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

[Lenards, Andrew J - (lenards)]

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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