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From "Miller, Mark" <mmil...@sdsc.edu>
Subject RE: "input" and "output" subdirs in working directories
Date Tue, 23 Dec 2014 19:54:34 GMT
We do use a flat system. However, to return files in a very controlled way, since one has to
know precisely the names of input and output files, and maybe even restrict the user's ability
to name them. The codes we use produce files conditionally, depending on the command line,
and so unless you know the code super well, using explicit names can cause certain output
files to now be returned at all, an obvious bummer for user and developer alike. As a result,
I have elected in most cases to just return all files. This can be confusing for users, and
just binning input and output as coarse categories is something I wish I could do currently.

That was my motivation in responding....

Mark



-----Original Message-----
From: Marlon Pierce [mailto:marpierc@iu.edu] 
Sent: Tuesday, December 23, 2014 11:50 AM
To: dev@airavata.apache.org
Subject: Re: "input" and "output" subdirs in working directories

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: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/Consta
> nts.java 
> ./modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/c
> pi/BetterGfacImpl.java 
> ./modules/gfac/gfac-gram/src/main/java/org/apache/airavata/gfac/gram/u
> til/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/pro
> vider/impl/SSHProvider.java
>
> So we would need to clean these up if we remove the constants.
>
> Marlon
>


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