[EMBOSS] Jemboss unable to delete job directories if results.home is on NFS

[Rozenbaum, Daniel (Biocceleration Inc)]

My apologies - the part of the previous email where I described the modifications we made that appear to have helped resolve this problem was completely incorrect. I'm attaching a version of JembossServer.java (originally from the 6.4.0 distribution) with our modifications preceded with comments starting with "// Biocceleration: " . To reiterate, these modifications were mostly guesswork - trying to identify possible places where an explicit close() could have helped resolve the issue.
________________________________________
From: emboss-bounces at lists.open-bio.org [emboss-bounces at lists.open-bio.org] On Behalf Of Rozenbaum, Daniel (Biocceleration Inc)
Sent: Friday, September 21, 2012 10:55 PM
To: emboss at lists.open-bio.org
Subject: [EMBOSS] Jemboss unable to delete job directories if results.home is on NFS

Greetings,

We had run into the following problem: if Jemboss results directory (results.home in jemboss.properties) is a directory on NFS, Jemboss is unable to delete job directories, either from Saved Results or from File Manager (in the case of the latter I first delete the files in the directory from the File Manager - no problem there).

Here're the steps that reproduced the problem in our environment:

1. Run say "makeprotseq" in Jemboss. The resultant job directory contains files makeseq.fasta, .desc, and .finished.

2. Open File Manager, browse to the job directory in the Remote pane, and delete the file "makeseq.fasta". The file disappears, but when checking the contents of the directory on the server, it turns out that even though "makeseq.fasta" is no longer there, there's a file ".nfs0000000<random looking hexadecimal number>". Applying "lsof" on the file reveals that the it is being kept open by a "java" process corresponding to the Tomcat server.

3. Attempt to delete the directory from Jemboss File Manager. The directory disappears in File Manager view, but a check on the server side reveals that it's still there. Inside the directory, files .desc and .finished are gone but the file .nfs000000... is still there. After a "refresh" in Jemboss File Manager the directory reappears.

It was our understanding that the appearance of these ".nfs00000..." files after the attempt to delete the result files was the standard behavior of NFS when there's an attempt to delete an open file. People smarter than me then were able to resolve the problem by adding calls "in.close()" after the "while" loops in the following methods in JembossServer.java

show_acd
show_saved_result
list_saved_results
loadFilesContent (in two places)
update_result_status

We would really appreciate if you could please review these changes and confirm whether they're indeed correct and necessary.

With best regards,
Daniel

--
Daniel Rozenbaum
Biocceleration, Inc.
OCIO/ Office of Application Engineering & Development/ Patent System Division
600 Dulany St.
Alexandria, VA 22314




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