew wrote:
>
> Hello Trupal,
>
> I have installed Tripal and am starting to set up our database.  I am
> creating a website for RNA dependent RNA polymerases (RdRp) with many
> different mutants for different viruses species.  The goal of the database
> is to analysis structure, sequences, & molecular data and keep track of
> storage through a webpage.
>
> When I run the "Load OBO Gene Ontology" using cron I get an error.  I was
> able to instal other OBOs after this one, but for some reason I can not
> install this OBO.  I went into the obo_loader.php file to change line 564,
> but could not see how to change the file.  How would I fix this problem?
>
> The error code is: Calling: tripal_cv_load_obo_v1_2_id(4, 15)
> Downloading URL http://www.geneontology.org/ontology/gene_ontology.obo,
> saving to
> /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx
> Opening File
> /private/var/folders/_w/wff08fgx7pxbmkzkl24z9gh00000gp/T/obo_8Epunx
>
> Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to
> allocate 71 bytes) in
> /Users/andrew/Sites/drupal/sites/all/modules/tripal-6.x-0.3.1b/tripal_cv/obo_loader.php
> on line 564
>
> I also keep getting: Invalid argument supplied for foreach() in
> /Users/andrew/Sites/drupal/includes/form.inc on line 1217.  Does anybody
> know about this error?
>
> As I stated before, we will have many mutants for individual species.
> Looking at several websites that use GMOD, there does not seem to be a way
> to have different mutants just version of the same species.  Ho would I set
> up Tripal/Chado to allow for mutants?  How would I remove the other species
> that are found in Tripal?
>
> Thank you,
>
> Andrew Block
>
> Research Associate
> -------------------------------------------------------
> Colorado State University
> Dept. of Biochemistry & Molecular Biology
> Molecular and Radiological Biosciences 139
> 1870 Campus Delivery
> Colorado State University
> Ft. Collins, CO  80523-1870
> -------------------------------------------------------
> (970) 491-0271    Lab
> [hidden email]
> -------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
>
>
>
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>
>
>
> ------------------------------------------------------------------------------
> The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
> is your hub for all things parallel software development, from weekly
> thought
> leadership blogs to news, videos, case studies, tutorials, tech docs,
> whitepapers, evaluation guides, and opinion stories. Check out the most
> recent posts - join the conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
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> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
is your hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials, tech docs,
whitepapers, evaluation guides, and opinion stories. Check out the most
recent posts - join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
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