Well, I would say that not being to unlimit the stack size to some
reasonable value is the more dangerous feature. The reason to put large
arrays on the stack has to do with caching effects. So what you can do is
basically keep using the same memory that is already in the cache if you
work on data on the stack. This can actually make a measurable difference
in performance, and is why I have made a point of using stack workspace in
places in pmemd. I agree that an OS that does not handle larger stack sizes
certainly does put a crimp in this programming style, but at least to my
knowledge, this is a problem that can be worked around. Automatic arrays in
both c and fortran are, at least in my opinion, very nice capabilities, but
I am more focused on "make it really fast" than "make it run on anything in
the world with no trouble at all" (ie., I understand the difference of
opinion).
- Bob
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: "'AMBER Developers Mailing List'" <amber-developers.ambermd.org>
Sent: Monday, April 19, 2010 4:23 PM
Subject: RE: [AMBER-Developers] release plans
> Hi Dan,
>
>> -unlimit stack
>> +limit stacksize unlimited
>> +set STACK=`limit stacksize | awk '{print $2}'`
>> +if (! $?STACK || $STACK != "unlimited" || $STACK == "" ) then
>> + echo "This test requires a larger stack size. Exiting."
>> + exit(0)
>> +endif
>
> A 'lot' of machines do not allow the stack to be set to unlimited by
> non-root users and some not even by root. E.g. on Redhat EL4 AS:
>
> limit stacksize unlimited
> limit stacksize
> stacksize 524288 kbytes
>
> So I'm not sure this is a solution. A 'much better' one would be to go
> into
> the code and work out why it needs such a large stacksize. Typically this
> is
> due to people using automatic arrays (dangerous F90 feature in my opinion)
> when really they should be allocating them.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
> _______________________________________________
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> AMBER-Developers.ambermd.org
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>
>
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Received on Mon Apr 19 2010 - 14:00:04 PDT
