[Iplant-api-dev] DO NOT REPLY "error when using CloudStructure app"

[Wang, Liya]

Looks like Foundation API apps are failing to submit jobs to Lonestar. Several users experienced this and I got the similar errors below. Liya

apps-v1/jobs/66522 FAILED re-poll: 5s
Failed to submit job 66522: java.io.IOException: Error completing remote execution after:
s

On Jan 23, 2015, at 3:00 PM, Nicole Hopkins <nicole at iplantcollaborative.org<mailto:nicole at iplantcollaborative.org>> wrote:

Liya can you take a look at this?

---------- Forwarded message ----------
From: <ask at iplantcollaborative.org<mailto:ask at iplantcollaborative.org>>
Date: Fri, Jan 23, 2015 at 1:01 PM
Subject: DO NOT REPLY "error when using CloudStructure app"
To: nicole at iplantcollaborative.org<mailto:nicole at iplantcollaborative.org>




phdgrimm<http://ask.iplantcollaborative.org/users/123/phdgrimm/> posted a question<http://ask.iplantcollaborative.org/question/2955/error-when-using-cloudstructure-app/>.

Question : error when using CloudStructure app

Asked by phdgrimm:

Tags: DiscoveryEnvironment.

I have been getting multiple errors with the app with the most recent being hard to interpret. My structure file has no marker row and has genotype data on 2 lines per ind.

[file format ex.]

A=10,T=11,G=12,C=13

K10-G10.KUROILER 1 2 12 13 13 12 10 11 13 11 11 10 10 13 11 12 10 11 13 12 10 10 12

K10-G10.KUROILER 1 -9 12 13 13 10 12 11 13 11 13 10 13 13 11 12 12 13 13 12 10 10 10

When I look at the .err and .out files from the fail log I see:

[.err file] Failed to submit job 66488: java.io.IOException: Error completing remote execution after: s

[.out file] 0/1 - 0.00% of files done 0.000/0.000 MB - 0.00% of file sizes done Processing condor-stdout-0 - 0.000 MB 2015-01-23.05:45:59

[porklock] Applying metadata to /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 [porklock] Metadata tuples for /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 are ((ipc-execution-id 7afffda7-689d-4080-a082-5cc4cce78137 UUID) (ipc-analysis-id 0a243f34-adda-4721-8597-80e94bf8f9e6 UUID)) [porklock] Size of tuple (ipc-execution-id 7afffda7-689d-4080-a082-5cc4cce78137 UUID) is 3 [porklock] Might be adding metadata to /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 (ipc-execution-id 7afffda7-689d-4080-a082-5cc4cce78137 UUID) [porklock] AVU? /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 () [porklock] Adding metadata

======= Full thread summary =======

Question : error when using CloudStructure app

Asked by phdgrimm:

Tags: DiscoveryEnvironment.

I have been getting multiple errors with the app with the most recent being hard to interpret. My structure file has no marker row and has genotype data on 2 lines per ind.

[file format ex.]

A=10,T=11,G=12,C=13

K10-G10.KUROILER 1 2 12 13 13 12 10 11 13 11 11 10 10 13 11 12 10 11 13 12 10 10 12

K10-G10.KUROILER 1 -9 12 13 13 10 12 11 13 11 13 10 13 13 11 12 12 13 13 12 10 10 10

When I look at the .err and .out files from the fail log I see:

[.err file] Failed to submit job 66488: java.io.IOException: Error completing remote execution after: s

[.out file] 0/1 - 0.00% of files done 0.000/0.000 MB - 0.00% of file sizes done Processing condor-stdout-0 - 0.000 MB 2015-01-23.05:45:59

[porklock] Applying metadata to /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 [porklock] Metadata tuples for /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 are ((ipc-execution-id 7afffda7-689d-4080-a082-5cc4cce78137 UUID) (ipc-analysis-id 0a243f34-adda-4721-8597-80e94bf8f9e6 UUID)) [porklock] Size of tuple (ipc-execution-id 7afffda7-689d-4080-a082-5cc4cce78137 UUID) is 3 [porklock] Might be adding metadata to /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 (ipc-execution-id 7afffda7-689d-4080-a082-5cc4cce78137 UUID) [porklock] AVU? /iplant/home/phdgrimm/analyses/CloudSTRUCTURE_analysis1-2015-01-23-12-44-53.2/logs/condor-stdout-0 () [porklock] Adding metadata

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________________________________

Sincerely,
Administrator








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Nicole Hopkins
Scientific Initiatives Coordinator
iPlant Collaborative- University of Arizona
(520) 626-7390