Resource temporarily unavailable

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Resource temporarily unavailable

Durdevic, Marija

Dear developers,

 

From time to time I have issue on my Galaxy server. The problem is when job is done and results has to be written to the database something happened. The error message is: “/home/data/galaxy_database/files/024/dataset_24790.dat: Resource temporarily unavailable” where “/home/data/galaxy_database/files/024/dataset_24790.dat” is path to the output file. Although it produced reasonable output the job is shown as failed.

 

I am running galaxy over Slurm and we use NFS for connection with storage.  

 

Do anyone have idea what can be possible reason for such error?

 

Thanks in advance.

 

Best,

Marija


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Re: Resource temporarily unavailable

Nicola Soranzo-2
Hi Marija,
you can try to set

retry_job_output_collection = 3

in your config/galaxy.ini file and see if that helps.

Cheers,
Nicola

On 23/01/17 09:47, Durdevic, Marija wrote:

Dear developers,

 

From time to time I have issue on my Galaxy server. The problem is when job is done and results has to be written to the database something happened. The error message is: “/home/data/galaxy_database/files/024/dataset_24790.dat: Resource temporarily unavailable” where “/home/data/galaxy_database/files/024/dataset_24790.dat” is path to the output file. Although it produced reasonable output the job is shown as failed.

 

I am running galaxy over Slurm and we use NFS for connection with storage.  

 

Do anyone have idea what can be possible reason for such error?

 

Thanks in advance.

 

Best,

Marija



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/mailinglists/


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Re: Resource temporarily unavailable

Durdevic, Marija

Thank you Nicola,

 

it worked when I put retry_job_output_collection = 10, but only for some tools. For some of them is still the same. Especially if I run it on a data collections.

And if I run the tool locally , not over the Slurm, it worked well.

 

I am not sure if the problem is with Slurm maybe or some Galaxy-Slurm configuration?

 

Best,

Marija

 

Von: Nicola Soranzo [[hidden email]] Im Auftrag von Nicola Soranzo
Gesendet: Montag, 23. Jänner 2017 17:17
An: Durdevic, Marija; [hidden email]
Betreff: Re: [galaxy-dev] Resource temporarily unavailable

 

Hi Marija,
you can try to set

retry_job_output_collection = 3

in your config/galaxy.ini file and see if that helps.

Cheers,
Nicola

On 23/01/17 09:47, Durdevic, Marija wrote:

Dear developers,

 

From time to time I have issue on my Galaxy server. The problem is when job is done and results has to be written to the database something happened. The error message is: “/home/data/galaxy_database/files/024/dataset_24790.dat: Resource temporarily unavailable” where “/home/data/galaxy_database/files/024/dataset_24790.dat” is path to the output file. Although it produced reasonable output the job is shown as failed.

 

I am running galaxy over Slurm and we use NFS for connection with storage.  

 

Do anyone have idea what can be possible reason for such error?

 

Thanks in advance.

 

Best,

Marija



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/
 
To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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