[Biopython-dev] [Bug 2528] NCBIStandalone.blastall(): Replace os.popen3 with subprocess.Popen

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jun 25 16:09:24 UTC 2008


------- Comment #5 from mmokrejs at ribosome.natur.cuni.cz  2008-06-25 12:09 EST -------
(In reply to comment #4)
> Is there an easy way to replicate this issue?

I believe run under mod_python a blast search and try to display it on the web
the results, that's all I actually do. On the server the blastall processes did
not flush it's cache, so if you would connect to the running process by strace
utility you would see it has done write() of some line being not yet the last
one of the output. The process hangs like this for ages, until you do "kill
-HUP $pid", then it it flushes the write buffer and exits successfully. Happens
with blast 2.2.18 at least.

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