Thanks, Mark. What's your approach in CIPRES? Do you use a flat
structure for your working directories, or do you do something else?
Marlon
On 12/23/14, 2:45 PM, Miller, Mark wrote:
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:[email protected]]
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
