Mailing-List: contact dev-help@airavata.apache.org; run by ezmlm
Precedence: bulk
Reply-To: dev@airavata.apache.org
Received-SPF: pass (nike.apache.org: domain of marpierc@iu.edu designates
 129.79.1.194 as permitted sender)
Message-ID: <5499BBEF.2040104@iu.edu>
Date: Tue, 23 Dec 2014 14:01:03 -0500
From: Marlon Pierce <marpierc@iu.edu>
User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.9;
 rv:24.0) Gecko/20100101 Thunderbird/24.6.0
MIME-Version: 1.0
To: Airavata Dev <dev@airavata.apache.org>
Subject: "input" and "output" subdirs in working directories
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit

When Airavata executes a remote command (launching a SLURM job, for 
example), it creates a working directory on the target machine's scratch 
space and two subdirectories, "input" and "output".  Is there a good 
reason for creating these two subdirectories?  Why not just do all the 
work in the top level of the working directory?  It seems unnecessary.  
Also, I don't understand why these are in the GFAC module, as these 
should be constructed from Registry information.

Below is background information.
--------------
Below is an example working directory.

$ cd 
/oasis/scratch/trestles/ogce/temp_project/gta-work-dirs/TEST_8b10aa04-95c3-4695-af77-d3b3987c7ef9/
$ ls -tlr
total 20
drwxr-xr-x 2 ogce sds128 4096 Dec 23 07:17 output
-rw-r--r-- 1 ogce sds128  831 Dec 23 07:39 1203922204.pbs
-rw------- 1 ogce sds128   28 Dec 23 07:40 Gaussian.stdout
-rw------- 1 ogce sds128  663 Dec 23 07:40 Gaussian.stderr
drwxr-xr-x 2 ogce sds128 4096 Dec 23 07:47 input

The names of these subdirectories are specified in Constants.java (as 
OUTPUT_DATA_DIR_VAR_NAME and INPUT_DATA_DIR_VAR_NAME).   Below are the 
files in the GFAC module that use these two constants.

$ find ./modules/gfac -type f -exec grep -il "OUTPUT_DATA_DIR_VAR" {} \; 
| grep java|grep -v target

./modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Constants.java
./modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java
./modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/gram/util/GramRSLGenerator.java
./modules/gfac/gfac-local/src/main/java/org/apache/airavata/gfac/local/provider/impl/LocalProvider.java
./modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java

So we would need to clean these up if we remove the constants.

Marlon