[api-dev] error accessing shared files

Thu Mar 10 22:25:51 MST 2016

Hi Jon-

I was seeing those this afternoon after a user said that is what he is getting. There are some real data transfer problems. Matt and Nirav are working on it. We ran some tests this afternoon and transfer was very, very slow with irods. Hopefully this problem can be traced soon.

Roger

--
Roger A Barthelson, PhD
CyVerse
BIO5/University of Arizona
rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
520-977-5249<tel://520-977-5249>

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On March 10, 2016 at 10:19:58 PM, Duvick, Jonathan P [GDCBS] (jduvick at iastate.edu<mailto:jduvick at iastate.edu>) wrote:

Hi, still getting consistent errors, but now the  webhook returns "FAILED unable to stage inputs for job after 3 attempts".
Example:
3645922279708814875-242ac1110-0001-007
Thanks,
Jon
Sent from my iPad

On Mar 10, 2016, at 4:29 PM, John Fonner <jfonner at tacc.utexas.edu<mailto:jfonner at tacc.utexas.edu>> wrote:

Hi Cornel and Jon,

I suspect both of these errors were transient.  Are you still getting them?

I don't know what might have caused the "do not have permission" error, but i am able to pull down the file you referenced.  Jon, I've seen this error before when Agave can't reach the Datastore.  Let us know if you keep seeing this.  There was a window a couple of weeks ago where there was some lag in the connection between Agave and the Datastore that was enough to cause some timeouts.  In response, I believe they updated things to be more tolerant of latency.  So if it's an ongoing issue, we definitely want to know.

Thanks,
John

________________________________________
From: api-dev <api-dev-bounces at maillist.cyverse.org<mailto:api-dev-bounces at maillist.cyverse.org>> on behalf of Duvick, Jonathan P [GDCBS] <jduvick at iastate.edu<mailto:jduvick at iastate.edu>>
Sent: Thursday, March 10, 2016 11:32 AM
To: John Fonner
Cc: Volker Brendel; Discussion of CyVerse API development
Subject: Re: [api-dev] error accessing shared files

Similarly for me, job submissions and API calls are returning various errors, including:

{"status":"error","message":"Unable to locate application assets on remote system. Remote server responded with: Failed to authenticate to remote server.","version":"2.1.6-re4c012a"}

and on a job that submitted successfully:

"Attempt 3 failed to stage job inputs. Failed to transfer input /jduvick/xgdbvm/tmp/GDB014_hpcs/SCFDIR/GDB014gdna.fa "

 (although this file exists)

-Jon Duvick
________________________________________
From: api-dev <api-dev-bounces at maillist.cyverse.org<mailto:api-dev-bounces at maillist.cyverse.org>> on behalf of Ghiban, Cornel <ghiban at cshl.edu<mailto:ghiban at cshl.edu>>
Sent: Thursday, March 10, 2016 9:20 AM
To: Duvick, Jonathan P [GDCBS]
Cc: Discussion of CyVerse API development
Subject: [api-dev] error accessing shared files

Hi,

I'm seeing errors like these and not sure this is an Agave or iRODS
(multiple tries still give the same errors):

{"status":"error","message":"You do not have permission to access this
the input file or directory at
/shared/iplant_DNA_subway/genomes/zea_mays/annotation.gtf","version":"2
.1.6-re4c012a"}

{"status":"error","message":"You do not have permission to access this
the input file or directory at
/shared/iplant_DNA_subway/genomes/homo_sapiens/annotation.gtf","version
":"2.1.6-re4c012a"}

{"status":"error","message":"You do not have permission to access this
the input file or directory at
/shared/iplant_DNA_subway/genomes/caenorhabditis_elegans/annotation.gtf
","version":"2.1.6-re4c012a"}

{"status":"error","message":"You do not have permission to access this
the input file or directory at
/shared/iplant_DNA_subway/genomes/brassica_rapaFPsc/annotation.gff3","v
ersion":"2.1.6-re4c012a"}

{"status":"error","message":"You do not have permission to access this
the input file or directory at
/shared/iplant_DNA_subway/genomes/rattus_norvegicus/annotation.gtf","ve
rsion":"2.1.6-re4c012a"}

These files are public in the /shared/ folder.

Thanks,
Cornel

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