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From "Miller, Mark" <mmil...@sdsc.edu>
Subject RE: "input" and "output" subdirs in working directories
Date Tue, 23 Dec 2014 19:45:26 GMT
I am not sure of the reasoning behind the design, but off-hand it seems to me it would simplify
the job of returning to "input" and "output" files as discrete entities, so if you don't know
which files are which, you would have at least two coarse bins that can be returned under
separate banners.

Mark


-----Original Message-----
From: Marlon Pierce [mailto:marpierc@iu.edu] 
Sent: Tuesday, December 23, 2014 11:01 AM
To: Airavata Dev
Subject: "input" and "output" subdirs in working directories

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


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