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
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
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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 [mailto:nicola.soranzo@gmail.com] Im Auftrag von Nicola Soranzo Gesendet: Montag, 23. Jänner 2017 17:17 An: Durdevic, Marija; galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org 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
___________________________________________________________
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and other Galaxy lists, please use the interface at:
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