[Iplant-api-dev] Creating a system/app/job combo using CLI/FORK scheduler with AGAVE

[Matthew Vaughn]

I'll post an example tomorrow that we've been using for the Arabidopsis Information Portal project (I'm out of the office today)

Matt

--

Matthew W. Vaughn, Ph.D.
Director, Life Sciences Computing
Texas Advanced Computing Center
The University of Texas at Austin
(949) 436-6642


________________________________________
From: iplant-api-dev-bounces at iplantcollaborative.org [iplant-api-dev-bounces at iplantcollaborative.org] on behalf of Brian Corrie [bcorrie at sfu.ca]
Sent: Thursday, July 24, 2014 5:10 PM
To: Matthew Vaughn
Cc: Discussion of iPlant API development
Subject: [Iplant-api-dev] Creating a system/app/job combo using CLI/FORK        scheduler with AGAVE

Hello All,

I am trying to create a AGAVE system/app/job combination that uses the
FORK scheduler and the CLI executionType. I am using the AGAVE CLI
interface.

I am having trouble finding an example on the web site and I can't seem
to find the right combination of system, app, and job configurations.

Does anyone have such an example? My problems revolve around queues and
jobs submission. One fundamental question I have is. does a system that
uses CLI/FORK need a queue? I wouldn't think so, but thought I would check.

Here is my problem:

When I create a System without a queue, create an App that uses that
System, and submit a Job using that App, I get the following response
from the job submission:

Invalid nodeCount. No queue found on bugaboo-cli-bcorrie that support
jobs with 1 nodes.

So it looks like I need a queue.

If I create a system with a queue named default, when I submit a job the
job is successfully created but the submission phase of the job fails
three times and then the overall job fails. I am not sure what is wrong
at the submission phase.

bcorrie at itivm6$ jobs-history 0001406239429461-5056a550b8-0001-007
Job accepted and queued for submission.
Skipping staging. No input data associated with this job.
Preparing job for submission.
Attempt 1 to submit job
Attempt 1 failed to submit job. Failed to submit cli job.
Attempt 2 to submit job
Attempt 2 failed to submit job. Failed to submit cli job.
Attempt 3 to submit job
Attempt 3 failed to submit job. Failed to submit cli job.
Cleaning up remote work directory.
Completed cleaning up remote work directory.
Unable to submit job after 3 attempts. Job cancelled.

Does anyone have any advice or experience. Note, I have no problem
whatsoever running jobs as an HPC job using queues and the PBS scheduler
using AGAVE, it is the "simple" CLI/FORK jobs that are getting me.

I suspect I am missing something simple???

Thanks in advance for any help...

Brian






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