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From "Miller, Mark" <>
Subject RE: Partial results of an application run
Date Fri, 19 Sep 2014 21:40:43 GMT
Aha, Very interesting, I was not thinking about the full span of possibilities. You make a
good point.
In fact, CIPRES has a special system that manages files above a certain size, because otherwise
they just gum up our whole app and bring the server down.
These are regular result files.

I agree there may be cases where the Gateway needs/wants  to refuse certain files, such as
the example you mentioned. 
For us it possible, but a lot more work, to specify each file that needs to be returned. But
for apps with one or two codes that are well understood it would be very little effort.

I am wondering if the large files you mentioned are produced by gadget only in the failure
And how will/does  Airavata manage files that are very large in the success case? 
And how large of files can we manage in Airavata?

But now that's a whole new thread I fear....


-----Original Message-----
From: Raminder Singh [] 
Sent: Friday, September 19, 2014 2:28 PM
Subject: Re: Partial results of an application run

Thanks Mark for the feedback. I agree with you that SciGap should provide all the information
to the gateway to debug a job. Followup question is, we should make this a default behavior
or gateway configured behavior? I had worked with codes like Gadget in the past which produce
huge intermediate files. In that case, we don't want to transfer all the files. I would suggest
gateway to provide details about the file it needs to debug a job failure, if not the real
intermediate output name some regular expression to find them and transfer to the gateway

Other way of dealing with this can be transfer intermediate files on demand. Gateway admins
or users get the list of intermediate files in the working folder. Airavata only transfer
files based on the user selection. Just an idea. 


On Sep 19, 2014, at 12:18 PM, Marlon Pierce <> wrote:

> Great feedback, Mark--
> Marlon
> On 9/19/14, 12:03 PM, Miller, Mark wrote:
>> Hi Raminder,
>> If I understand the issue, I have a comment.
>> The stdout/stderr files are absolutely critical to a gateway runner and the every
end user for debugging issues, even simple ones like a typo that breaks the infile formatting.
>> There are two levels of benefit: first, the savvy user reads these docs and solves
their own problem more quickly, if it is on their side, and notifies me of the message when
it isn't on their side. This saves time for everyone.
>> Second, when the non-savvy user reports an issue but can't figure out what's wrong,,
this is the first place I look to identify the issue. It also makes it possible at all to
debug on a reasonably large user population. removing these files takes away the levers both
users and gateway owners have to manage issues. If I understand the issue correctly, I don't
think that SciGap wants to inherit the job of debugging job runs for all its constituent Gateways,
and not passing these files along would do just that.
>> I strongly feel, again assuming I understand correctly, that all the files available
from every failed job should be passed along to the Gateway by SciGap. If the Gateway owners
wish to debug every user issue on their own, they can pass only certain files along to the
>> In our time with CIPRES I think I have used almost every file we or the users job
has created to debug an issue at one time or another.
>> Sometimes the absence of a file alone tells me what the issue is. On the other hand,
many of code produce both STDOUT as a file, and stdout.txt as a file.
>> If SciGap wanted to be responsible for eliminating that ambiguity, 
>> that might be fine. But delivering both copies puts the effort back on the Gateway
developer to decide how to handle it, and perhaps that is again the best solution. And it
requires no effort on the part of SciGap, which already has many things to take care of.
>> So my vote is to return everything to the Gateway for every job.
>> The exception with this might be SciGap-created files that do not have any relevance
to the Gateway. I still think they would be of benefit to the Gateway developer (at least)
because then they can report the issue to SciGap directly and explicitly.
>> That means the admin on the SciGap side does not have to look up the job, maneuver
to the directory, and open files to find the error message. It conserves many keystrokes/clicks.
If we have 50 client Gateways, we will be grateful when a User reports the SciGap error message
and job number, rather than just saying they have an issue.
>> Those are my thoughts.
>> Best,
>> Mark
>> From: Raminder Singh []
>> Sent: Friday, September 19, 2014 7:56 AM
>> To:
>> Subject: Partial results of an application run
>> Hi Dev,
>> Currently we are not moving partial results (stdout/stderr and other files) to the
gateway incase of application failure (failed to produce output). This can be fixed but question
is do we want it to be the default behavior or based on some user flag in experiment. To make
it work properly, we need user input to provide regular expressions or other details about
required files, incase of failure. Any suggestions on these changes in Application catalog
and Airavata API. We also need APIs functions to get job working directory and other details.
I created a JIRA for this.
>> Thanks
>> Raminder

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