#308 knitr rules hang waiting for input

[Anonymous]

Certain source files can cause knitr to prompt and wait for input, and when this happens in a WW make job, for some reason it doesn't terminate after the 5 minutes that is currently the time limit on our wikis.

[Lee Worden]

Oh, and possibly it crashes the server... I waited 5 minutes for it to terminate on n06, and now n06 isn't accepting ssh connections

[Lee Worden]

but is still responding to http requests

[Lee Worden]

At least, the initial report I received seemed to say that knitr was prompting for input. When I make a pdf from the problem file on my laptop, it does not prompt, but it does go into an infinite make recursion. Since that should never happen, I'm going to fix that and then see what we have.

[Lee Worden]

I have dealt with the make recursion. That could bring a server to its knees. But pe-make is supposed to be using rlimit to keep that from happening. I will have to look into that.

[Lee Worden]

OK - now that I have the project on my laptop, and all the utilities installed that it uses (AFAICT), I am finding that it invokes xppaut which prompts and waits. Why this should fail to get terminated, and possibly cause server crashes, I don't know.

[Lee Worden]

When I do it with pe-make on my laptop, it terminates the process at the time limit.

[Lee Worden]

And when I do it with pe-make on n06

env time-limit=30 /usr/local/workingwiki/WorkingWiki/ProjectEngine/pe-make thesis.pdf

it terminates after 30 seconds.

But in thesis.pdf.make.log in the WW directory is a horror, endlessly repeating

(c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un (c)d (l)ist (r)un

"(r)un (c)d (l)ist " is the prompt from xppaut, that doesn't get a response. Maybe xppaut doesn't behave well when its output is being piped?

env time-limit=30 /usr/local/src/WorkingWiki/ProjectEngine/pe-make thesis.pdf >& /dev/tty

(back on my laptop) just prints the prompt once and gets killed at 30 seconds. It also behaves well when I pipe it into a file and run it in the background, both at home and on the cluster, and also when I use 'sudo -u apache -i' to run it in the background as apache into a file. I am puzzled.

[Lee Worden]

So, got the project running in my home wiki and it does the repetitive output thing there - so I can use that to diagnose the problem without crashing yushan nodes.

[Lee Worden]

</dev/null does not help

[Lee Worden]

When it runs amok on my laptop, it gets killed at the time limit, at least if I set the time limit to 20 seconds. I could see having more trouble when it runs for 5 minutes. The log file generated on n06 is 3G.

[Lee Worden]

The problem behavior of xppaut can be reproduced outside the wikis by running

xppaut -silent missing.ode </dev/null

where missing.ode is not an actual file.