[Iplant-api-dev] Filesystem issues with Foundation API?

[Andy Edmonds]

The smallest amount of available scratch space on the iplant condor 
nodes is 320GB.

Thanks...
-Andy-

-- 
Andy Edmonds
University of Arizona
iPlant Collaborative
Core Services
Email: aedmonds at iplantcollaborative.org
Phone: 520-626-4279

On 03/04/2013 03:38 PM, Lenards, Andrew J - (lenards) wrote:
> Please disregard for now.
>
> It looks like I made a mistake in my triage.
>
> The BASH script the DE creates to execute an App (regardless of its' 
> target, local condor vs. Foundation API), it does a make directory 
> (mkdir) and that appears to be what is failing:
>
> #### EXAMPLE SNIPPET
>
> #!/bin/bash
> cd ~
> mkdir -p iplant-de-jobs/lenards/jd887b1e1-0534-4eaa-a534-f259f1201b88
> pushd iplant-de-jobs/lenards/jd887b1e1-0534-4eaa-a534-f259f1201b88
> mkdir -p logs
> EXITSTATUS=0
> PATH=/usr/local/bin/:/usr/local2/bin/:/usr/bin/ 
> /usr/local/bin/porklock mkdir --user lenards --destination 
> '/iplant/home/lenards/analyses/ask_ipc_repro-2013-03-04-14-15-24.592' 
> 1> logs/imkdir-stdout 2> logs/imkdir-stderr
> if [ ! "$?" -eq "0" ]; then
>     EXITSTATUS=1
> fi
>
> ------------------------------------------------------------------------
> *From:* iplant-api-dev-bounces at iplantcollaborative.org 
> [iplant-api-dev-bounces at iplantcollaborative.org] on behalf of Lenards, 
> Andrew J - (lenards) [lenards at email.arizona.edu]
> *Sent:* Monday, March 04, 2013 2:27 PM
> *To:* iplant-api-dev at iplantcollaborative.org
> *Cc:* support at iplantcollaborative.org
> *Subject:* [Iplant-api-dev] Filesystem issues with Foundation API?
>
> Hi,
>
> It looks like users of the Discovery Environment are getting App 
> failures for anything that is run via the Foundation API:
>
> http://ask.iplantcollaborative.org/question/529/read-only-file-system-error/?answer=531#post-id-531
>
> I was able to reproduce the error by running two DE Apps: 
> Scythe-adapter-trimming, FastQC 0.10.1
>
> The errors seem to indicate that the system user (ipcservices, or 
> whichever) does not have permissions to create the directory structure 
> to place the outputs of the jobs.
>
> -----
>
> The Scythe-adapter-trimming job produces the following error in the 
> ``script-error.log`` file returned in logs:
>
> mkdir: cannot create directory 
> `iplant-de-jobs/lenards/j20ac77e1-18ed-42d8-84ce-a39579d8fc34': 
> Read-only file system
> /condor01/scratch/lenards/ask_ipc_repro-2013-03-04-14-14-22.752/logs/iplant.sh: 
> line 4: pushd: 
> iplant-de-jobs/lenards/j20ac77e1-18ed-42d8-84ce-a39579d8fc34: No such 
> file or directory
> /condor01/scratch/lenards/ask_ipc_repro-2013-03-04-14-14-22.752/logs/iplant.sh: 
> line 31: popd: directory stack empty
> rm: cannot remove 
> `iplant-de-jobs/lenards/j20ac77e1-18ed-42d8-84ce-a39579d8fc34': No 
> such file or directory
>
> -----
>
> The FastQC 0.10.1 job produces the following error in the 
> ``script-error.log`` file returned in logs:
>
> mkdir: cannot create directory 
> `iplant-de-jobs/lenards/jd887b1e1-0534-4eaa-a534-f259f1201b88': 
> Read-only file system
> /condor01/scratch/lenards/ask_ipc_repro-2013-03-04-14-15-24.592/logs/iplant.sh: 
> line 4: pushd: 
> iplant-de-jobs/lenards/jd887b1e1-0534-4eaa-a534-f259f1201b88: No such 
> file or directory
> /condor01/scratch/lenards/ask_ipc_repro-2013-03-04-14-15-24.592/logs/iplant.sh: 
> line 26: popd: directory stack empty
> rm: cannot remove 
> `iplant-de-jobs/lenards/jd887b1e1-0534-4eaa-a534-f259f1201b88': No 
> such file or directory
>
> -----
>
> I don't think this is an issue of ``ipcservices`` not having read 
> access to the inputs (though that crossed my mind).
>
> Thanks in advance for any help we can provide this community member.
>
> Andy
>
>
>
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